diff --git a/Applications/PluginGenerator/CMakeLists.txt b/Applications/PluginGenerator/CMakeLists.txt
index aebbe5def5..0fa99551a6 100644
--- a/Applications/PluginGenerator/CMakeLists.txt
+++ b/Applications/PluginGenerator/CMakeLists.txt
@@ -1,73 +1,73 @@
if (${CMAKE_SOURCE_DIR} EQUAL ${PROJECT_SOURCE_DIR})
- cmake_minimum_required(VERSION 3.14.5 FATAL_ERROR)
+ cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
endif()
project(MitkPluginGenerator)
set(VERSION_MAJOR 1)
set(VERSION_MINOR 5)
set(VERSION_PATCH 0)
set(VERSION_STRING "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
set(standalone_build 1)
else()
set(standalone_build 0)
endif()
#-----------------------------------------------------------------------------
# Prerequisites
#-----------------------------------------------------------------------------
find_package(Qt5Core REQUIRED)
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/PluginGeneratorConfig.h.in"
"${CMAKE_CURRENT_BINARY_DIR}/PluginGeneratorConfig.h" @ONLY)
include_directories("${CMAKE_CURRENT_BINARY_DIR}")
#-----------------------------------------------------------------------------
# Executable
#-----------------------------------------------------------------------------
set(src_files
PluginGenerator.cpp
ctkCommandLineParser.cpp
)
qt5_wrap_cpp(src_files ctkCommandLineParser.h OPTIONS -DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION)
qt5_add_resources(src_files plugin_template.qrc project_template.qrc)
set(exec_target ${PROJECT_NAME})
add_executable(${exec_target} ${src_files})
set_property(TARGET ${exec_target} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Applications/PluginGenerator")
target_link_libraries(${exec_target} Qt5::Core)
#-----------------------------------------------------------------------------
# Win32 Convenience
#-----------------------------------------------------------------------------
if(WIN32 AND NOT standalone_build)
file(TO_NATIVE_PATH "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}" native_runtime_dir)
add_custom_target(NewPlugin start "MITK PluginGenerator" /D "${native_runtime_dir}" cmd /K ${exec_target}.exe -h
DEPENDS ${exec_target})
set_property(TARGET NewPlugin PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Applications/PluginGenerator")
endif()
#-----------------------------------------------------------------------------
# Testing
#-----------------------------------------------------------------------------
if(NOT standalone_build)
# Test the plugin generator
include(mitkTestPluginGenerator)
endif()
#-----------------------------------------------------------------------------
# Packaging support
#-----------------------------------------------------------------------------
if(standalone_build)
include(SetupPackaging.cmake)
endif()
diff --git a/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt b/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt
index 1618e04c80..572d4ebd54 100644
--- a/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt
+++ b/Applications/PluginGenerator/ProjectTemplate/CMakeLists.txt
@@ -1,329 +1,329 @@
-cmake_minimum_required(VERSION 3.14.5 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
# Change project and application name to your own
set(MY_PROJECT_NAME $(project-name))
set(MY_APP_NAME $(project-app-name))
#-----------------------------------------------------------------------------
# Set the language standard (MITK requires C++14)
#-----------------------------------------------------------------------------
set(CMAKE_CXX_STANDARD 14)
set(CMAKE_CXX_STANDARD_REQUIRED 1)
set(CMAKE_CXX_EXTENSIONS 0)
#-----------------------------------------------------------------------------
# Set a default build type if none was specified
#-----------------------------------------------------------------------------
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
message(STATUS "Setting build type to 'Debug' as none was specified.")
set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY
STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
endif()
#-----------------------------------------------------------------------------
# Superbuild Option - Enabled by default
#-----------------------------------------------------------------------------
option(${MY_PROJECT_NAME}_USE_SUPERBUILD "Build ${MY_PROJECT_NAME} and the projects it depends on via SuperBuild.cmake." ON)
if(${MY_PROJECT_NAME}_USE_SUPERBUILD)
project(${MY_PROJECT_NAME}-superbuild)
set(${MY_PROJECT_NAME}_SOURCE_DIR ${PROJECT_SOURCE_DIR})
set(${MY_PROJECT_NAME}_BINARY_DIR ${PROJECT_BINARY_DIR})
else()
project(${MY_PROJECT_NAME})
endif()
#-----------------------------------------------------------------------------
# See http://cmake.org/cmake/help/cmake-2-8-docs.html#section_Policies for details
#-----------------------------------------------------------------------------
set(project_policies
CMP0001 # NEW: CMAKE_BACKWARDS_COMPATIBILITY should no longer be used.
CMP0002 # NEW: Logical target names must be globally unique.
CMP0003 # NEW: Libraries linked via full path no longer produce linker search paths.
CMP0004 # NEW: Libraries linked may NOT have leading or trailing whitespace.
CMP0005 # NEW: Preprocessor definition values are now escaped automatically.
CMP0006 # NEW: Installing MACOSX_BUNDLE targets requires a BUNDLE DESTINATION.
CMP0007 # NEW: List command no longer ignores empty elements.
CMP0008 # NEW: Libraries linked by full-path must have a valid library file name.
CMP0009 # NEW: FILE GLOB_RECURSE calls should not follow symlinks by default.
CMP0010 # NEW: Bad variable reference syntax is an error.
CMP0011 # NEW: Included scripts do automatic cmake_policy PUSH and POP.
CMP0012 # NEW: if() recognizes numbers and boolean constants.
CMP0013 # NEW: Duplicate binary directories are not allowed.
CMP0014 # NEW: Input directories must have CMakeLists.txt
CMP0020 # NEW: Automatically link Qt executables to qtmain target on Windows.
CMP0028 # NEW: Double colon in target name means ALIAS or IMPORTED target.
)
foreach(policy ${project_policies})
if(POLICY ${policy})
cmake_policy(SET ${policy} NEW)
endif()
endforeach()
#-----------------------------------------------------------------------------
# Update CMake module path
#------------------------------------------------------------------------------
set(CMAKE_MODULE_PATH
${${MY_PROJECT_NAME}_SOURCE_DIR}/CMake
${CMAKE_MODULE_PATH}
)
#-----------------------------------------------------------------------------
# CMake Function(s) and Macro(s)
#-----------------------------------------------------------------------------
include(CTest)
include(MacroEmptyExternalProject)
#-----------------------------------------------------------------------------
# Output directories.
#-----------------------------------------------------------------------------
foreach(type LIBRARY RUNTIME ARCHIVE)
set(output_dir ${${MY_PROJECT_NAME}_BINARY_DIR}/bin)
set(CMAKE_${type}_OUTPUT_DIRECTORY ${output_dir} CACHE INTERNAL "Single output directory for building all libraries.")
mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY)
endforeach()
#-----------------------------------------------------------------------------
# Additional Options (also shown during superbuild)
#-----------------------------------------------------------------------------
option(BUILD_SHARED_LIBS "Build ${MY_PROJECT_NAME} with shared libraries" ON)
option(WITH_COVERAGE "Enable/Disable coverage" OFF)
option(BUILD_TESTING "Test the project" ON)
option(${MY_PROJECT_NAME}_BUILD_ALL_PLUGINS "Build all ${MY_PROJECT_NAME} plugins" OFF)
mark_as_advanced(${MY_PROJECT_NAME}_INSTALL_RPATH_RELATIVE
${MY_PROJECT_NAME}_BUILD_ALL_PLUGINS
)
#-----------------------------------------------------------------------------
# Superbuild script
#-----------------------------------------------------------------------------
if(${MY_PROJECT_NAME}_USE_SUPERBUILD)
include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
return()
endif()
#*****************************************************************************
#**************************** END OF SUPERBUILD ****************************
#*****************************************************************************
#-----------------------------------------------------------------------------
# Prerequesites
#-----------------------------------------------------------------------------
set(${PROJECT_NAME}_MODULES_PACKAGE_DEPENDS_DIR "${PROJECT_SOURCE_DIR}/CMake/PackageDepends")
set(MODULES_PACKAGE_DEPENDS_DIRS ${${PROJECT_NAME}_MODULES_PACKAGE_DEPENDS_DIR})
find_package(MITK 2018.04.99 REQUIRED)
if(COMMAND mitkFunctionCheckMitkCompatibility)
mitkFunctionCheckMitkCompatibility(VERSIONS MITK_VERSION_PLUGIN_SYSTEM 1 REQUIRED)
else()
message(SEND_ERROR "Your MITK version is too old. Please use Git hash b86bf28 or newer")
endif()
link_directories(${MITK_LINK_DIRECTORIES})
#-----------------------------------------------------------------------------
# CMake Function(s) and Macro(s)
#-----------------------------------------------------------------------------
set(CMAKE_MODULE_PATH
${MITK_SOURCE_DIR}/CMake
${CMAKE_MODULE_PATH}
)
include(mitkFunctionCheckCompilerFlags)
include(mitkFunctionGetGccVersion)
include(mitkFunctionGetVersion)
#-----------------------------------------------------------------------------
# Set project specific options and variables (NOT available during superbuild)
#-----------------------------------------------------------------------------
set(${PROJECT_NAME}_VERSION_MAJOR "0")
set(${PROJECT_NAME}_VERSION_MINOR "1")
set(${PROJECT_NAME}_VERSION_PATCH "1")
set(${PROJECT_NAME}_VERSION_STRING "${${PROJECT_NAME}_VERSION_MAJOR}.${${PROJECT_NAME}_VERSION_MINOR}.${${PROJECT_NAME}_VERSION_PATCH}")
# Ask the user if a console window should be shown with the applications
option(${PROJECT_NAME}_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting GUI Applications" ON)
mark_as_advanced(${PROJECT_NAME}_SHOW_CONSOLE_WINDOW)
if(NOT UNIX)
set(MITK_WIN32_FORCE_STATIC "STATIC")
endif()
#-----------------------------------------------------------------------------
# Get project version info
#-----------------------------------------------------------------------------
mitkFunctionGetVersion(${PROJECT_SOURCE_DIR} ${PROJECT_NAME})
#-----------------------------------------------------------------------------
# Installation preparation
#
# These should be set before any MITK install macros are used
#-----------------------------------------------------------------------------
# on macOS all CTK plugins get copied into every
# application bundle (.app directory) specified here
set(MACOSX_BUNDLE_NAMES)
if(APPLE)
list(APPEND MACOSX_BUNDLE_NAMES ${MY_APP_NAME})
endif(APPLE)
#-----------------------------------------------------------------------------
# Set symbol visibility Flags
#-----------------------------------------------------------------------------
if(CMAKE_COMPILER_IS_GNUCXX)
# The MITK module build system does not yet support default hidden visibility
set(VISIBILITY_CXX_FLAGS ) # "-fvisibility=hidden -fvisibility-inlines-hidden")
endif()
#-----------------------------------------------------------------------------
# Set coverage Flags
#-----------------------------------------------------------------------------
if(WITH_COVERAGE)
if(CMAKE_COMPILER_IS_GNUCXX)
set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG")
set(COVERAGE_CXX_FLAGS ${coverage_flags})
set(COVERAGE_C_FLAGS ${coverage_flags})
endif()
endif()
#-----------------------------------------------------------------------------
# Project C/CXX Flags
#-----------------------------------------------------------------------------
set(${PROJECT_NAME}_C_FLAGS "${MITK_C_FLAGS} ${COVERAGE_C_FLAGS}")
set(${PROJECT_NAME}_C_FLAGS_DEBUG ${MITK_C_FLAGS_DEBUG})
set(${PROJECT_NAME}_C_FLAGS_RELEASE ${MITK_C_FLAGS_RELEASE})
set(${PROJECT_NAME}_CXX_FLAGS "${MITK_CXX_FLAGS} ${VISIBILITY_CXX_FLAGS} ${COVERAGE_CXX_FLAGS}")
set(${PROJECT_NAME}_CXX_FLAGS_DEBUG ${MITK_CXX_FLAGS_DEBUG})
set(${PROJECT_NAME}_CXX_FLAGS_RELEASE ${MITK_CXX_FLAGS_RELEASE})
set(${PROJECT_NAME}_EXE_LINKER_FLAGS ${MITK_EXE_LINKER_FLAGS})
set(${PROJECT_NAME}_SHARED_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS})
set(${PROJECT_NAME}_MODULE_LINKER_FLAGS ${MITK_MODULE_LINKER_FLAGS})
#-----------------------------------------------------------------------------
# Set C/CXX Flags
#-----------------------------------------------------------------------------
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${${PROJECT_NAME}_C_FLAGS}")
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} ${${PROJECT_NAME}_C_FLAGS_DEBUG}")
set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} ${${PROJECT_NAME}_C_FLAGS_RELEASE}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${${PROJECT_NAME}_CXX_FLAGS}")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${${PROJECT_NAME}_CXX_FLAGS_DEBUG}")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${${PROJECT_NAME}_CXX_FLAGS_RELEASE}")
set(CMAKE_EXE_LINKER_FLAGS ${${PROJECT_NAME}_EXE_LINKER_FLAGS})
set(CMAKE_SHARED_LINKER_FLAGS ${${PROJECT_NAME}_SHARED_LINKER_FLAGS})
set(CMAKE_MODULE_LINKER_FLAGS ${${PROJECT_NAME}_MODULE_LINKER_FLAGS})
#-----------------------------------------------------------------------------
# Testing
#-----------------------------------------------------------------------------
if(BUILD_TESTING)
# Configuration for the CMake-generated test driver
set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include <stdexcept>")
set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "
try
{")
set(CMAKE_TESTDRIVER_AFTER_TESTMAIN "
}
catch (const std::exception& e)
{
fprintf(stderr, \"%s\\n\", e.what());
return EXIT_FAILURE;
}
catch (...)
{
printf(\"Exception caught in the test driver\\n\");
return EXIT_FAILURE;
}")
endif()
#-----------------------------------------------------------------------------
# ${MY_PROJECT_NAME}_SUPERBUILD_BINARY_DIR
#-----------------------------------------------------------------------------
# If ${MY_PROJECT_NAME}_SUPERBUILD_BINARY_DIR isn't defined, it means this project is
# *NOT* build using Superbuild. In that specific case, ${MY_PROJECT_NAME}_SUPERBUILD_BINARY_DIR
# should default to PROJECT_BINARY_DIR
if(NOT DEFINED ${PROJECT_NAME}_SUPERBUILD_BINARY_DIR)
set(${PROJECT_NAME}_SUPERBUILD_BINARY_DIR ${PROJECT_BINARY_DIR})
endif()
#-----------------------------------------------------------------------------
# MITK modules
#-----------------------------------------------------------------------------
#add_subdirectory(Modules)
#-----------------------------------------------------------------------------
# CTK plugins
#-----------------------------------------------------------------------------
# The CMake code in this section *must* be in the top-level CMakeLists.txt file
macro(GetMyTargetLibraries all_target_libraries varname)
set(re_ctkplugin "^$(project-plugin-base)_[a-zA-Z0-9_]+$")
set(_tmp_list)
list(APPEND _tmp_list ${all_target_libraries})
ctkMacroListFilter(_tmp_list re_ctkplugin OUTPUT_VARIABLE ${varname})
endmacro()
include(${CMAKE_CURRENT_SOURCE_DIR}/Plugins/Plugins.cmake)
ctkMacroSetupPlugins(${PROJECT_PLUGINS}
BUILD_OPTION_PREFIX ${MY_PROJECT_NAME}_
BUILD_ALL ${${MY_PROJECT_NAME}_BUILD_ALL_PLUGINS})
#-----------------------------------------------------------------------------
# Add subdirectories
#-----------------------------------------------------------------------------
add_subdirectory(Apps/$(project-app-name))
#-----------------------------------------------------------------------------
# Installation
#-----------------------------------------------------------------------------
# set MITK cpack variables
include(mitkSetupCPack)
# Customize CPack variables for this project
include(CPackSetup)
list(APPEND CPACK_CREATE_DESKTOP_LINKS "${MY_APP_NAME}")
configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in
${PROJECT_BINARY_DIR}/${PROJECT_NAME}CPackOptions.cmake @ONLY)
set(CPACK_PROJECT_CONFIG_FILE "${PROJECT_BINARY_DIR}/${PROJECT_NAME}CPackOptions.cmake")
# include CPack model once all variables are set
include(CPack)
# Additional installation rules
include(mitkInstallRules)
#-----------------------------------------------------------------------------
# Last configuration steps
#-----------------------------------------------------------------------------
diff --git a/CMake/BuildConfigurations/All.cmake b/CMake/BuildConfigurations/All.cmake
index 2bbbfaf858..6a3b24125e 100644
--- a/CMake/BuildConfigurations/All.cmake
+++ b/CMake/BuildConfigurations/All.cmake
@@ -1,51 +1,45 @@
set(MITK_CONFIG_PACKAGES )
set(_apple_package_excludes)
set(_package_excludes
${_apple_package_excludes}
OpenCL
OpenMP
SYSTEM_Boost
Boost_LIBRARIES
SYSTEM_PYTHON
SUPERBUILD
- BiophotonicsHardware_SpectroCam
POLHEMUS_TRACKER
-
- US_DiPhAS_SDK
- GALIL_HARDWARE
- OPHIR_PYRO_HARDWARE
-
MICROBIRD_TRACKER
MICROBIRD_TRACKER_INCLUDE_DIR
MICROBIRD_TRACKER_LIB
MICRON_TRACKER
OPTITRACK_TRACKER
SPACENAVIGATOR
TOF_KINECT
TOF_KINECTV2
TOF_MESASR4000
TOF_PMDCAMBOARD
TOF_PMDCAMCUBE
TOF_PMDO3
US_TELEMED_SDK
videoInput
WIIMOTE
)
get_cmake_property(_cache_vars CACHE_VARIABLES)
foreach(_cache_var ${_cache_vars})
string(REGEX REPLACE "MITK_USE_(.+)" "\\1" _package "${_cache_var}")
if(_package AND NOT _package STREQUAL _cache_var)
list(FIND _package_excludes ${_package} _index)
if(_index EQUAL -1)
list(APPEND MITK_CONFIG_PACKAGES ${_package})
endif()
endif()
endforeach()
set(MITK_BUILD_ALL_APPS ON CACHE BOOL "Build all MITK applications" FORCE)
set(MITK_BUILD_ALL_PLUGINS ON CACHE BOOL "Build all MITK plugins" FORCE)
set(MITK_BUILD_EXAMPLES ON CACHE BOOL "Build the MITK examples" FORCE)
set(BLUEBERRY_BUILD_ALL_PLUGINS ON CACHE BOOL "Build all BlueBerry plugins" FORCE)
diff --git a/CMake/BuildConfigurations/camiPhotoacousticsSetup.cmake b/CMake/BuildConfigurations/camiPhotoacousticsSetup.cmake
deleted file mode 100644
index 4a881e5fb6..0000000000
--- a/CMake/BuildConfigurations/camiPhotoacousticsSetup.cmake
+++ /dev/null
@@ -1,25 +0,0 @@
-message(STATUS "Configuring MITK Photoacoustics Setup Build")
-
-# Enable open cv and open igt link, which is a necessary configuration
-set(MITK_USE_OpenCV ON CACHE BOOL "MITK Use OpenCV Library" FORCE)
-set(MITK_USE_OpenIGTLink ON CACHE BOOL "MITK Use OpenIGTLink Library" FORCE)
-set(MITK_USE_US_DiPhAS_SDK ON CACHE BOOL "Use DiPhAS SDK" FORCE)
-set(MITK_US_DiPhAS_SDK_PATH "C:/Users/dkfz/Source/Repos/UltrasoundResearchPlatform_SDK/UltrasoundResearchPlatformSDK_Cpp/x64" CACHE PATH "DiPhAS SDK Path")
-
-set(MITK_USE_OPHIR_PYRO_HARDWARE ON CACHE BOOL "Use the Ophir sensor build-in in OPOTEK Phocus Mobile" FORCE)
-set(MITK_OPHIR_API_PATH "C:/OphirCppWrapper" CACHE PATH "Ophir API Path")
-
-set(MITK_USE_GALIL_HARDWARE ON CACHE BOOL "Use hardware build-in in OPOTEK Phocus Mobile" FORCE)
-set(MITK_GALIL_API_PATH "C:/Program Files (x86)/Galil/gclib" CACHE PATH "Galil API Path")
-
-# Enable default plugins and the navigation modules
-set(MITK_CONFIG_PLUGINS
- org.mitk.gui.qt.datamanager
- org.mitk.gui.qt.stdmultiwidgeteditor
- org.mitk.gui.qt.imagenavigator
- org.mitk.gui.qt.properties
- org.mitk.gui.qt.viewnavigator
- org.mitk.gui.qt.ultrasound
- org.mitk.gui.qt.lasercontrol
-)
-
diff --git a/CMake/BuildConfigurations/camiPhotoacousticsWorkstation.cmake b/CMake/BuildConfigurations/camiPhotoacousticsWorkstation.cmake
deleted file mode 100644
index 0b05599c4e..0000000000
--- a/CMake/BuildConfigurations/camiPhotoacousticsWorkstation.cmake
+++ /dev/null
@@ -1,22 +0,0 @@
-message(STATUS "Configuring MITK Photoacoustics Setup Build")
-
-# Enable open cv and open igt link, which is a necessary configuration
-set(MITK_USE_OpenCV ON CACHE BOOL "MITK Use OpenCV Library" FORCE)
-set(MITK_USE_OpenIGTLink ON CACHE BOOL "MITK Use OpenIGTLink Library" FORCE)
-
-set(MITK_USE_OpenCL ON CACHE BOOL "MITK Use OpenCL Library" FORCE)
-
-# Also enable plugins often used in photoacoustics
-set(MITK_CONFIG_PLUGINS
- org.mitk.gui.qt.datamanager
- org.mitk.gui.qt.stdmultiwidgeteditor
- org.mitk.gui.qt.imagenavigator
- org.mitk.gui.qt.properties
- org.mitk.gui.qt.viewnavigator
- org.mitk.gui.qt.ultrasound
- org.mitk.gui.qt.photoacoustics.imageprocessing
- org.mitk.gui.qt.measurementtoolbox
- org.mitk.gui.qt.pointsetinteraction
-)
-
-set(BUILD_PhotoacousticBeamformingTool ON CACHE BOOL "Build commandline tools for Beamforming" FORCE)
diff --git a/CMake/MITKDashboardScript.download.cmake b/CMake/MITKDashboardScript.download.cmake
index 7ff24c8582..a6f9daa5b3 100644
--- a/CMake/MITKDashboardScript.download.cmake
+++ b/CMake/MITKDashboardScript.download.cmake
@@ -1,698 +1,698 @@
#[============================================================================[
Helper functions
]============================================================================]
function(get_macos_codename)
set(macos_codename "")
set(software_license_file "\
/System/Library/CoreServices/Setup Assistant.app\
/Contents/Resources/en.lproj/OSXSoftwareLicense.rtf")
if(EXISTS "${software_license_file}")
file(READ "${software_license_file}" software_license)
if(software_license MATCHES "SOFTWARE LICENSE AGREEMENT FOR macOS ([^\n]+)")
set(macos_codename "${CMAKE_MATCH_1}")
endif()
endif()
set(${ARGV0} ${macos_codename} PARENT_SCOPE)
endfunction()
function(get_macos_name)
set(macos_name "macOS")
get_macos_codename(macos_codename)
if(macos_codename)
set(macos_name "${macos_name} ${macos_codename}")
endif()
execute_process(
RESULT_VARIABLE error_code
OUTPUT_VARIABLE version
OUTPUT_STRIP_TRAILING_WHITESPACE
COMMAND "sw_vers" "-productVersion")
if(0 EQUAL error_code AND version)
set(macos_name "${macos_name} ${version}")
endif()
set(${ARGV0} ${macos_name} PARENT_SCOPE)
endfunction()
function(get_linux_name)
set(linux_name "Linux")
set(os_release_file "/etc/os-release")
if(EXISTS "${os_release_file}")
file(STRINGS "${os_release_file}" os_release)
set(name "")
set(version_id "")
foreach(line ${os_release})
if(NOT name AND line MATCHES "^NAME=[\"]?([^\"]+)")
set(name "${CMAKE_MATCH_1}")
continue()
endif()
if(NOT version_id AND line MATCHES "^VERSION_ID=\"?([^\"]+)")
set(version_id "${CMAKE_MATCH_1}")
continue()
endif()
if(name AND version_id)
break()
endif()
endforeach()
if(name)
set(linux_name "${name}")
endif()
if(version_id)
set(linux_name "${linux_name} ${version_id}")
endif()
endif()
set(${ARGV0} ${linux_name} PARENT_SCOPE)
endfunction()
function(get_windows_name)
set(windows_name "Windows")
execute_process(
RESULT_VARIABLE error_code
OUTPUT_VARIABLE version
OUTPUT_STRIP_TRAILING_WHITESPACE
COMMAND "wmic" "os" "get" "Version" "-value")
if(0 EQUAL error_code AND version)
if(version MATCHES "Version=([0-9]+)\\.([0-9]+)")
set(windows_name "${windows_name} ${CMAKE_MATCH_1}")
if(NOT 0 EQUAL CMAKE_MATCH_2)
set(windows_name "${windows_name}.${CMAKE_MATCH_2}")
endif()
endif()
endif()
set(${ARGV0} ${windows_name} PARENT_SCOPE)
endfunction()
function(get_os_name)
set(os_name "")
if(APPLE)
get_macos_name(os_name)
elseif(UNIX)
get_linux_name(os_name)
elseif(WIN32)
get_windows_name(os_name)
endif()
set(${ARGV0} ${os_name} PARENT_SCOPE)
endfunction()
function(download_string)
cmake_parse_arguments(PARSE_ARGV 0 ARG "" "URL;OUTPUT_VARIABLE" "")
get_temp_directory(temp_dir)
string(RANDOM random_filename)
while(EXISTS "${temp_dir}/${random_filename}")
string(RANDOM random_filename)
endwhile()
set(temp_output_file "${temp_dir}/${random_filename}")
download_file(
URL ${ARG_URL}
OUTPUT_FILE ${temp_output_file}
ERROR_CODE error_code)
set(output "")
if(EXISTS "${temp_output_file}")
file(READ "${temp_output_file}" output)
file(REMOVE "${temp_output_file}")
endif()
set(${ARG_OUTPUT_VARIABLE} ${output} PARENT_SCOPE)
endfunction()
function(find_vswhere)
get_temp_directory(temp_dir)
set(latest_vswhere "${temp_dir}/vswhere.exe")
set(vswhere "vswhere.exe-NOTFOUND")
if(EXISTS "${latest_vswhere}")
set(vswhere "${latest_vswhere}")
else()
set(program_files_x86 "PROGRAMFILES(X86)")
set(program_files_x86 "$ENV{${program_files_x86}}")
set(system_vswhere "${program_files_x86}/Microsoft Visual Studio/Installer/vswhere.exe")
if(EXISTS "${system_vswhere}")
set(vswhere "${system_vswhere}")
else()
download_string(
URL "https://api.github.com/repos/microsoft/vswhere/releases/latest"
OUTPUT_VARIABLE latest_vswhere_json)
if(latest_vswhere_json MATCHES "\"browser_download_url\": *\"([^\"]*)\"")
download_file(
URL "${CMAKE_MATCH_1}"
OUTPUT_FILE "${latest_vswhere}"
ERROR_CODE error_code)
if (0 EQUAL error_code)
set(vswhere "${latest_vswhere}")
endif()
endif()
endif()
endif()
set(${ARGV0} "${vswhere}" PARENT_SCOPE)
endfunction()
function(vswhere)
cmake_parse_arguments(PARSE_ARGV 0 ARG "" "PROPERTY;OUTPUT_VARIABLE" "")
set(property_value "")
if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio ([0-9]+)")
set(major_version "${CMAKE_MATCH_1}")
math(EXPR next_major_version "${major_version} + 1")
find_vswhere(vswhere)
if (vswhere)
execute_process(
OUTPUT_VARIABLE property_value
OUTPUT_STRIP_TRAILING_WHITESPACE
COMMAND ${vswhere}
"-requires" "Microsoft.VisualStudio.Workload.NativeDesktop"
"-version" "[${major_version},${next_major_version})"
"-property" "${ARG_PROPERTY}"
"-format" "value")
endif()
endif()
set(${ARG_OUTPUT_VARIABLE} ${property_value} PARENT_SCOPE)
endfunction()
function(get_visual_studio_name)
set(visual_studio_name "Visual Studio")
if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)")
set(product_line_version "${CMAKE_MATCH_1}")
set(visual_studio_name "${visual_studio_name} ${product_line_version}")
vswhere(PROPERTY "catalog_productDisplayVersion" OUTPUT_VARIABLE product_display_version)
if(product_display_version)
set(visual_studio_name "${visual_studio_name} ${product_display_version}")
endif()
endif()
set(${ARGV0} ${visual_studio_name} PARENT_SCOPE)
endfunction()
function(get_compiler_name)
set(compiler_name "")
if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio")
get_visual_studio_name(compiler_name)
else()
get_temp_directory(temp_dir)
file(WRITE "${temp_dir}/src/CMakeLists.txt" "\
project(probe C)
message(STATUS \"CMAKE_C_COMPILER_ID=\\\"\${CMAKE_C_COMPILER_ID}\\\"\")
message(STATUS \"CMAKE_C_COMPILER_VERSION=\\\"\${CMAKE_C_COMPILER_VERSION}\\\"\")")
file(REMOVE_RECURSE "${temp_dir}/build")
unset(options)
foreach(option ${MITK_SUPERBUILD_OPTIONS})
list(APPEND options "-D" "${option}")
endforeach()
execute_process(
RESULT_VARIABLE error_code
OUTPUT_VARIABLE compiler
ERROR_QUIET
COMMAND ${CMAKE_COMMAND}
"-S" "${temp_dir}/src"
"-B" "${temp_dir}/build"
"-G" "${CTEST_CMAKE_GENERATOR}"
${options})
if(0 EQUAL error_code)
if(compiler MATCHES "CMAKE_C_COMPILER_ID=\"([^\"]*)\"")
set(compiler_name "${CMAKE_MATCH_1}")
if(compiler MATCHES "CMAKE_C_COMPILER_VERSION=\"([^\"]*)\"")
set(version "${CMAKE_MATCH_1}")
if(version MATCHES "^([0-9]+\\.[0-9]+\\.[0-9]+)")
set(version "${CMAKE_MATCH_1}")
endif()
string(REGEX REPLACE "\\.0$" "" version "${version}")
set(compiler_name "${compiler_name} ${version}")
endif()
endif()
endif()
endif()
set(${ARGV0} ${compiler_name} PARENT_SCOPE)
endfunction()
function(get_default_build_name)
get_os_name(default_build_name)
get_compiler_name(compiler_name)
if(compiler_name)
set(default_build_name "${default_build_name} ${compiler_name}")
endif()
set(default_build_name "${default_build_name} ${CTEST_BUILD_CONFIGURATION}")
if(MITK_BUILD_CONFIGURATION)
set(default_build_name "${default_build_name} ${MITK_BUILD_CONFIGURATION}")
endif()
if(MITK_BUILD_NAME_SUFFIX)
set(default_build_name "${default_build_name} ${MITK_BUILD_NAME_SUFFIX}")
endif()
set(${ARGV0} ${default_build_name} PARENT_SCOPE)
endfunction()
function(git)
cmake_parse_arguments(PARSE_ARGV 0 ARG "" "WORKING_DIRECTORY;OUTPUT_VARIABLE;RESULT_VARIABLE" "")
if(NOT ARG_WORKING_DIRECTORY)
set(ARG_WORKING_DIRECTORY "${CTEST_SOURCE_DIRECTORY}")
endif()
get_filename_component(ARG_WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" ABSOLUTE)
execute_process(
WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}"
RESULT_VARIABLE error_code
OUTPUT_VARIABLE output
OUTPUT_STRIP_TRAILING_WHITESPACE
COMMAND "${CTEST_GIT_COMMAND}" ${ARG_UNPARSED_ARGUMENTS})
if(ARG_OUTPUT_VARIABLE)
set(${ARG_OUTPUT_VARIABLE} ${output} PARENT_SCOPE)
endif()
if(ARG_RESULT_VARIABLE)
set(${ARG_RESULT_VARIABLE} ${error_code} PARENT_SCOPE)
endif()
endfunction()
function(git_log)
cmake_parse_arguments(PARSE_ARGV 0 ARG "" "WORKING_DIRECTORY;COMMIT_HASH;COMMITTER;SUBJECT" "")
if(NOT ARG_WORKING_DIRECTORY)
set(ARG_WORKING_DIRECTORY "${CTEST_SOURCE_DIRECTORY}")
endif()
get_filename_component(ARG_WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" ABSOLUTE)
set(args WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" "log" "-1")
if(ARG_COMMIT_HASH)
unset(commit_hash)
git(OUTPUT_VARIABLE commit_hash ${args} "--pretty=%h" )
if(commit_hash)
set(${ARG_COMMIT_HASH} ${commit_hash} PARENT_SCOPE)
endif()
endif()
if(ARG_COMMITTER)
unset(committer)
git(OUTPUT_VARIABLE committer ${args} "--pretty=%cn" )
if(committer)
set(${ARG_COMMITTER} ${committer} PARENT_SCOPE)
endif()
endif()
if(ARG_SUBJECT)
unset(subject)
git(OUTPUT_VARIABLE subject ${args} "--pretty=%s" )
if(subject)
set(${ARG_SUBJECT} ${subject} PARENT_SCOPE)
endif()
endif()
endfunction()
function(rm)
execute_process(COMMAND ${CMAKE_COMMAND} "-E" "rm" "-rf" ${ARGN})
endfunction()
function(submit)
cmake_parse_arguments(PARSE_ARGV 0 ARG "" "" "PARTS")
if(MITK_SUBMIT_URL)
set(submit_url "SUBMIT_URL" "${MITK_SUBMIT_URL}")
else()
unset(submit_url)
endif()
if(MITK_AUTH_TOKEN)
set(http_header HTTPHEADER "Authorization: Bearer ${MITK_AUTH_TOKEN}")
else()
unset(http_header)
endif()
ctest_submit(${submit_url} ${http_header} RETRY_COUNT 3 RETRY_DELAY 5 PARTS ${ARG_PARTS})
endfunction()
#[============================================================================[
Actual script
]============================================================================]
-cmake_minimum_required(VERSION 3.15 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.18 FATAL_ERROR)
find_program(CTEST_GIT_COMMAND git)
if(NOT CTEST_GIT_COMMAND)
message(FATAL_ERROR "Git not found")
endif()
if(NOT CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio")
unset(CTEST_CMAKE_GENERATOR_PLATFORM)
endif()
if(CTEST_CMAKE_GENERATOR MATCHES "^(Unix Makefiles|Ninja)$")
set(CTEST_USE_LAUNCHERS ON)
endif()
if(NOT CTEST_SITE)
unset(CTEST_SITE)
site_name(CTEST_SITE)
endif()
if(NOT CTEST_BUILD_NAME)
get_default_build_name(CTEST_BUILD_NAME)
endif()
set(CTEST_SOURCE_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/src/MITK")
set(CTEST_BINARY_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/build")
set(indent " ")
message("CTest settings")
if(MITK_SUBMIT_URL)
message("${indent}Submit URL: ${MITK_SUBMIT_URL}")
endif()
message("\
${indent}Dashboard model: ${CTEST_DASHBOARD_MODEL}
${indent}Build name: ${CTEST_BUILD_NAME}
${indent}Site: ${CTEST_SITE}")
if(MITK_CLEAN_SOURCE_DIR OR MITK_CLEAN_BINARY_DIR)
message("Clean")
if(MITK_CLEAN_SOURCE_DIR)
set(clean_dir "${CMAKE_CURRENT_SOURCE_DIR}/src")
message("${indent}Source directory: ${clean_dir}")
rm("${clean_dir}")
endif()
if(MITK_CLEAN_BINARY_DIR)
set(clean_dir "${CMAKE_CURRENT_SOURCE_DIR}/build")
message("${indent}Binary directory: ${clean_dir}")
rm("${clean_dir}")
endif()
endif()
message("MITK repository")
if(NOT EXISTS "${CTEST_SOURCE_DIRECTORY}")
message("\
${indent}Clone repository: ${MITK_REPOSITORY}
${indent}Branch: ${MITK_BRANCH}")
set(CTEST_CHECKOUT_COMMAND "\"${CTEST_GIT_COMMAND}\" clone --branch=${MITK_BRANCH} -- ${MITK_REPOSITORY} MITK")
ctest_start(${CTEST_DASHBOARD_MODEL})
else()
git_log(COMMIT_HASH old_revision COMMITTER committer SUBJECT subject)
message("\
${indent}Update repository: ${CTEST_SOURCE_DIRECTORY}
${indent}Branch: ${MITK_BRANCH}
${indent}Old revision: ${old_revision} (committed by ${committer})
${indent}${indent}${subject}")
ctest_start(${CTEST_DASHBOARD_MODEL})
- set(CTEST_UPDATE_OPTIONS "origin ${MITK_BRANCH}")
+ set(CTEST_UPDATE_OPTIONS "--tags origin ${MITK_BRANCH}")
ctest_update(RETURN_VALUE return_value)
if(-1 EQUAL return_value)
return()
endif()
git_log(COMMIT_HASH new_revision)
if(new_revision STREQUAL old_revision)
message("${indent}New revision: up-to-date")
else()
git_log(COMMITTER committer SUBJECT subject)
message("\
${indent}New revision: ${new_revision} (committed by ${committer})
${indent}${indent}${subject}")
endif()
endif()
unset(extension_dirs)
if(MITK_EXTENSIONS)
list(LENGTH MITK_EXTENSIONS mitk_extensions_size)
math(EXPR max_index "${mitk_extensions_size} - 1")
foreach(name_index RANGE 0 ${max_index} 3)
list(GET MITK_EXTENSIONS ${name_index} name)
math(EXPR url_index "${name_index} + 1")
list(GET MITK_EXTENSIONS ${url_index} url)
math(EXPR branch_index "${name_index} + 2")
list(GET MITK_EXTENSIONS ${branch_index} branch)
message("${name} repository")
set(extension_dir "${CMAKE_CURRENT_SOURCE_DIR}/src/${name}")
list(APPEND extension_dirs "${extension_dir}")
if(NOT EXISTS "${extension_dir}")
message("\
${indent}Clone repository: ${url}
${indent}Branch: ${branch}")
git("clone" "--quiet" "--branch=${branch}" "${url}" "${name}"
WORKING_DIRECTORY "${extension_dir}/..")
else()
git_log(COMMIT_HASH old_revision COMMITTER committer SUBJECT subject
WORKING_DIRECTORY "${extension_dir}")
message("\
${indent}Update repository: ${extension_dir}
${indent}Branch: ${branch}
${indent}Old revision: ${old_revision} (committed by ${committer})
${indent}${indent}${subject}")
- git("fetch" "--quiet" "origin" "${branch}"
+ git("fetch" "--quiet" "--tags" "origin" "${branch}"
WORKING_DIRECTORY "${extension_dir}")
git("diff" "--quiet" "HEAD" "FETCH_HEAD"
WORKING_DIRECTORY "${extension_dir}"
RESULT_VARIABLE error_code)
if(NOT error_code EQUAL 0)
git("reset" "--quiet" "--hard" "FETCH_HEAD"
WORKING_DIRECTORY "${extension_dir}")
endif()
git_log(COMMIT_HASH new_revision
WORKING_DIRECTORY "${extension_dir}")
if(new_revision STREQUAL old_revision)
message("${indent}New revision: up-to-date")
else()
git_log(COMMITTER committer SUBJECT subject
WORKING_DIRECTORY "${extension_dir}")
message("\
${indent}New revision: ${new_revision} (committed by ${committer})
${indent}${indent}${subject}")
endif()
endif()
endforeach()
endif()
submit(PARTS Update)
set(options
"-D" "MITK_CTEST_SCRIPT_MODE:STRING=${CTEST_DASHBOARD_MODEL}"
# "-D" "SUPERBUILD_EXCLUDE_MITKBUILD_TARGET:BOOL=TRUE"
)
if(extension_dirs)
string (REPLACE ";" "\\\;" extension_dirs "${extension_dirs}")
list(APPEND options "-D" "MITK_EXTENSION_DIRS:STRING=${extension_dirs}")
endif()
if(MITK_BUILD_CONFIGURATION)
list(APPEND options "-D" "MITK_BUILD_CONFIGURATION:STRING=${MITK_BUILD_CONFIGURATION}")
endif()
if(MITK_BUILD_OPTIONS)
get_temp_directory(temp_dir)
set(mitk_initial_cache_file "${temp_dir}/MITKInitialCache.cmake")
file(WRITE "${mitk_initial_cache_file}" "")
foreach(mitk_option ${MITK_BUILD_OPTIONS})
if(mitk_option MATCHES "^([^:]+):([^=]+)=(.*)")
set(var "${CMAKE_MATCH_1}")
set(type "${CMAKE_MATCH_2}")
set(value "${CMAKE_MATCH_3}")
file(APPEND "${mitk_initial_cache_file}" "set(${var} \"${value}\" CACHE ${type} \"\" FORCE)\n")
endif()
endforeach()
list(APPEND options "-D" "MITK_INITIAL_CACHE_FILE:FILEPATH=${mitk_initial_cache_file}")
endif()
foreach(option ${MITK_SUPERBUILD_OPTIONS})
list(APPEND options "-D" "${option}")
endforeach()
ctest_configure(OPTIONS "${options}" RETURN_VALUE return_value)
submit(PARTS Configure)
if(NOT 0 EQUAL return_value)
submit(PARTS Done)
return()
endif()
include("${CTEST_BINARY_DIRECTORY}/SuperBuildTargets.cmake")
if(NOT SUPERBUILD_TARGETS)
submit(PARTS Done)
message(FATAL_ERROR "SUPERBUILD_TARGETS variable not set in SuperBuildTargets.cmake")
else()
set(mitk_targets
MITK-Data
MITK-Utilities
MITK-Configure
MITK-build
)
list(LENGTH SUPERBUILD_TARGETS n)
list(LENGTH mitk_targets num_mitk_targets)
math(EXPR n "${n} + ${num_mitk_targets}")
set(i 1)
unset(append)
foreach(target ${SUPERBUILD_TARGETS} ${mitk_targets})
message("MITK superbuild - [${i}/${n}] Build ${target}")
if(NOT target IN_LIST mitk_targets)
list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION ".*")
set(pop_warning_exception TRUE)
else()
set(pop_warning_exception FALSE)
endif()
ctest_build(TARGET ${target}
NUMBER_ERRORS num_build_errors
NUMBER_WARNINGS num_build_warnings
RETURN_VALUE return_value
${append})
if(pop_warning_exception)
list(POP_BACK CTEST_CUSTOM_WARNING_EXCEPTION)
endif()
submit(PARTS Build)
if(0 LESS num_build_warnings)
message("${indent}${num_build_warnings} warning(s)")
endif()
if(NOT (0 EQUAL return_value AND 0 EQUAL num_build_errors))
submit(PARTS Done)
message("${indent}${num_build_errors} error(s)")
return()
else()
message("${indent}${target} was built successfully")
endif()
if(NOT append)
set(append APPEND)
endif()
math(EXPR i "${i} + 1")
endforeach()
endif()
if(MITK_BUILD_DOCUMENTATION)
message("MITK build - Build documentation")
list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION ".*")
ctest_build(TARGET doc
BUILD "${CTEST_BINARY_DIRECTORY}/MITK-build"
NUMBER_ERRORS num_doc_errors
NUMBER_WARNINGS num_doc_warnings
RETURN_VALUE return_value
APPEND
)
list(POP_BACK CTEST_CUSTOM_WARNING_EXCEPTION)
submit(PARTS Build)
if(0 LESS num_doc_warnings)
message("${indent}${num_doc_warnings} warning(s)")
endif()
if(NOT (0 EQUAL return_value AND 0 EQUAL num_doc_errors))
submit(PARTS Done)
message("${indent}${num_doc_errors} error(s)")
return()
else()
message("${indent}Documentation was built successfully")
endif()
endif()
message("Run unit tests...")
set(CTEST_CONFIGURATION_TYPE "${CTEST_BUILD_CONFIGURATION}")
ctest_test(
BUILD "${CTEST_BINARY_DIRECTORY}/MITK-build"
PARALLEL_LEVEL 4)
submit(PARTS Test Done)
message("Done")
diff --git a/CMake/NSIS.template.in b/CMake/NSIS.template.in
index f111eadbc1..47f5d675ff 100644
--- a/CMake/NSIS.template.in
+++ b/CMake/NSIS.template.in
@@ -1,1086 +1,1014 @@
; CPack install script designed for a nmake build
;--------------------------------
; You must define these values
!define VERSION "@CPACK_PACKAGE_VERSION@"
!define PATCH "@CPACK_PACKAGE_VERSION_PATCH@"
!define INST_DIR "@CPACK_TEMPORARY_DIRECTORY@"
;--------------------------------
;Variables
Var MUI_TEMP
Var STARTMENU_FOLDER
Var SV_ALLUSERS
Var START_MENU
Var DO_NOT_ADD_TO_PATH
Var ADD_TO_PATH_ALL_USERS
Var ADD_TO_PATH_CURRENT_USER
Var INSTALL_DESKTOP
Var IS_DEFAULT_INSTALLDIR
;--------------------------------
;Include Modern UI
!include "MUI.nsh"
;Default installation folder
InstallDir "@CPACK_NSIS_INSTALL_ROOT@\@CPACK_PACKAGE_INSTALL_DIRECTORY@"
;Allow for very long title on the welcome page
!define MUI_WELCOMEPAGE_TITLE_3LINES
;--------------------------------
;General
;Name and file
Name "@CPACK_NSIS_PACKAGE_NAME@"
OutFile "@CPACK_TOPLEVEL_DIRECTORY@/@CPACK_OUTPUT_FILE_NAME@"
;Set compression
SetCompressor @CPACK_NSIS_COMPRESSOR@
RequestExecutionLevel user
@CPACK_NSIS_DEFINES@
!include Sections.nsh
;--- Component support macros: ---
; The code for the add/remove functionality is from:
; http://nsis.sourceforge.net/Add/Remove_Functionality
; It has been modified slightly and extended to provide
; inter-component dependencies.
Var AR_SecFlags
Var AR_RegFlags
@CPACK_NSIS_SECTION_SELECTED_VARS@
; Loads the "selected" flag for the section named SecName into the
; variable VarName.
!macro LoadSectionSelectedIntoVar SecName VarName
SectionGetFlags ${${SecName}} $${VarName}
IntOp $${VarName} $${VarName} & ${SF_SELECTED} ;Turn off all other bits
!macroend
; Loads the value of a variable... can we get around this?
!macro LoadVar VarName
IntOp $R0 0 + $${VarName}
!macroend
; Sets the value of a variable
!macro StoreVar VarName IntValue
IntOp $${VarName} 0 + ${IntValue}
!macroend
!macro InitSection SecName
; This macro reads component installed flag from the registry and
;changes checked state of the section on the components page.
;Input: section index constant name specified in Section command.
ClearErrors
;Reading component status from registry
ReadRegDWORD $AR_RegFlags HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@\Components\${SecName}" "Installed"
IfErrors "default_${SecName}"
;Status will stay default if registry value not found
;(component was never installed)
IntOp $AR_RegFlags $AR_RegFlags & ${SF_SELECTED} ;Turn off all other bits
SectionGetFlags ${${SecName}} $AR_SecFlags ;Reading default section flags
IntOp $AR_SecFlags $AR_SecFlags & 0xFFFE ;Turn lowest (enabled) bit off
IntOp $AR_SecFlags $AR_RegFlags | $AR_SecFlags ;Change lowest bit
; Note whether this component was installed before
!insertmacro StoreVar ${SecName}_was_installed $AR_RegFlags
IntOp $R0 $AR_RegFlags & $AR_RegFlags
;Writing modified flags
SectionSetFlags ${${SecName}} $AR_SecFlags
"default_${SecName}:"
!insertmacro LoadSectionSelectedIntoVar ${SecName} ${SecName}_selected
!macroend
!macro FinishSection SecName
; This macro reads section flag set by user and removes the section
;if it is not selected.
;Then it writes component installed flag to registry
;Input: section index constant name specified in Section command.
SectionGetFlags ${${SecName}} $AR_SecFlags ;Reading section flags
;Checking lowest bit:
IntOp $AR_SecFlags $AR_SecFlags & ${SF_SELECTED}
IntCmp $AR_SecFlags 1 "leave_${SecName}"
;Section is not selected:
;Calling Section uninstall macro and writing zero installed flag
!insertmacro "Remove_${${SecName}}"
WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@\Components\${SecName}" \
"Installed" 0
Goto "exit_${SecName}"
"leave_${SecName}:"
;Section is selected:
WriteRegDWORD HKLM "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@\Components\${SecName}" \
"Installed" 1
"exit_${SecName}:"
!macroend
; NSIS example code to only include some code if a file exists at compile time (whereas IfFileExists works at runtime)
; See http://nsis.sourceforge.net/Check_if_a_file_exists_at_compile_time for documentation
!macro !defineifexist _VAR_NAME _FILE_NAME
!tempfile _TEMPFILE
!system 'if exist "${_FILE_NAME}" echo !define ${_VAR_NAME} > "${_TEMPFILE}"'
!include '${_TEMPFILE}'
!delfile '${_TEMPFILE}'
!undef _TEMPFILE
!macroend
!define !defineifexist "!insertmacro !defineifexist"
; Determine whether the selection of SecName changed
!macro MaybeSelectionChanged SecName
!insertmacro LoadVar ${SecName}_selected
SectionGetFlags ${${SecName}} $R1
IntOp $R1 $R1 & ${SF_SELECTED} ;Turn off all other bits
; See if the status has changed:
IntCmp $R0 $R1 "${SecName}_unchanged"
!insertmacro LoadSectionSelectedIntoVar ${SecName} ${SecName}_selected
IntCmp $R1 ${SF_SELECTED} "${SecName}_was_selected"
!insertmacro "Deselect_required_by_${SecName}"
goto "${SecName}_unchanged"
"${SecName}_was_selected:"
!insertmacro "Select_${SecName}_depends"
"${SecName}_unchanged:"
!macroend
;--- End of Add/Remove macros ---
;--------------------------------
;Interface Settings
!define MUI_HEADERIMAGE
!define MUI_ABORTWARNING
;--------------------------------
; path functions
!verbose 3
!include "WinMessages.NSH"
!verbose 4
;----------------------------------------
; based upon a script of "Written by KiCHiK 2003-01-18 05:57:02"
;----------------------------------------
!verbose 3
!include "WinMessages.NSH"
!verbose 4
;====================================================
; get_NT_environment
; Returns: the selected environment
; Output : head of the stack
;====================================================
!macro select_NT_profile UN
Function ${UN}select_NT_profile
StrCmp $ADD_TO_PATH_ALL_USERS "1" 0 environment_single
DetailPrint "Selected environment for all users"
Push "all"
Return
environment_single:
DetailPrint "Selected environment for current user only."
Push "current"
Return
FunctionEnd
!macroend
!insertmacro select_NT_profile ""
!insertmacro select_NT_profile "un."
;----------------------------------------------------
!define NT_current_env 'HKCU "Environment"'
!define NT_all_env 'HKLM "SYSTEM\CurrentControlSet\Control\Session Manager\Environment"'
!ifndef WriteEnvStr_RegKey
!ifdef ALL_USERS
!define WriteEnvStr_RegKey \
'HKLM "SYSTEM\CurrentControlSet\Control\Session Manager\Environment"'
!else
!define WriteEnvStr_RegKey 'HKCU "Environment"'
!endif
!endif
; AddToPath - Adds the given dir to the search path.
; Input - head of the stack
; Note - Win9x systems requires reboot
Function AddToPath
Exch $0
Push $1
Push $2
Push $3
# don't add if the path doesn't exist
IfFileExists "$0\*.*" "" AddToPath_done
ReadEnvStr $1 PATH
; if the path is too long for a NSIS variable NSIS will return a 0
; length string. If we find that, then warn and skip any path
; modification as it will trash the existing path.
StrLen $2 $1
IntCmp $2 0 CheckPathLength_ShowPathWarning CheckPathLength_Done CheckPathLength_Done
CheckPathLength_ShowPathWarning:
DetailPrint "Warning: Could not modify PATH variable - current PATH is too long.\n\
This does not impact the functionality of MITK itself, but you will not be able to start\
it from anywhere via command line."
; The message box is probably too much of an escalation, most users won't care or notice
;Messagebox MB_OK|MB_ICONEXCLAMATION "Warning! PATH too long installer unable to modify PATH!"
Goto AddToPath_done
CheckPathLength_Done:
Push "$1;"
Push "$0;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
Push "$1;"
Push "$0\;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
GetFullPathName /SHORT $3 $0
Push "$1;"
Push "$3;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
Push "$1;"
Push "$3\;"
Call StrStr
Pop $2
StrCmp $2 "" "" AddToPath_done
Call IsNT
Pop $1
StrCmp $1 1 AddToPath_NT
; Not on NT
StrCpy $1 $WINDIR 2
FileOpen $1 "$1\autoexec.bat" a
FileSeek $1 -1 END
FileReadByte $1 $2
IntCmp $2 26 0 +2 +2 # DOS EOF
FileSeek $1 -1 END # write over EOF
FileWrite $1 "$\r$\nSET PATH=%PATH%;$3$\r$\n"
FileClose $1
SetRebootFlag true
Goto AddToPath_done
AddToPath_NT:
StrCmp $ADD_TO_PATH_ALL_USERS "1" ReadAllKey
ReadRegStr $1 ${NT_current_env} "PATH"
Goto DoTrim
ReadAllKey:
ReadRegStr $1 ${NT_all_env} "PATH"
DoTrim:
StrCmp $1 "" AddToPath_NTdoIt
Push $1
Call Trim
Pop $1
StrCpy $0 "$1;$0"
AddToPath_NTdoIt:
StrCmp $ADD_TO_PATH_ALL_USERS "1" WriteAllKey
WriteRegExpandStr ${NT_current_env} "PATH" $0
Goto DoSend
WriteAllKey:
WriteRegExpandStr ${NT_all_env} "PATH" $0
DoSend:
SendMessage ${HWND_BROADCAST} ${WM_WININICHANGE} 0 "STR:Environment" /TIMEOUT=5000
AddToPath_done:
Pop $3
Pop $2
Pop $1
Pop $0
FunctionEnd
; RemoveFromPath - Remove a given dir from the path
; Input: head of the stack
Function un.RemoveFromPath
Exch $0
Push $1
Push $2
Push $3
Push $4
Push $5
Push $6
IntFmt $6 "%c" 26 # DOS EOF
Call un.IsNT
Pop $1
StrCmp $1 1 unRemoveFromPath_NT
; Not on NT
StrCpy $1 $WINDIR 2
FileOpen $1 "$1\autoexec.bat" r
GetTempFileName $4
FileOpen $2 $4 w
GetFullPathName /SHORT $0 $0
StrCpy $0 "SET PATH=%PATH%;$0"
Goto unRemoveFromPath_dosLoop
unRemoveFromPath_dosLoop:
FileRead $1 $3
StrCpy $5 $3 1 -1 # read last char
StrCmp $5 $6 0 +2 # if DOS EOF
StrCpy $3 $3 -1 # remove DOS EOF so we can compare
StrCmp $3 "$0$\r$\n" unRemoveFromPath_dosLoopRemoveLine
StrCmp $3 "$0$\n" unRemoveFromPath_dosLoopRemoveLine
StrCmp $3 "$0" unRemoveFromPath_dosLoopRemoveLine
StrCmp $3 "" unRemoveFromPath_dosLoopEnd
FileWrite $2 $3
Goto unRemoveFromPath_dosLoop
unRemoveFromPath_dosLoopRemoveLine:
SetRebootFlag true
Goto unRemoveFromPath_dosLoop
unRemoveFromPath_dosLoopEnd:
FileClose $2
FileClose $1
StrCpy $1 $WINDIR 2
Delete "$1\autoexec.bat"
CopyFiles /SILENT $4 "$1\autoexec.bat"
Delete $4
Goto unRemoveFromPath_done
unRemoveFromPath_NT:
StrCmp $ADD_TO_PATH_ALL_USERS "1" unReadAllKey
ReadRegStr $1 ${NT_current_env} "PATH"
Goto unDoTrim
unReadAllKey:
ReadRegStr $1 ${NT_all_env} "PATH"
unDoTrim:
StrCpy $5 $1 1 -1 # copy last char
StrCmp $5 ";" +2 # if last char != ;
StrCpy $1 "$1;" # append ;
Push $1
Push "$0;"
Call un.StrStr ; Find `$0;` in $1
Pop $2 ; pos of our dir
StrCmp $2 "" unRemoveFromPath_done
; else, it is in path
# $0 - path to add
# $1 - path var
StrLen $3 "$0;"
StrLen $4 $2
StrCpy $5 $1 -$4 # $5 is now the part before the path to remove
StrCpy $6 $2 "" $3 # $6 is now the part after the path to remove
StrCpy $3 $5$6
StrCpy $5 $3 1 -1 # copy last char
StrCmp $5 ";" 0 +2 # if last char == ;
StrCpy $3 $3 -1 # remove last char
StrCmp $ADD_TO_PATH_ALL_USERS "1" unWriteAllKey
WriteRegExpandStr ${NT_current_env} "PATH" $3
Goto unDoSend
unWriteAllKey:
WriteRegExpandStr ${NT_all_env} "PATH" $3
unDoSend:
SendMessage ${HWND_BROADCAST} ${WM_WININICHANGE} 0 "STR:Environment" /TIMEOUT=5000
unRemoveFromPath_done:
Pop $6
Pop $5
Pop $4
Pop $3
Pop $2
Pop $1
Pop $0
FunctionEnd
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Uninstall stuff
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
###########################################
# Utility Functions #
###########################################
;====================================================
; IsNT - Returns 1 if the current system is NT, 0
; otherwise.
; Output: head of the stack
;====================================================
; IsNT
; no input
; output, top of the stack = 1 if NT or 0 if not
;
; Usage:
; Call IsNT
; Pop $R0
; ($R0 at this point is 1 or 0)
!macro IsNT un
Function ${un}IsNT
Push $0
ReadRegStr $0 HKLM "SOFTWARE\Microsoft\Windows NT\CurrentVersion" CurrentVersion
StrCmp $0 "" 0 IsNT_yes
; we are not NT.
Pop $0
Push 0
Return
IsNT_yes:
; NT!!!
Pop $0
Push 1
FunctionEnd
!macroend
!insertmacro IsNT ""
!insertmacro IsNT "un."
; StrStr
; input, top of stack = string to search for
; top of stack-1 = string to search in
; output, top of stack (replaces with the portion of the string remaining)
; modifies no other variables.
;
; Usage:
; Push "this is a long ass string"
; Push "ass"
; Call StrStr
; Pop $R0
; ($R0 at this point is "ass string")
!macro StrStr un
Function ${un}StrStr
Exch $R1 ; st=haystack,old$R1, $R1=needle
Exch ; st=old$R1,haystack
Exch $R2 ; st=old$R1,old$R2, $R2=haystack
Push $R3
Push $R4
Push $R5
StrLen $R3 $R1
StrCpy $R4 0
; $R1=needle
; $R2=haystack
; $R3=len(needle)
; $R4=cnt
; $R5=tmp
loop:
StrCpy $R5 $R2 $R3 $R4
StrCmp $R5 $R1 done
StrCmp $R5 "" done
IntOp $R4 $R4 + 1
Goto loop
done:
StrCpy $R1 $R2 "" $R4
Pop $R5
Pop $R4
Pop $R3
Pop $R2
Exch $R1
FunctionEnd
!macroend
!insertmacro StrStr ""
!insertmacro StrStr "un."
Function Trim ; Added by Pelaca
Exch $R1
Push $R2
Loop:
StrCpy $R2 "$R1" 1 -1
StrCmp "$R2" " " RTrim
StrCmp "$R2" "$\n" RTrim
StrCmp "$R2" "$\r" RTrim
StrCmp "$R2" ";" RTrim
GoTo Done
RTrim:
StrCpy $R1 "$R1" -1
Goto Loop
Done:
Pop $R2
Exch $R1
FunctionEnd
Function ConditionalAddToRegisty
Pop $0
Pop $1
StrCmp "$0" "" ConditionalAddToRegisty_EmptyString
WriteRegStr SHCTX "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" \
"$1" "$0"
;MessageBox MB_OK "Set Registry: '$1' to '$0'"
DetailPrint "Set install registry entry: '$1' to '$0'"
ConditionalAddToRegisty_EmptyString:
FunctionEnd
;--------------------------------
!ifdef CPACK_USES_DOWNLOAD
Function DownloadFile
IfFileExists $INSTDIR\* +2
CreateDirectory $INSTDIR
Pop $0
; Skip if already downloaded
IfFileExists $INSTDIR\$0 0 +2
Return
StrCpy $1 "@CPACK_DOWNLOAD_SITE@"
try_again:
NSISdl::download "$1/$0" "$INSTDIR\$0"
Pop $1
StrCmp $1 "success" success
StrCmp $1 "Cancelled" cancel
MessageBox MB_OK "Download failed: $1"
cancel:
Return
success:
FunctionEnd
!endif
;--------------------------------
; Installation types
@CPACK_NSIS_INSTALLATION_TYPES@
;--------------------------------
; Component sections
@CPACK_NSIS_COMPONENT_SECTIONS@
;--------------------------------
; Define some macro setting for the gui
@CPACK_NSIS_INSTALLER_MUI_ICON_CODE@
@CPACK_NSIS_INSTALLER_ICON_CODE@
@CPACK_NSIS_INSTALLER_MUI_COMPONENTS_DESC@
@CPACK_NSIS_INSTALLER_MUI_FINISHPAGE_RUN_CODE@
;--------------------------------
;Pages
!insertmacro MUI_PAGE_WELCOME
!insertmacro MUI_PAGE_LICENSE "@CPACK_RESOURCE_FILE_LICENSE@"
Page custom InstallOptionsPage
!insertmacro MUI_PAGE_DIRECTORY
;Start Menu Folder Page Configuration
!define MUI_STARTMENUPAGE_REGISTRY_ROOT "SHCTX"
!define MUI_STARTMENUPAGE_REGISTRY_KEY "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@"
!define MUI_STARTMENUPAGE_REGISTRY_VALUENAME "Start Menu Folder"
!insertmacro MUI_PAGE_STARTMENU Application $STARTMENU_FOLDER
@CPACK_NSIS_PAGE_COMPONENTS@
!insertmacro MUI_PAGE_INSTFILES
!insertmacro MUI_PAGE_FINISH
!insertmacro MUI_UNPAGE_CONFIRM
!insertmacro MUI_UNPAGE_INSTFILES
;--------------------------------
;Languages
!insertmacro MUI_LANGUAGE "English" ;first language is the default language
!insertmacro MUI_LANGUAGE "Albanian"
!insertmacro MUI_LANGUAGE "Arabic"
!insertmacro MUI_LANGUAGE "Basque"
!insertmacro MUI_LANGUAGE "Belarusian"
!insertmacro MUI_LANGUAGE "Bosnian"
!insertmacro MUI_LANGUAGE "Breton"
!insertmacro MUI_LANGUAGE "Bulgarian"
!insertmacro MUI_LANGUAGE "Croatian"
!insertmacro MUI_LANGUAGE "Czech"
!insertmacro MUI_LANGUAGE "Danish"
!insertmacro MUI_LANGUAGE "Dutch"
!insertmacro MUI_LANGUAGE "Estonian"
!insertmacro MUI_LANGUAGE "Farsi"
!insertmacro MUI_LANGUAGE "Finnish"
!insertmacro MUI_LANGUAGE "French"
!insertmacro MUI_LANGUAGE "German"
!insertmacro MUI_LANGUAGE "Greek"
!insertmacro MUI_LANGUAGE "Hebrew"
!insertmacro MUI_LANGUAGE "Hungarian"
!insertmacro MUI_LANGUAGE "Icelandic"
!insertmacro MUI_LANGUAGE "Indonesian"
!insertmacro MUI_LANGUAGE "Irish"
!insertmacro MUI_LANGUAGE "Italian"
!insertmacro MUI_LANGUAGE "Japanese"
!insertmacro MUI_LANGUAGE "Korean"
!insertmacro MUI_LANGUAGE "Kurdish"
!insertmacro MUI_LANGUAGE "Latvian"
!insertmacro MUI_LANGUAGE "Lithuanian"
!insertmacro MUI_LANGUAGE "Luxembourgish"
!insertmacro MUI_LANGUAGE "Macedonian"
!insertmacro MUI_LANGUAGE "Malay"
!insertmacro MUI_LANGUAGE "Mongolian"
!insertmacro MUI_LANGUAGE "Norwegian"
!insertmacro MUI_LANGUAGE "Polish"
!insertmacro MUI_LANGUAGE "Portuguese"
!insertmacro MUI_LANGUAGE "PortugueseBR"
!insertmacro MUI_LANGUAGE "Romanian"
!insertmacro MUI_LANGUAGE "Russian"
!insertmacro MUI_LANGUAGE "Serbian"
!insertmacro MUI_LANGUAGE "SerbianLatin"
!insertmacro MUI_LANGUAGE "SimpChinese"
!insertmacro MUI_LANGUAGE "Slovak"
!insertmacro MUI_LANGUAGE "Slovenian"
!insertmacro MUI_LANGUAGE "Spanish"
!insertmacro MUI_LANGUAGE "Swedish"
!insertmacro MUI_LANGUAGE "Thai"
!insertmacro MUI_LANGUAGE "TradChinese"
!insertmacro MUI_LANGUAGE "Turkish"
!insertmacro MUI_LANGUAGE "Ukrainian"
!insertmacro MUI_LANGUAGE "Welsh"
;--------------------------------
;Reserve Files
;These files should be inserted before other files in the data block
;Keep these lines before any File command
;Only for solid compression (by default, solid compression is enabled for BZIP2 and LZMA)
ReserveFile "NSIS.InstallOptions.ini"
!insertmacro MUI_RESERVEFILE_INSTALLOPTIONS
;--------------------------------
;Installer Sections
Section "-Core installation"
;Use the entire tree produced by the INSTALL target. Keep the
;list of directories here in sync with the RMDir commands below.
SetOutPath "$INSTDIR"
@CPACK_NSIS_FULL_INSTALL@
- ; Check whether redistributables need to be installed
- Call RedistributablePage
-
;Store installation folder
WriteRegStr SHCTX "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@" "" $INSTDIR
;Create uninstaller
WriteUninstaller "$INSTDIR\Uninstall.exe"
Push "DisplayName"
Push "@CPACK_NSIS_DISPLAY_NAME@"
Call ConditionalAddToRegisty
Push "DisplayVersion"
Push "@CPACK_PACKAGE_VERSION@"
Call ConditionalAddToRegisty
Push "Publisher"
Push "@CPACK_PACKAGE_VENDOR@"
Call ConditionalAddToRegisty
Push "UninstallString"
Push "$INSTDIR\Uninstall.exe"
Call ConditionalAddToRegisty
Push "NoRepair"
Push "1"
Call ConditionalAddToRegisty
!ifdef CPACK_NSIS_ADD_REMOVE
;Create add/remove functionality
Push "ModifyPath"
Push "$INSTDIR\AddRemove.exe"
Call ConditionalAddToRegisty
!else
Push "NoModify"
Push "1"
Call ConditionalAddToRegisty
!endif
; Optional registration
Push "DisplayIcon"
Push "$INSTDIR\@CPACK_NSIS_INSTALLED_ICON_NAME@"
Call ConditionalAddToRegisty
Push "HelpLink"
Push "@CPACK_NSIS_HELP_LINK@"
Call ConditionalAddToRegisty
Push "URLInfoAbout"
Push "@CPACK_NSIS_URL_INFO_ABOUT@"
Call ConditionalAddToRegisty
Push "Contact"
Push "@CPACK_NSIS_CONTACT@"
Call ConditionalAddToRegisty
!insertmacro MUI_INSTALLOPTIONS_READ $INSTALL_DESKTOP "NSIS.InstallOptions.ini" "Field 5" "State"
!insertmacro MUI_STARTMENU_WRITE_BEGIN Application
;Create shortcuts
CreateDirectory "$SMPROGRAMS\$STARTMENU_FOLDER"
@CPACK_NSIS_CREATE_ICONS@
@CPACK_NSIS_CREATE_ICONS_EXTRA@
CreateShortCut "$SMPROGRAMS\$STARTMENU_FOLDER\Uninstall.lnk" "$INSTDIR\Uninstall.exe"
;Read a value from an InstallOptions INI file
!insertmacro MUI_INSTALLOPTIONS_READ $DO_NOT_ADD_TO_PATH "NSIS.InstallOptions.ini" "Field 2" "State"
!insertmacro MUI_INSTALLOPTIONS_READ $ADD_TO_PATH_ALL_USERS "NSIS.InstallOptions.ini" "Field 3" "State"
!insertmacro MUI_INSTALLOPTIONS_READ $ADD_TO_PATH_CURRENT_USER "NSIS.InstallOptions.ini" "Field 4" "State"
; Write special uninstall registry entries
Push "StartMenu"
Push "$STARTMENU_FOLDER"
Call ConditionalAddToRegisty
Push "DoNotAddToPath"
Push "$DO_NOT_ADD_TO_PATH"
Call ConditionalAddToRegisty
Push "AddToPathAllUsers"
Push "$ADD_TO_PATH_ALL_USERS"
Call ConditionalAddToRegisty
Push "AddToPathCurrentUser"
Push "$ADD_TO_PATH_CURRENT_USER"
Call ConditionalAddToRegisty
Push "InstallToDesktop"
Push "$INSTALL_DESKTOP"
Call ConditionalAddToRegisty
!insertmacro MUI_STARTMENU_WRITE_END
@CPACK_NSIS_EXTRA_INSTALL_COMMANDS@
SectionEnd
Section "-Add to path"
Push $INSTDIR\bin
StrCmp "@CPACK_NSIS_MODIFY_PATH@" "ON" 0 doNotAddToPath
StrCmp $DO_NOT_ADD_TO_PATH "1" doNotAddToPath 0
Call AddToPath
doNotAddToPath:
SectionEnd
;--------------------------------
; Create custom pages
Function InstallOptionsPage
!insertmacro MUI_HEADER_TEXT "Install Options" "Choose options for installing @CPACK_NSIS_PACKAGE_NAME@"
!insertmacro MUI_INSTALLOPTIONS_DISPLAY "NSIS.InstallOptions.ini"
FunctionEnd
; Author: Lilla (lilla@earthlink.net) 2003-06-13
; function IsUserAdmin uses plugin \NSIS\PlusgIns\UserInfo.dll
; This function is based upon code in \NSIS\Contrib\UserInfo\UserInfo.nsi
; This function was tested under NSIS 2 beta 4 (latest CVS as of this writing).
;
; Usage:
; Call IsUserAdmin
; Pop $R0 ; at this point $R0 is "true" or "false"
;
Function IsUserAdmin
Push $R0
Push $R1
Push $R2
ClearErrors
UserInfo::GetName
IfErrors Win9x
Pop $R1
UserInfo::GetAccountType
Pop $R2
StrCmp $R2 "Admin" 0 Continue
; Observation: I get here when running Win98SE. (Lilla)
; The functions UserInfo.dll looks for are there on Win98 too,
; but just don't work. So UserInfo.dll, knowing that admin isn't required
; on Win98, returns admin anyway. (per kichik)
; MessageBox MB_OK 'User "$R1" is in the Administrators group'
StrCpy $R0 "true"
Goto Done
Continue:
; You should still check for an empty string because the functions
; UserInfo.dll looks for may not be present on Windows 95. (per kichik)
StrCmp $R2 "" Win9x
StrCpy $R0 "false"
;MessageBox MB_OK 'User "$R1" is in the "$R2" group'
Goto Done
Win9x:
; comment/message below is by UserInfo.nsi author:
; This one means you don't need to care about admin or
; not admin because Windows 9x doesn't either
;MessageBox MB_OK "Error! This DLL can't run under Windows 9x!"
StrCpy $R0 "true"
Done:
;MessageBox MB_OK 'User= "$R1" AccountType= "$R2" IsUserAdmin= "$R0"'
Pop $R2
Pop $R1
Exch $R0
FunctionEnd
-Function RedistributablePage
- ; Check whether the appropriate redistributable for this installer has been installed
- StrCmp '@CPACK_LIBRARY_ARCHITECTURE@' 'x64' 0 +3
- SetRegView 64
- Goto done
- StrCmp '@CPACK_LIBRARY_ARCHITECTURE@' 'x86' 0 +3
- SetRegView 32
- Goto done
- ; The following line should not be reached, use for debugging
- ; MessageBox MB_OK "Could not determine x86/x64 architecture during CPack installer configuration."
- done:
- ReadRegDword $1 HKLM "SOFTWARE\Microsoft\DevDiv\vc\Servicing\@CPACK_VISUAL_STUDIO_VERSION_MAJOR@.0\RuntimeMinimum" "Install"
-
- ; If installed show installed, else offer installation
- StrCmp $1 1 RedistInstalled
-
- ; Offer Installation
- ; MessageBox MB_YESNO "MITK requires the @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ Redistributable to function. Do you wish to install it?" /SD IDYES IDNO endInstallationMissingRedist
-
- ; Verify that user has admin privileges
- ; Otherwise they are not able to install the redistributable
- Call IsUserAdmin
- Exch $R0
- StrCmp $R0 "false" NoAdminRights
- Pop $R0
-
- SetOutPath $INSTDIR\thirdpartyinstallers
-
- ; We need compile time information on whether the redistributable installer exists.
- ; If it does not exist using the "File" command will lead to errors.
- ${!defineifexist} REDIST_INSTALLER_PRESENT @CPACK_PACKAGE_FILE_NAME@\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@
-
- !ifdef REDIST_INSTALLER_PRESENT
- ; Check at runtime whether the redistributable installer is available
- IfFileExists $INSTDIR\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@ InstallRedist NoRedistInstaller
-
- InstallRedist:
-
- ClearErrors
- File "@CPACK_PACKAGE_FILE_NAME@\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@"
- ExecWait '"$INSTDIR\thirdpartyinstallers\@CPACK_REDISTRIBUTABLE_FILE_NAME@" /passive /norestart'
- IfErrors endInstallationMissingRedist
-
- Goto RedistInstalled
-
- endInstallationMissingRedist:
- Abort "Installation aborted. Missing required @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable"
- !endif
-
- ; We are missing the redistributable installer, inform the user
- NoRedistInstaller:
- MessageBox MB_OK "Missing required @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable. You need to install it to use MITK."
- Goto End
-
- ; The user does not have the required rights to install redistributables
- NoAdminRights:
- MessageBox MB_OK|MB_ICONSTOP "This MITK version requires the @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable.$\r$\n\
- Your user account does not have administrator privileges.$\r$\n\
- Please ask your system administrator to install the @CPACK_VISUAL_STUDIO_PRODUCT_NAME@ @CPACK_LIBRARY_ARCHITECTURE@ Redistributable."
- Pop $R0
- Goto End
-
- ; No need to do anything
- RedistInstalled:
- Goto End
-
- End:
-FunctionEnd
-
;--------------------------------
; determine admin versus local install
Function un.onInit
ClearErrors
UserInfo::GetName
IfErrors noLM
Pop $0
UserInfo::GetAccountType
Pop $1
StrCmp $1 "Admin" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Admin group'
Goto done
StrCmp $1 "Power" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Power Users group'
Goto done
noLM:
;Get installation folder from registry if available
done:
FunctionEnd
;--- Add/Remove callback functions: ---
!macro SectionList MacroName
;This macro used to perform operation on multiple sections.
;List all of your components in following manner here.
@CPACK_NSIS_COMPONENT_SECTION_LIST@
!macroend
Section -FinishComponents
;Removes unselected components and writes component status to registry
!insertmacro SectionList "FinishSection"
!ifdef CPACK_NSIS_ADD_REMOVE
; Get the name of the installer executable
System::Call 'kernel32::GetModuleFileNameA(i 0, t .R0, i 1024) i r1'
StrCpy $R3 $R0
; Strip off the last 13 characters, to see if we have AddRemove.exe
StrLen $R1 $R0
IntOp $R1 $R0 - 13
StrCpy $R2 $R0 13 $R1
StrCmp $R2 "AddRemove.exe" addremove_installed
; We're not running AddRemove.exe, so install it
CopyFiles $R3 $INSTDIR\AddRemove.exe
addremove_installed:
!endif
SectionEnd
;--- End of Add/Remove callback functions ---
;--------------------------------
; Component dependencies
Function .onSelChange
!insertmacro SectionList MaybeSelectionChanged
FunctionEnd
;--------------------------------
;Uninstaller Section
Section "Uninstall"
ReadRegStr $START_MENU SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "StartMenu"
;MessageBox MB_OK "Start menu is in: $START_MENU"
ReadRegStr $DO_NOT_ADD_TO_PATH SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "DoNotAddToPath"
ReadRegStr $ADD_TO_PATH_ALL_USERS SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "AddToPathAllUsers"
ReadRegStr $ADD_TO_PATH_CURRENT_USER SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "AddToPathCurrentUser"
;MessageBox MB_OK "Add to path: $DO_NOT_ADD_TO_PATH all users: $ADD_TO_PATH_ALL_USERS"
ReadRegStr $INSTALL_DESKTOP SHCTX \
"Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@" "InstallToDesktop"
;MessageBox MB_OK "Install to desktop: $INSTALL_DESKTOP "
@CPACK_NSIS_EXTRA_UNINSTALL_COMMANDS@
;Remove files we installed.
;Keep the list of directories here in sync with the File commands above.
@CPACK_NSIS_DELETE_FILES@
@CPACK_NSIS_DELETE_DIRECTORIES@
!ifdef CPACK_NSIS_ADD_REMOVE
;Remove the add/remove program
Delete "$INSTDIR\AddRemove.exe"
!endif
;Remove the uninstaller itself.
Delete "$INSTDIR\Uninstall.exe"
DeleteRegKey SHCTX "Software\Microsoft\Windows\CurrentVersion\Uninstall\@CPACK_PACKAGE_NAME@"
;Remove the installation directory if it is empty.
RMDir "$INSTDIR"
; Remove the registry entries.
DeleteRegKey SHCTX "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@"
; Removes all optional components
!insertmacro SectionList "RemoveSection"
!insertmacro MUI_STARTMENU_GETFOLDER Application $MUI_TEMP
Delete "$SMPROGRAMS\$MUI_TEMP\Uninstall.lnk"
@CPACK_NSIS_DELETE_ICONS@
@CPACK_NSIS_DELETE_ICONS_EXTRA@
;Delete empty start menu parent diretories
StrCpy $MUI_TEMP "$SMPROGRAMS\$MUI_TEMP"
startMenuDeleteLoop:
ClearErrors
RMDir $MUI_TEMP
GetFullPathName $MUI_TEMP "$MUI_TEMP\.."
IfErrors startMenuDeleteLoopDone
StrCmp "$MUI_TEMP" "$SMPROGRAMS" startMenuDeleteLoopDone startMenuDeleteLoop
startMenuDeleteLoopDone:
; If the user changed the shortcut, then untinstall may not work. This should
; try to fix it.
StrCpy $MUI_TEMP "$START_MENU"
Delete "$SMPROGRAMS\$MUI_TEMP\Uninstall.lnk"
@CPACK_NSIS_DELETE_ICONS_EXTRA@
;Delete empty start menu parent diretories
StrCpy $MUI_TEMP "$SMPROGRAMS\$MUI_TEMP"
secondStartMenuDeleteLoop:
ClearErrors
RMDir $MUI_TEMP
GetFullPathName $MUI_TEMP "$MUI_TEMP\.."
IfErrors secondStartMenuDeleteLoopDone
StrCmp "$MUI_TEMP" "$SMPROGRAMS" secondStartMenuDeleteLoopDone secondStartMenuDeleteLoop
secondStartMenuDeleteLoopDone:
DeleteRegKey /ifempty SHCTX "Software\@CPACK_PACKAGE_VENDOR@\@CPACK_PACKAGE_INSTALL_REGISTRY_KEY@"
Push $INSTDIR\bin
StrCmp $DO_NOT_ADD_TO_PATH_ "1" doNotRemoveFromPath 0
Call un.RemoveFromPath
doNotRemoveFromPath:
SectionEnd
;--------------------------------
; determine admin versus local install
; Is install for "AllUsers" or "JustMe"?
; Default to "JustMe" - set to "AllUsers" if admin or on Win9x
; This function is used for the very first "custom page" of the installer.
; This custom page does not show up visibly, but it executes prior to the
; first visible page and sets up $INSTDIR properly...
; Choose different default installation folder based on SV_ALLUSERS...
; "Program Files" for AllUsers, "My Documents" for JustMe...
Function .onInit
; Reads components status for registry
!insertmacro SectionList "InitSection"
; check to see if /D has been used to change
; the install directory by comparing it to the
; install directory that is expected to be the
; default
StrCpy $IS_DEFAULT_INSTALLDIR 0
StrCmp "$INSTDIR" "@CPACK_NSIS_INSTALL_ROOT@\@CPACK_PACKAGE_INSTALL_DIRECTORY@" 0 +2
StrCpy $IS_DEFAULT_INSTALLDIR 1
StrCpy $SV_ALLUSERS "JustMe"
; if default install dir then change the default
; if it is installed for JustMe
StrCmp "$IS_DEFAULT_INSTALLDIR" "1" 0 +2
StrCpy $INSTDIR "$DOCUMENTS\@CPACK_PACKAGE_INSTALL_DIRECTORY@"
ClearErrors
UserInfo::GetName
IfErrors noLM
Pop $0
UserInfo::GetAccountType
Pop $1
StrCmp $1 "Admin" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Admin group'
StrCpy $SV_ALLUSERS "AllUsers"
Goto done
StrCmp $1 "Power" 0 +3
SetShellVarContext all
;MessageBox MB_OK 'User "$0" is in the Power Users group'
StrCpy $SV_ALLUSERS "AllUsers"
Goto done
noLM:
StrCpy $SV_ALLUSERS "AllUsers"
;Get installation folder from registry if available
done:
StrCmp $SV_ALLUSERS "AllUsers" 0 +3
StrCmp "$IS_DEFAULT_INSTALLDIR" "1" 0 +2
StrCpy $INSTDIR "@CPACK_NSIS_INSTALL_ROOT@\@CPACK_PACKAGE_INSTALL_DIRECTORY@"
StrCmp "@CPACK_NSIS_MODIFY_PATH@" "ON" 0 noOptionsPage
!insertmacro MUI_INSTALLOPTIONS_EXTRACT "NSIS.InstallOptions.ini"
noOptionsPage:
FunctionEnd
diff --git a/CMake/PackageDepends/MITK_Boost_Config.cmake b/CMake/PackageDepends/MITK_Boost_Config.cmake
index 967e1e8124..b152bfa4f5 100644
--- a/CMake/PackageDepends/MITK_Boost_Config.cmake
+++ b/CMake/PackageDepends/MITK_Boost_Config.cmake
@@ -1,17 +1,13 @@
-if(MITK_USE_Boost_LIBRARIES)
- find_package(Boost 1.68.0 REQUIRED COMPONENTS ${MITK_USE_Boost_LIBRARIES} QUIET)
-else()
- find_package(Boost 1.68.0 REQUIRED QUIET)
+find_package(Boost REQUIRED COMPONENTS ${Boost_REQUIRED_COMPONENTS_BY_MODULE})
+
+if(Boost_REQUIRED_COMPONENTS_BY_MODULE)
+ foreach(boost_component ${Boost_REQUIRED_COMPONENTS_BY_MODULE})
+ list(APPEND ALL_LIBRARIES "Boost::${boost_component}")
+ endforeach()
endif()
-list(APPEND ALL_INCLUDE_DIRECTORIES ${Boost_INCLUDE_DIRS})
+list(APPEND ALL_LIBRARIES "Boost::boost")
-if(Boost_LIBRARIES)
- if(WIN32)
- # Force dynamic linking
- list(APPEND ALL_COMPILE_OPTIONS -DBOOST_ALL_DYN_LINK)
- else()
- # Boost has an auto link feature (pragma comment lib) for Windows
- list(APPEND ALL_LIBRARIES ${Boost_LIBRARIES})
- endif()
+if(MSVC)
+ list(APPEND ALL_LIBRARIES "Boost::dynamic_linking" "bcrypt")
endif()
diff --git a/CMake/PackageDepends/MITK_ITK_Config.cmake b/CMake/PackageDepends/MITK_ITK_Config.cmake
index 7daf7b4d65..1e2b401f82 100644
--- a/CMake/PackageDepends/MITK_ITK_Config.cmake
+++ b/CMake/PackageDepends/MITK_ITK_Config.cmake
@@ -1,4 +1,16 @@
-find_package(ITK COMPONENTS ${ITK_REQUIRED_COMPONENTS_BY_MODULE} REQUIRED)
+foreach(itk_component ${ITK_REQUIRED_COMPONENTS_BY_MODULE})
+ if(NOT itk_component MATCHES "^ITK")
+ set(itk_component "ITK${itk_component}")
+ endif()
+ list(APPEND _itk_required_components_by_module ${itk_component})
+endforeach()
-list(APPEND ALL_LIBRARIES ${ITK_LIBRARIES})
-list(APPEND ALL_INCLUDE_DIRECTORIES ${ITK_INCLUDE_DIRS})
+find_package(ITK COMPONENTS ${_itk_required_components_by_module} REQUIRED)
+
+foreach(itk_component ${_itk_required_components_by_module})
+ if(${itk_component}_LIBRARIES)
+ list(APPEND ALL_LIBRARIES ${${itk_component}_LIBRARIES})
+ else()
+ list(APPEND ALL_LIBRARIES ${itk_component})
+ endif()
+endforeach()
diff --git a/CMake/PackageDepends/MITK_OpenGL_Config.cmake b/CMake/PackageDepends/MITK_OpenGL_Config.cmake
index a322942bd5..0925ef472b 100644
--- a/CMake/PackageDepends/MITK_OpenGL_Config.cmake
+++ b/CMake/PackageDepends/MITK_OpenGL_Config.cmake
@@ -1,5 +1,3 @@
set(OpenGL_GL_PREFERENCE LEGACY)
find_package(OpenGL REQUIRED)
-list(APPEND ALL_INCLUDE_DIRECTORIES ${OPENGL_INCLUDE_DIR})
-list(APPEND ALL_LIBRARIES ${OPENGL_LIBRARIES})
-
+list(APPEND ALL_LIBRARIES OpenGL::GL)
diff --git a/CMake/PackageDepends/MITK_OpenMP_Config.cmake b/CMake/PackageDepends/MITK_OpenMP_Config.cmake
index e69de29bb2..8ca95d08c1 100644
--- a/CMake/PackageDepends/MITK_OpenMP_Config.cmake
+++ b/CMake/PackageDepends/MITK_OpenMP_Config.cmake
@@ -0,0 +1 @@
+set(ALL_LIBRARIES OpenMP::OpenMP_CXX)
diff --git a/CMake/PackageDepends/MITK_OpenMesh_Config.cmake b/CMake/PackageDepends/MITK_OpenMesh_Config.cmake
index e69de29bb2..85d06a71dd 100644
--- a/CMake/PackageDepends/MITK_OpenMesh_Config.cmake
+++ b/CMake/PackageDepends/MITK_OpenMesh_Config.cmake
@@ -0,0 +1,7 @@
+find_package(OpenMesh COMPONENTS ${OpenMesh_REQUIRED_COMPONENTS_BY_MODULE} REQUIRED)
+
+foreach(openmesh_component ${OpenMesh_REQUIRED_COMPONENTS_BY_MODULE})
+ list(APPEND ALL_LIBRARIES "OpenMesh${openmesh_component}")
+endforeach()
+
+set(ALL_COMPILE_DEFINITIONS -D_USE_MATH_DEFINES)
diff --git a/CMake/PackageDepends/MITK_OpenSSL_Config.cmake b/CMake/PackageDepends/MITK_OpenSSL_Config.cmake
new file mode 100644
index 0000000000..ade27a6dc0
--- /dev/null
+++ b/CMake/PackageDepends/MITK_OpenSSL_Config.cmake
@@ -0,0 +1,5 @@
+find_package(OpenSSL COMPONENTS ${OpenSSL_REQUIRED_COMPONENTS_BY_MODULE} REQUIRED)
+
+foreach(openssl_component ${OpenSSL_REQUIRED_COMPONENTS_BY_MODULE})
+ list(APPEND ALL_LIBRARIES "OpenSSL::${openssl_component}")
+endforeach()
diff --git a/CMake/PackageDepends/MITK_Poco_Config.cmake b/CMake/PackageDepends/MITK_Poco_Config.cmake
index cf5397f2d7..96f8a3c19d 100644
--- a/CMake/PackageDepends/MITK_Poco_Config.cmake
+++ b/CMake/PackageDepends/MITK_Poco_Config.cmake
@@ -1,7 +1,9 @@
-set(Poco_LIBRARIES)
if(NOT Poco_REQUIRED_COMPONENTS_BY_MODULE)
set(Poco_REQUIRED_COMPONENTS_BY_MODULE Foundation)
endif()
+
find_package(Poco PATHS ${Poco_DIR} COMPONENTS ${Poco_REQUIRED_COMPONENTS_BY_MODULE} CONFIG REQUIRED)
-list(APPEND ALL_LIBRARIES ${Poco_LIBRARIES})
+foreach(poco_component ${Poco_REQUIRED_COMPONENTS_BY_MODULE})
+ list(APPEND ALL_LIBRARIES "Poco::${poco_component}")
+endforeach()
diff --git a/CMake/PackageDepends/MITK_Python3_Config.cmake b/CMake/PackageDepends/MITK_Python3_Config.cmake
index e69de29bb2..7324aa0d44 100644
--- a/CMake/PackageDepends/MITK_Python3_Config.cmake
+++ b/CMake/PackageDepends/MITK_Python3_Config.cmake
@@ -0,0 +1,3 @@
+foreach(python3_component ${Python3_REQUIRED_COMPONENTS_BY_MODULE})
+ list(APPEND ALL_LIBRARIES "Python3::${python3_component}")
+endforeach()
diff --git a/CMake/PackageDepends/MITK_Qt5_Config.cmake b/CMake/PackageDepends/MITK_Qt5_Config.cmake
index 37f08b5160..cda0e217cd 100644
--- a/CMake/PackageDepends/MITK_Qt5_Config.cmake
+++ b/CMake/PackageDepends/MITK_Qt5_Config.cmake
@@ -1,4 +1,5 @@
find_package(Qt5 COMPONENTS ${Qt5_REQUIRED_COMPONENTS_BY_MODULE} REQUIRED QUIET)
-foreach(_component ${Qt5_REQUIRED_COMPONENTS_BY_MODULE})
- list(APPEND ALL_LIBRARIES ${Qt5${_component}_LIBRARIES})
+
+foreach(qt5_component ${Qt5_REQUIRED_COMPONENTS_BY_MODULE})
+ list(APPEND ALL_LIBRARIES Qt5::${qt5_component})
endforeach()
diff --git a/CMake/PackageDepends/MITK_VPX_Config.cmake b/CMake/PackageDepends/MITK_VPX_Config.cmake
deleted file mode 100644
index ec51ff8dc7..0000000000
--- a/CMake/PackageDepends/MITK_VPX_Config.cmake
+++ /dev/null
@@ -1,9 +0,0 @@
-set( VPX_LIB "" CACHE FILEPATH "Search for the vpx library file" )
-set( VPX_HEADER_DIR "" CACHE PATH "The path containing vpy headers" )
-set( VPX_FOUND FALSE )
-
-if(VPX_LIB AND VPX_HEADER_DIR)
- list(APPEND ALL_LIBRARIES ${VPX_LIB})
- list(APPEND ALL_INCLUDE_DIRECTORIES ${VPX_HEADER_DIR})
- set( VPX_FOUND TRUE )
-endif()
diff --git a/CMake/PackageDepends/MITK_VTK_Config.cmake b/CMake/PackageDepends/MITK_VTK_Config.cmake
index f13834dd55..74a9a3be22 100644
--- a/CMake/PackageDepends/MITK_VTK_Config.cmake
+++ b/CMake/PackageDepends/MITK_VTK_Config.cmake
@@ -1,8 +1,9 @@
find_package(VTK COMPONENTS ${VTK_REQUIRED_COMPONENTS_BY_MODULE} REQUIRED)
-if(MITK_USE_Qt5)
- find_package(Qt5Widgets REQUIRED QUIET)
-endif()
+foreach(vtk_module ${VTK_REQUIRED_COMPONENTS_BY_MODULE})
+ list(APPEND ALL_LIBRARIES "VTK::${vtk_module}")
+endforeach()
-list(APPEND ALL_INCLUDE_DIRECTORIES ${VTK_INCLUDE_DIRS})
-list(APPEND ALL_LIBRARIES ${VTK_LIBRARIES})
+if(ALL_LIBRARIES)
+ vtk_module_autoinit(TARGETS ${MODULE_NAME} MODULES ${ALL_LIBRARIES})
+endif()
diff --git a/CMake/PackageDepends/MITK_cpprestsdk_Config.cmake b/CMake/PackageDepends/MITK_cpprestsdk_Config.cmake
index e69de29bb2..7764cec563 100644
--- a/CMake/PackageDepends/MITK_cpprestsdk_Config.cmake
+++ b/CMake/PackageDepends/MITK_cpprestsdk_Config.cmake
@@ -0,0 +1 @@
+set(ALL_LIBRARIES cpprestsdk::cpprest)
diff --git a/CMake/PackageDepends/MITK_tinyxml2_Config.cmake b/CMake/PackageDepends/MITK_tinyxml2_Config.cmake
new file mode 100644
index 0000000000..b08632d240
--- /dev/null
+++ b/CMake/PackageDepends/MITK_tinyxml2_Config.cmake
@@ -0,0 +1 @@
+set(ALL_LIBRARIES "tinyxml2::tinyxml2")
diff --git a/CMake/PackageDepends/MITK_tinyxml_Config.cmake b/CMake/PackageDepends/MITK_tinyxml_Config.cmake
deleted file mode 100644
index ee84a8ae1a..0000000000
--- a/CMake/PackageDepends/MITK_tinyxml_Config.cmake
+++ /dev/null
@@ -1,4 +0,0 @@
-list(APPEND ALL_LIBRARIES ${tinyxml_LIBRARIES})
-if(tinyxml_INCLUDE_DIRS)
- list(APPEND ALL_INCLUDE_DIRECTORIES ${tinyxml_INCLUDE_DIRS})
-endif()
diff --git a/CMake/RunInstalledApp.bat b/CMake/RunInstalledApp.bat
new file mode 100644
index 0000000000..8ca0361f5c
--- /dev/null
+++ b/CMake/RunInstalledApp.bat
@@ -0,0 +1 @@
+start "" /B /D bin bin/%~n0.exe %*
diff --git a/CMake/mitkFunctionCreateBlueBerryApplication.cmake b/CMake/mitkFunctionCreateBlueBerryApplication.cmake
index 9f4001b778..8869470500 100644
--- a/CMake/mitkFunctionCreateBlueBerryApplication.cmake
+++ b/CMake/mitkFunctionCreateBlueBerryApplication.cmake
@@ -1,229 +1,231 @@
#!
#! Create a BlueBerry application.
#!
#! \brief This function will create a BlueBerry application together with all
#! necessary provisioning and configuration data and install support.
#!
#! \param NAME (required) The name of the executable.
#! \param DESCRIPTION (optional) A human-readable description of your application.
#! The usage depends on the CPack generator (on Windows, this is a descriptive
#! text for the created shortcuts).
#! \param SOURCES (optional) A list of source files to compile into your executable. Defaults
#! to <name>.cpp.
#! \param PLUGINS (optional) A list of required plug-ins. Defaults to all known plug-ins.
#! \param EXCLUDE_PLUGINS (optional) A list of plug-ins which should not be used. Mainly
#! useful if PLUGINS was not used.
#! \param LINK_LIBRARIES A list of libraries to be linked with the executable.
#! \param LIBRARY_DIRS A list of directories to pass through to MITK_INSTALL_TARGETS
#! \param NO_PROVISIONING (option) Do not create provisioning files.
#! \param NO_INSTALL (option) Do not install this executable
#!
#! Assuming that there exists a file called <code>MyApp.cpp</code>, an example call looks like:
#! \code
#! mitkFunctionCreateBlueBerryApplication(
#! NAME MyApp
#! DESCRIPTION "MyApp - New ways to explore medical data"
#! EXCLUDE_PLUGINS org.mitk.gui.qt.extapplication
#! )
#! \endcode
#!
function(mitkFunctionCreateBlueBerryApplication)
cmake_parse_arguments(_APP "NO_PROVISIONING;NO_INSTALL" "NAME;DESCRIPTION" "SOURCES;PLUGINS;EXCLUDE_PLUGINS;LINK_LIBRARIES;LIBRARY_DIRS" ${ARGN})
if(NOT _APP_NAME)
message(FATAL_ERROR "NAME argument cannot be empty.")
endif()
if(NOT _APP_SOURCES)
set(_APP_SOURCES ${_APP_NAME}.cpp)
endif()
if(NOT _APP_PLUGINS)
ctkFunctionGetAllPluginTargets(_APP_PLUGINS)
else()
set(_plugins ${_APP_PLUGINS})
set(_APP_PLUGINS)
foreach(_plugin ${_plugins})
string(REPLACE "." "_" _plugin_target ${_plugin})
list(APPEND _APP_PLUGINS ${_plugin_target})
endforeach()
# get all plug-in dependencies
ctkFunctionGetPluginDependencies(_plugin_deps PLUGINS ${_APP_PLUGINS} ALL)
# add the dependencies to the list of application plug-ins
list(APPEND _APP_PLUGINS ${_plugin_deps})
endif()
# -----------------------------------------------------------------------
# Set up include and link dirs for the executable
# -----------------------------------------------------------------------
include_directories(
${org_blueberry_core_runtime_INCLUDE_DIRS}
)
# -----------------------------------------------------------------------
# Add executable icon (Windows)
# -----------------------------------------------------------------------
set(WINDOWS_ICON_RESOURCE_FILE "")
if(WIN32)
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/icons/${_APP_NAME}.rc")
set(WINDOWS_ICON_RESOURCE_FILE "${CMAKE_CURRENT_SOURCE_DIR}/icons/${_APP_NAME}.rc")
endif()
endif()
# -----------------------------------------------------------------------
# Create the executable and link libraries
# -----------------------------------------------------------------------
set(_app_compile_flags )
if(WIN32)
set(_app_compile_flags "${_app_compile_flags} -DPOCO_NO_UNWINDOWS -DWIN32_LEAN_AND_MEAN")
endif()
if(MITK_SHOW_CONSOLE_WINDOW)
add_executable(${_APP_NAME} MACOSX_BUNDLE ${_APP_SOURCES} ${WINDOWS_ICON_RESOURCE_FILE})
else()
add_executable(${_APP_NAME} MACOSX_BUNDLE WIN32 ${_APP_SOURCES} ${WINDOWS_ICON_RESOURCE_FILE})
endif()
if(NOT CMAKE_CURRENT_SOURCE_DIR MATCHES "^${CMAKE_SOURCE_DIR}.*")
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
if(CMAKE_CURRENT_SOURCE_DIR MATCHES "^${MITK_EXTENSION_DIR}.*")
get_filename_component(MITK_EXTENSION_ROOT_FOLDER "${MITK_EXTENSION_DIR}" NAME)
set_property(TARGET ${_APP_NAME} PROPERTY FOLDER "${MITK_EXTENSION_ROOT_FOLDER}/Applications")
break()
endif()
endforeach()
else()
set_property(TARGET ${_APP_NAME} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Applications")
endif()
mitk_use_modules(TARGET ${_APP_NAME} MODULES MitkAppUtil)
set_target_properties(${_APP_NAME} PROPERTIES
COMPILE_FLAGS "${_app_compile_flags}")
target_link_libraries(${_APP_NAME} PRIVATE org_blueberry_core_runtime ${_APP_LINK_LIBRARIES})
if(WIN32)
target_link_libraries(${_APP_NAME} PRIVATE ${QT_QTMAIN_LIBRARY})
endif()
# -----------------------------------------------------------------------
# Add executable icon and bundle name (Mac)
# -----------------------------------------------------------------------
if(APPLE)
if( _APP_DESCRIPTION)
set_target_properties(${_APP_NAME} PROPERTIES MACOSX_BUNDLE_NAME "${_APP_DESCRIPTION}")
else()
set_target_properties(${_APP_NAME} PROPERTIES MACOSX_BUNDLE_NAME "${_APP_NAME}")
endif()
set(icon_name "icon.icns")
set(icon_full_path "${CMAKE_CURRENT_SOURCE_DIR}/icons/${icon_name}")
if(EXISTS "${icon_full_path}")
set_target_properties(${_APP_NAME} PROPERTIES MACOSX_BUNDLE_ICON_FILE "${icon_name}")
file(COPY ${icon_full_path} DESTINATION "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.app/Contents/Resources/")
INSTALL (FILES ${icon_full_path} DESTINATION "${_APP_NAME}.app/Contents/Resources/")
endif()
endif()
# -----------------------------------------------------------------------
# Set build time dependencies
# -----------------------------------------------------------------------
# This ensures that all enabled plug-ins are up-to-date when the
# executable is build.
if(_APP_PLUGINS)
ctkMacroGetAllProjectTargetLibraries("${_APP_PLUGINS}" _project_plugins)
if(_APP_EXCLUDE_PLUGINS AND _project_plugins)
set(_exclude_targets)
foreach(_exclude_plugin ${_APP_EXCLUDE_PLUGINS})
string(REPLACE "." "_" _exclude_target ${_exclude_plugin})
list(APPEND _exclude_targets ${_exclude_target})
endforeach()
list(REMOVE_ITEM _project_plugins ${_exclude_targets})
endif()
if(_project_plugins)
add_dependencies(${_APP_NAME} ${_project_plugins})
endif()
endif()
# -----------------------------------------------------------------------
# Additional files needed for the executable
# -----------------------------------------------------------------------
if(NOT _APP_NO_PROVISIONING)
# Create a provisioning file, listing all plug-ins
set(_prov_file "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.provisioning")
mitkFunctionCreateProvisioningFile(FILE ${_prov_file}
PLUGINS ${_APP_PLUGINS}
EXCLUDE_PLUGINS ${_APP_EXCLUDE_PLUGINS}
)
endif()
# Create a .ini file for initial parameters
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${_APP_NAME}.ini")
configure_file(${_APP_NAME}.ini
${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.ini)
endif()
# Create batch and VS user files for Windows platforms
include(mitkFunctionCreateWindowsBatchScript)
if(WIN32)
set(template_name "start${_APP_NAME}.bat.in")
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${template_name}")
foreach(BUILD_TYPE debug release)
mitkFunctionCreateWindowsBatchScript(${template_name}
${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/start${_APP_NAME}_${BUILD_TYPE}.bat
${BUILD_TYPE})
endforeach()
endif()
mitkFunctionConfigureVisualStudioUserProjectFile(
NAME ${_APP_NAME}
)
endif(WIN32)
# -----------------------------------------------------------------------
# Install support
# -----------------------------------------------------------------------
if(NOT _APP_NO_INSTALL)
# This installs all third-party CTK plug-ins
mitkFunctionInstallThirdPartyCTKPlugins(${_APP_PLUGINS} EXCLUDE ${_APP_EXCLUDE_PLUGINS})
if(COMMAND BlueBerryApplicationInstallHook)
set(_real_app_plugins ${_APP_PLUGINS})
if(_APP_EXCLUDE_PLUGINS)
list(REMOVE_ITEM _real_app_plugins ${_APP_EXCLUDE_PLUGINS})
endif()
BlueBerryApplicationInstallHook(APP_NAME ${_APP_NAME} PLUGINS ${_real_app_plugins})
endif()
# Install the executable
MITK_INSTALL_TARGETS(EXECUTABLES ${_APP_NAME} LIBRARY_DIRS ${_APP_LIBRARY_DIRS} GLOB_PLUGINS )
if(NOT _APP_NO_PROVISIONING)
# Install the provisioning file
mitkFunctionInstallProvisioningFiles(${_prov_file})
endif()
# On Linux, create a shell script to start a relocatable application
if(UNIX AND NOT APPLE)
- install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${_APP_NAME}.sh)
+ install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME "${_APP_NAME}.sh")
+ elseif(WIN32)
+ install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.bat" DESTINATION "." RENAME "${_APP_NAME}.bat")
endif()
# Tell cpack the executables that you want in the start menu as links
set(MITK_CPACK_PACKAGE_EXECUTABLES ${MITK_CPACK_PACKAGE_EXECUTABLES} "${_APP_NAME};${_APP_DESCRIPTION}" CACHE INTERNAL "Collecting windows shortcuts to executables")
endif()
endfunction()
function(FunctionCreateBlueBerryApplication)
message(SEND_ERROR "The function FunctionCreateBlueBerryApplication was renamed to mitkFunctionCreateBlueBerryApplication in MITK 2015.05")
endfunction()
diff --git a/CMake/mitkFunctionCreateCommandLineApp.cmake b/CMake/mitkFunctionCreateCommandLineApp.cmake
index 139d6d53ef..949e57e848 100644
--- a/CMake/mitkFunctionCreateCommandLineApp.cmake
+++ b/CMake/mitkFunctionCreateCommandLineApp.cmake
@@ -1,55 +1,58 @@
#!
#! Create a Command Line App.
#!
#! \brief This function will create a command line executable and the scripts required to run it
#!
#! \param NAME (required) Name of the command line app
#! \param DEPENDS (optional) Required MITK modules beyond MitkCommandLine
#! \param PACKAGE_DEPENDS (optional) list of "packages" this command line app depends on (e.g. ITK, VTK, etc.)
+#! \param TARGET_DEPENDS (optional) list of additional CMake targets this command line app depends on
#! \param CPP_FILES (optional) list of cpp files, if it is not given NAME.cpp is assumed
#!
#! Assuming that there exists a file called <code>MyApp.cpp</code>, an example call looks like:
#! \code
#! mitkFunctionCreateCommandLineApp(
#! NAME MyApp
#! DEPENDS MitkCore MitkPlanarFigure
#! PACKAGE_DEPENDS ITK VTK
#! )
#! \endcode
#!
function(mitkFunctionCreateCommandLineApp)
set(_function_params
NAME # Name of the command line app
)
set(_function_multiparams
DEPENDS # list of modules this command line app depends on
PACKAGE_DEPENDS # list of "packages" this command line app depends on (e.g. ITK, VTK, etc.)
+ TARGET_DEPENDS # list of additional CMake targets this command line app depends on
CPP_FILES # (optional) list of cpp files, if it is not given NAME.cpp is assumed
)
set(_function_options
WARNINGS_NO_ERRORS
)
cmake_parse_arguments(CMDAPP "${_function_options}" "${_function_params}" "${_function_multiparams}" ${ARGN})
if(NOT CMDAPP_NAME)
message(FATAL_ERROR "NAME argument cannot be empty.")
endif()
if(NOT CMDAPP_CPP_FILES)
set(CMDAPP_CPP_FILES ${CMDAPP_NAME}.cpp)
endif()
if(CMDAPP_WARNINGS_NO_ERRORS)
LIST(APPEND _CMDAPP_OPTIONS WARNINGS_NO_ERRORS)
endif()
mitk_create_executable(${CMDAPP_NAME}
DEPENDS MitkCommandLine ${CMDAPP_DEPENDS}
PACKAGE_DEPENDS ${CMDAPP_PACKAGE_DEPENDS}
+ TARGET_DEPENDS ${TARGET_DEPENDS}
CPP_FILES ${CMDAPP_CPP_FILES}
${_CMDAPP_OPTIONS}
)
endfunction()
diff --git a/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake b/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake
index 85ea849bb2..7478718143 100644
--- a/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake
+++ b/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake
@@ -1,108 +1,114 @@
#!
#! Create a Command Line App.
#!
#! \brief This function will create a command line executable and the scripts required to run it
#!
#! \param NAME (required) Name of the algorithm / cmake target
#! \param DEPENDS (optional) Required MITK modules beyond MitkCommandLine
#! \param PACKAGE_DEPENDS (optional) list of "packages" this command line app depends on (e.g. ITK, VTK, etc.)
+#! \param TARGET_DEPENDS (optional) list of additional CMake targets this command line app depends on
#! \param CPP_FILES (optional) list of cpp files, if it is not given NAME.cpp is assumed
#! \param INCLUDE_DIRS (optional): All directories that should be added as include dirs to the project
#! \param PROFILE (optional): The profile file that should be used for the algorithm. If not set it is "./<algname>.profile".
#! \param NO_PROFILE_GEN (optional): Flag. If set no profile resource will be generated.
#! \param ADDITIONAL_LIBS (optional) List of additional private libraries linked to this module.
#! The folder containing the library will be added to the global list of library search paths.
#! \param H_FILES (optional) List of public header files for this module.
#! Assuming that there exists a file called <code>MyApp.cpp</code>, an example call looks like:
#! \code
#! mitkFunctionCreateCommandLineApp(
#! NAME MyApp
#! DEPENDS MitkCore MitkPlanarFigure
#! PACKAGE_DEPENDS ITK VTK
#! )
#! \endcode
#!
function(mitkFunctionCreateMatchPointDeployedAlgorithm)
set(_function_params
NAME # Name of the algorithm/target
PROFILE # Profile of the algorithm that should be used
)
set(_function_multiparams
DEPENDS # list of modules this command line app depends on
PACKAGE_DEPENDS # list of "packages" this command line app depends on (e.g. ITK, VTK, etc.)
+ TARGET_DEPENDS # list of CMake targets this command line app depends on
CPP_FILES # (optional) list of cpp files, if it is not given NAME.cpp is assumed
INCLUDE_DIRS # include directories: [PUBLIC|PRIVATE|INTERFACE] <list>
ADDITIONAL_LIBS # list of addidtional private libraries linked to this module.
H_FILES # list of header files: [PUBLIC|PRIVATE] <list>
)
set(_function_options
NO_PROFILE_GEN #Flag that indicates that no profile resource should be generated.
)
cmake_parse_arguments(ALG "${_function_options}" "${_function_params}" "${_function_multiparams}" ${ARGN})
if( NOT (DEFINED MITK_USE_MatchPoint) OR NOT (${MITK_USE_MatchPoint}))
message(FATAL_ERROR "Need package Matchpoint to deploy MatchPoint Algorithms.")
endif()
if(NOT ALG_NAME)
message(FATAL_ERROR "NAME argument cannot be empty.")
endif()
SET(ALG_TARGET "MDRA_${ALG_NAME}")
if(NOT ALG_CPP_FILES)
set(ALG_CPP_FILES "${ALG_NAME}.cpp")
endif()
IF(NOT ALG_PROFILE)
set(ALG_PROFILE "${ALG_NAME}.profile")
ENDIF(NOT ALG_PROFILE)
IF(NOT ALG_NO_PROFILE_GEN)
MESSAGE(STATUS "... generate MDRA profile for ${ALG_NAME} (from ${ALG_PROFILE})...")
include(${MatchPoint_SOURCE_DIR}/CMake/mapFunctionCreateAlgorithmProfile.cmake)
CREATE_ALGORITHM_PROFILE(${ALG_NAME} ${ALG_PROFILE})
MESSAGE(STATUS "... algorithm UID: ${ALGORITHM_PROFILE_UID}")
ENDIF(NOT ALG_NO_PROFILE_GEN)
MESSAGE(STATUS "... deploy MDRA algorithm ${ALG_NAME}...")
ADD_LIBRARY(${ALG_TARGET} SHARED ${ALG_CPP_FILES} ${ALGORITHM_PROFILE_FILE})
SET_TARGET_PROPERTIES(${ALG_TARGET} PROPERTIES
OUTPUT_NAME "mdra-${MatchPoint_VERSION_MAJOR}-${MatchPoint_VERSION_MINOR}_${ALG_NAME}"
OUTPUT_NAME_DEBUG "mdra-D-${MatchPoint_VERSION_MAJOR}-${MatchPoint_VERSION_MINOR}_${ALG_NAME}"
PREFIX ""
FOLDER "${MITK_ROOT_FOLDER}/Modules/MatchPointAlgorithms")
mitk_use_modules(TARGET ${ALG_TARGET}
MODULES ${ALG_DEPENDS}
- PACKAGES PRIVATE ITK MatchPoint ${ALG_PACKAGE_DEPENDS}
+ PACKAGES PRIVATE MatchPoint ${ALG_PACKAGE_DEPENDS}
)
+ if(ALG_TARGET_DEPENDS)
+ target_link_libraries(${ALG_TARGET} ${ALG_TARGET_DEPENDS})
+ endif()
+
target_include_directories(${ALG_TARGET} PRIVATE ${ALG_INCLUDE_DIRS} ${CMAKE_CURRENT_BINARY_DIR})
if(ALG_ADDITIONAL_LIBS)
target_link_libraries(${ALG_TARGET} PRIVATE ${ALG_ADDITIONAL_LIBS})
get_property(_mitk_additional_library_search_paths GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS)
foreach(_lib_filepath ${ALG_ADDITIONAL_LIBS})
get_filename_component(_search_path "${_lib_filepath}" PATH)
if(_search_path)
list(APPEND _mitk_additional_library_search_paths "${_search_path}")
endif()
endforeach()
if(_mitk_additional_library_search_paths)
list(REMOVE_DUPLICATES _mitk_additional_library_search_paths)
set_property(GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS ${_mitk_additional_library_search_paths})
endif()
endif()
MITK_INSTALL(TARGETS ${ALG_TARGET})
endfunction()
diff --git a/CMake/mitkFunctionCreateModule.cmake b/CMake/mitkFunctionCreateModule.cmake
index 4fe684de2f..f7b334c80b 100644
--- a/CMake/mitkFunctionCreateModule.cmake
+++ b/CMake/mitkFunctionCreateModule.cmake
@@ -1,651 +1,651 @@
##################################################################
#
# mitk_create_module
#
#! Creates a module for the automatic module dependency system within MITK.
#!
#! Example:
#!
#! \code
#! mitk_create_module(
#! DEPENDS PUBLIC MitkCore
#! PACKAGE_DEPENDS
#! PRIVATE Qt5|Xml+Networking
-#! PUBLIC ITK|Watershed
+#! PUBLIC ITK|Watersheds
#! \endcode
#!
#! The <moduleName> parameter specifies the name of the module which is used
#! to create a logical target name. The parameter is optional in case the
#! MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME variable evaluates to TRUE. The
#! module name will then be derived from the directory name in which this
#! function is called.
#!
#! If set, the following variables will be used to validate the module name:
#!
#! MITK_MODULE_NAME_REGEX_MATCH The module name must match this regular expression.
#! MITK_MODULE_NAME_REGEX_NOT_MATCH The module name must not match this regular expression.
#!
#! If the MITK_MODULE_NAME_PREFIX variable is set, the module name will be prefixed
#! with its contents.
#!
#! A modules source files are specified in a separate CMake file usually
#! called files.cmake, located in the module root directory. The
#! mitk_create_module() macro evaluates the following CMake variables
#! from the files.cmake file:
#!
#! - CPP_FILES A list of .cpp files
#! - H_FILES A list of .h files without a corresponding .cpp file
#! - TXX_FILES A list of .txx files
#! - RESOURCE_FILES A list of files (resources) which are embedded into the module
#! - MOC_H_FILES A list of Qt header files which should be processed by the MOC
#! - UI_FILES A list of .ui Qt UI files
#! - QRC_FILES A list of .qrc Qt resource files
#! - DOX_FILES A list of .dox Doxygen files
#!
#! List of variables available after the function is called:
#! - MODULE_NAME
#! - MODULE_TARGET
#! - MODULE_IS_ENABLED
#!
#! \sa mitk_create_executable
#!
#! Parameters (all optional):
#!
#! \param <moduleName> The module name (also used as target name)
#! \param FILES_CMAKE File name of a CMake file setting source list variables
#! (defaults to files.cmake)
#! \param VERSION Module version number, e.g. "1.2.0"
#! \param AUTOLOAD_WITH A module target name identifying the module which will
#! trigger the automatic loading of this module
#! \param DEPRECATED_SINCE Marks this modules as deprecated since <arg>
#! \param DESCRIPTION A description for this module
#!
#! Multi-value Parameters (all optional):
#!
#! \param INCLUDE_DIRS Include directories for this module:
#! \verbatim
#! [[PUBLIC|PRIVATE|INTERFACE] <dir1>...]...
#! \endverbatim
#! The default scope for include directories is PUBLIC.
#! \param DEPENDS List of module dependencies:
#! \verbatim
#! [[PUBLIC|PRIVATE|INTERFACE] <module1>...]...
#! \endverbatim
#! The default scope for module dependencies is PUBLIC.
#! \param PACKAGE_DEPENDS List of public packages dependencies (e.g. Qt, VTK, etc.).
#! Package dependencies have the following syntax:
#! \verbatim
#! [PUBLIC|PRIVATE|INTERFACE] PACKAGE[|COMPONENT1[+COMPONENT2]...]
#! \endverbatim
#! The default scope for package dependencies is PRIVATE.
#! \param ADDITIONAL_LIBS List of additional private libraries linked to this module.
#! The folder containing the library will be added to the global list of library search paths.
#! \param CPP_FILES List of source files for this module. If the list is non-empty,
#! the module does not need to provide a files.cmake file or FILES_CMAKE argument.
#! \param H_FILES List of public header files for this module. It is recommended to use
#! a files.cmake file instead.
#!
#! Options (optional)
#!
#! \param FORCE_STATIC Force building this module as a static library
#! \param GCC_DEFAULT_VISIBILITY Do not use gcc visibility flags - all
#! symbols will be exported
#! \param NO_INIT Do not create CppMicroServices initialization code
#! \param NO_FEATURE_INFO Do not create a feature info by calling add_feature_info()
#! \param WARNINGS_NO_ERRORS Do not treat compiler warnings as errors
#
##################################################################
function(mitk_create_module)
set(_macro_params
VERSION # module version number, e.g. "1.2.0"
EXPORT_DEFINE # export macro name for public symbols of this module (DEPRECATED)
AUTOLOAD_WITH # a module target name identifying the module which will trigger the
# automatic loading of this module
FILES_CMAKE # file name of a CMake file setting source list variables
# (defaults to files.cmake)
DEPRECATED_SINCE # marks this modules as deprecated
DESCRIPTION # a description for this module
)
set(_macro_multiparams
SUBPROJECTS # list of CDash labels (deprecated)
INCLUDE_DIRS # include directories: [PUBLIC|PRIVATE|INTERFACE] <list>
INTERNAL_INCLUDE_DIRS # include dirs internal to this module (DEPRECATED)
DEPENDS # list of modules this module depends on: [PUBLIC|PRIVATE|INTERFACE] <list>
DEPENDS_INTERNAL # list of modules this module internally depends on (DEPRECATED)
PACKAGE_DEPENDS # list of "packages this module depends on (e.g. Qt, VTK, etc.): [PUBLIC|PRIVATE|INTERFACE] <package-list>
- TARGET_DEPENDS # list of CMake targets this module should depend on
+ TARGET_DEPENDS # list of CMake targets this module should depend on: [PUBLIC|PRIVATE|INTERFACE] <list>
ADDITIONAL_LIBS # list of addidtional private libraries linked to this module.
CPP_FILES # list of cpp files
H_FILES # list of header files: [PUBLIC|PRIVATE] <list>
)
set(_macro_options
FORCE_STATIC # force building this module as a static library
HEADERS_ONLY # this module is a headers-only library
GCC_DEFAULT_VISIBILITY # do not use gcc visibility flags - all symbols will be exported
NO_DEFAULT_INCLUDE_DIRS # do not add default include directories like "include" or "."
NO_INIT # do not create CppMicroServices initialization code
NO_FEATURE_INFO # do not create a feature info by calling add_feature_info()
WARNINGS_NO_ERRORS # do not treat compiler warnings as errors
EXECUTABLE # create an executable; do not use directly, use mitk_create_executable() instead
C_MODULE # compile all source files as C sources
CXX_MODULE # compile all source files as C++ sources
)
cmake_parse_arguments(MODULE "${_macro_options}" "${_macro_params}" "${_macro_multiparams}" ${ARGN})
set(MODULE_NAME ${MODULE_UNPARSED_ARGUMENTS})
# -----------------------------------------------------------------
# Sanity checks
if(NOT MODULE_NAME)
if(MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME)
get_filename_component(MODULE_NAME ${CMAKE_CURRENT_SOURCE_DIR} NAME)
else()
message(SEND_ERROR "The module name must not be empty")
endif()
endif()
- set(_deprecated_args INTERNAL_INCLUDE_DIRS DEPENDS_INTERNAL EXPORT_DEFINE TARGET_DEPENDS HEADERS_ONLY)
+ set(_deprecated_args INTERNAL_INCLUDE_DIRS DEPENDS_INTERNAL EXPORT_DEFINE HEADERS_ONLY)
foreach(_deprecated_arg ${_deprecated_args})
if(MODULE_${_deprecated_arg})
message(WARNING "The ${_deprecated_arg} argument is deprecated")
endif()
endforeach()
set(_module_type module)
set(_Module_type Module)
if(MODULE_EXECUTABLE)
set(_module_type executable)
set(_Module_type Executable)
endif()
if(MITK_MODULE_NAME_REGEX_MATCH)
if(NOT ${MODULE_NAME} MATCHES ${MITK_MODULE_NAME_REGEX_MATCH})
message(SEND_ERROR "The ${_module_type} name \"${MODULE_NAME}\" does not match the regular expression \"${MITK_MODULE_NAME_REGEX_MATCH}\".")
endif()
endif()
if(MITK_MODULE_NAME_REGEX_NOT_MATCH)
if(${MODULE_NAME} MATCHES ${MITK_MODULE_NAME_REGEX_NOT_MATCH})
message(SEND_ERROR "The ${_module_type} name \"${MODULE_NAME}\" must not match the regular expression \"${MITK_MODULE_NAME_REGEX_NOT_MATCH}\".")
endif()
endif()
if(MITK_MODULE_NAME_PREFIX AND NOT MODULE_NAME MATCHES "^${MITK_MODULE_NAME_PREFIX}.*$")
set(MODULE_NAME "${MITK_MODULE_NAME_PREFIX}${MODULE_NAME}")
endif()
if(NOT MODULE_FILES_CMAKE)
set(MODULE_FILES_CMAKE files.cmake)
endif()
if(NOT IS_ABSOLUTE ${MODULE_FILES_CMAKE})
set(MODULE_FILES_CMAKE ${CMAKE_CURRENT_SOURCE_DIR}/${MODULE_FILES_CMAKE})
endif()
# -----------------------------------------------------------------
# Check if module should be build
set(MODULE_TARGET ${MODULE_NAME})
# assume worst case
set(MODULE_IS_ENABLED 0)
# first we check if we have an explicit module build list
if(MITK_MODULES_TO_BUILD)
list(FIND MITK_MODULES_TO_BUILD ${MODULE_NAME} _MOD_INDEX)
if(_MOD_INDEX EQUAL -1)
set(MODULE_IS_EXCLUDED 1)
endif()
endif()
if(NOT MODULE_IS_EXCLUDED)
# first of all we check for the dependencies
_mitk_parse_package_args(${MODULE_PACKAGE_DEPENDS})
mitk_check_module_dependencies(MODULES ${MODULE_DEPENDS}
PACKAGES ${PACKAGE_NAMES}
MISSING_DEPENDENCIES_VAR _MISSING_DEP
PACKAGE_DEPENDENCIES_VAR PACKAGE_NAMES)
if(_MISSING_DEP)
if(MODULE_NO_FEATURE_INFO)
message("${_Module_type} ${MODULE_NAME} won't be built, missing dependency: ${_MISSING_DEP}")
endif()
set(MODULE_IS_ENABLED 0)
else()
foreach(dep ${MODULE_DEPENDS})
if(TARGET ${dep})
get_target_property(AUTLOAD_DEP ${dep} MITK_AUTOLOAD_DIRECTORY)
if (AUTLOAD_DEP)
message(SEND_ERROR "Module \"${MODULE_NAME}\" has an invalid dependency on autoload module \"${dep}\". Check MITK_CREATE_MODULE usage for \"${MODULE_NAME}\".")
endif()
endif()
endforeach(dep)
set(MODULE_IS_ENABLED 1)
# now check for every package if it is enabled. This overlaps a bit with
# MITK_CHECK_MODULE ...
foreach(_package ${PACKAGE_NAMES})
if((DEFINED MITK_USE_${_package}) AND NOT (MITK_USE_${_package}))
message("${_Module_type} ${MODULE_NAME} won't be built. Turn on MITK_USE_${_package} if you want to use it.")
set(MODULE_IS_ENABLED 0)
break()
endif()
endforeach()
endif()
endif()
# -----------------------------------------------------------------
# Start creating the module
if(MODULE_IS_ENABLED)
# clear variables defined in files.cmake
set(RESOURCE_FILES )
set(CPP_FILES )
set(H_FILES )
set(TXX_FILES )
set(DOX_FILES )
set(UI_FILES )
set(MOC_H_FILES )
set(QRC_FILES )
# clear other variables
set(Q${KITNAME}_GENERATED_CPP )
set(Q${KITNAME}_GENERATED_MOC_CPP )
set(Q${KITNAME}_GENERATED_QRC_CPP )
set(Q${KITNAME}_GENERATED_UI_CPP )
# check and set-up auto-loading
if(MODULE_AUTOLOAD_WITH)
if(NOT TARGET "${MODULE_AUTOLOAD_WITH}")
message(SEND_ERROR "The module target \"${MODULE_AUTOLOAD_WITH}\" specified as the auto-loading module for \"${MODULE_NAME}\" does not exist")
endif()
endif()
set(_module_autoload_meta_target "${CMAKE_PROJECT_NAME}-autoload")
# create a meta-target if it does not already exist
if(NOT TARGET ${_module_autoload_meta_target})
add_custom_target(${_module_autoload_meta_target})
set_property(TARGET ${_module_autoload_meta_target} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules/Autoload")
endif()
if(NOT MODULE_EXPORT_DEFINE)
set(MODULE_EXPORT_DEFINE ${MODULE_NAME}_EXPORT)
endif()
if(MITK_GENERATE_MODULE_DOT)
message("MODULEDOTNAME ${MODULE_NAME}")
foreach(dep ${MODULE_DEPENDS})
message("MODULEDOT \"${MODULE_NAME}\" -> \"${dep}\" ; ")
endforeach(dep)
endif(MITK_GENERATE_MODULE_DOT)
if (EXISTS ${MODULE_FILES_CMAKE})
include(${MODULE_FILES_CMAKE})
endif()
if(MODULE_CPP_FILES)
list(APPEND CPP_FILES ${MODULE_CPP_FILES})
endif()
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/src")
# Preprend the "src" directory to the cpp file list
set(_cpp_files ${CPP_FILES})
set(CPP_FILES )
foreach(_cpp_file ${_cpp_files})
list(APPEND CPP_FILES "src/${_cpp_file}")
endforeach()
endif()
if(CPP_FILES OR RESOURCE_FILES OR UI_FILES OR MOC_H_FILES OR QRC_FILES)
set(MODULE_HEADERS_ONLY 0)
if(MODULE_C_MODULE)
set_source_files_properties(${CPP_FILES} PROPERTIES LANGUAGE C)
elseif(MODULE_CXX_MODULE)
set_source_files_properties(${CPP_FILES} PROPERTIES LANGUAGE CXX)
endif()
else()
set(MODULE_HEADERS_ONLY 1)
if(MODULE_AUTOLOAD_WITH)
message(SEND_ERROR "A headers only module cannot be auto-loaded")
endif()
endif()
set(module_c_flags )
set(module_c_flags_debug )
set(module_c_flags_release )
set(module_cxx_flags )
set(module_cxx_flags_debug )
set(module_cxx_flags_release )
if(MODULE_GCC_DEFAULT_VISIBILITY OR NOT CMAKE_COMPILER_IS_GNUCXX)
# We only support hidden visibility for gcc for now. Clang still has troubles with
# correctly marking template declarations and explicit template instantiations as exported.
# See http://comments.gmane.org/gmane.comp.compilers.clang.scm/50028
# and http://llvm.org/bugs/show_bug.cgi?id=10113
set(CMAKE_CXX_VISIBILITY_PRESET default)
set(CMAKE_VISIBILITY_INLINES_HIDDEN 0)
else()
set(CMAKE_CXX_VISIBILITY_PRESET hidden)
set(CMAKE_VISIBILITY_INLINES_HIDDEN 1)
endif()
if(NOT MODULE_WARNINGS_NO_ERRORS)
if(MSVC_VERSION)
mitkFunctionCheckCAndCXXCompilerFlags("/WX" module_c_flags module_cxx_flags)
# this would turn on unused parameter warnings, but unfortunately MSVC cannot
# distinguish yet between internal and external headers so this would be triggered
# a lot by external code. There is support for it on the way so this line could be
# reactivated after https://gitlab.kitware.com/cmake/cmake/issues/17904 has been fixed.
# mitkFunctionCheckCAndCXXCompilerFlags("/w34100" module_c_flags module_cxx_flags)
else()
mitkFunctionCheckCAndCXXCompilerFlags(-Werror module_c_flags module_cxx_flags)
# The flag "c++0x-static-nonintegral-init" has been renamed in newer Clang
# versions to "static-member-init", see
# http://clang-developers.42468.n3.nabble.com/Wc-0x-static-nonintegral-init-gone-td3999651.html
#
# Also, older Clang and seemingly all gcc versions do not warn if unknown
# "-no-*" flags are used, so CMake will happily append any -Wno-* flag to the
# command line. This may get confusing if unrelated compiler errors happen and
# the error output then additionally contains errors about unknown flags (which
# is not the case if there were no compile errors).
#
# So instead of using -Wno-* we use -Wno-error=*, which will be properly rejected by
# the compiler and if applicable, prints the specific warning as a real warning and
# not as an error (although -Werror was given).
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=c++0x-static-nonintegral-init" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=static-member-init" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=unknown-warning" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=gnu" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=class-memaccess" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=inconsistent-missing-override" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-copy" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=cast-function-type" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" module_c_flags module_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=type-limits" module_c_flags module_cxx_flags)
endif()
endif()
if(MODULE_FORCE_STATIC)
set(_STATIC STATIC)
else()
set(_STATIC )
endif(MODULE_FORCE_STATIC)
if(NOT MODULE_HEADERS_ONLY)
if(NOT MODULE_NO_INIT OR RESOURCE_FILES)
find_package(CppMicroServices QUIET NO_MODULE REQUIRED)
endif()
if(NOT MODULE_NO_INIT)
usFunctionGenerateModuleInit(CPP_FILES)
endif()
set(binary_res_files )
set(source_res_files )
if(RESOURCE_FILES)
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/resource")
set(res_dir resource)
elseif(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/Resources")
set(res_dir Resources)
else()
message(SEND_ERROR "Resources specified but ${CMAKE_CURRENT_SOURCE_DIR}/resource directory not found.")
endif()
foreach(res_file ${RESOURCE_FILES})
if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/${res_dir}/${res_file})
list(APPEND binary_res_files "${res_file}")
else()
list(APPEND source_res_files "${res_file}")
endif()
endforeach()
# Add a source level dependencies on resource files
usFunctionGetResourceSource(TARGET ${MODULE_TARGET} OUT CPP_FILES)
endif()
endif()
if(MITK_USE_Qt5)
if(UI_FILES)
qt5_wrap_ui(Q${KITNAME}_GENERATED_UI_CPP ${UI_FILES})
endif()
if(MOC_H_FILES)
qt5_wrap_cpp(Q${KITNAME}_GENERATED_MOC_CPP ${MOC_H_FILES} OPTIONS -DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION)
endif()
if(QRC_FILES)
qt5_add_resources(Q${KITNAME}_GENERATED_QRC_CPP ${QRC_FILES})
endif()
endif()
set(Q${KITNAME}_GENERATED_CPP ${Q${KITNAME}_GENERATED_CPP} ${Q${KITNAME}_GENERATED_UI_CPP} ${Q${KITNAME}_GENERATED_MOC_CPP} ${Q${KITNAME}_GENERATED_QRC_CPP})
mitkFunctionOrganizeSources(
SOURCE ${CPP_FILES}
HEADER ${H_FILES}
TXX ${TXX_FILES}
DOC ${DOX_FILES}
UI ${UI_FILES}
QRC ${QRC_FILES}
MOC ${Q${KITNAME}_GENERATED_MOC_CPP}
GEN_QRC ${Q${KITNAME}_GENERATED_QRC_CPP}
GEN_UI ${Q${KITNAME}_GENERATED_UI_CPP}
)
set(coverage_sources
${CPP_FILES} ${H_FILES} ${GLOBBED__H_FILES} ${CORRESPONDING__H_FILES} ${TXX_FILES}
${TOOL_CPPS} ${TOOL_GUI_CPPS})
# ---------------------------------------------------------------
# Create the actual module target
if(MODULE_HEADERS_ONLY)
add_library(${MODULE_TARGET} INTERFACE)
# INTERFACE_LIBRARY targets may only have whitelisted properties. The property "FOLDER" is not allowed.
# set_property(TARGET ${MODULE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules")
else()
if(MODULE_EXECUTABLE)
if(MITK_SHOW_CONSOLE_WINDOW)
set(_SHOW_CONSOLE_OPTION "")
else()
set(_SHOW_CONSOLE_OPTION WIN32)
endif()
add_executable(${MODULE_TARGET} ${_SHOW_CONSOLE_OPTION}
${MODULE_CPP_FILES} ${coverage_sources} ${CPP_FILES_GENERATED} ${Q${KITNAME}_GENERATED_CPP}
${DOX_FILES} ${UI_FILES} ${QRC_FILES} ${WINDOWS_ICON_RESOURCE_FILE})
set_property(TARGET ${MODULE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules/Executables")
set(_us_module_name main)
else()
add_library(${MODULE_TARGET} ${_STATIC}
${coverage_sources} ${CPP_FILES_GENERATED} ${Q${KITNAME}_GENERATED_CPP}
${DOX_FILES} ${UI_FILES} ${QRC_FILES})
set_property(TARGET ${MODULE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules")
set(_us_module_name ${MODULE_TARGET})
endif()
# Apply properties to the module target.
target_compile_definitions(${MODULE_TARGET} PRIVATE US_MODULE_NAME=${_us_module_name})
if(MODULE_C_MODULE)
if(module_c_flags)
string(REPLACE " " ";" module_c_flags "${module_c_flags}")
target_compile_options(${MODULE_TARGET} PRIVATE ${module_c_flags})
endif()
if(module_c_flags_debug)
string(REPLACE " " ";" module_c_flags_debug "${module_c_flags_debug}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Debug>:${module_c_flags_debug}>)
endif()
if(module_c_flags_release)
string(REPLACE " " ";" module_c_flags_release "${module_c_flags_release}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Release>:${module_c_flags_release}>)
endif()
else()
if(module_cxx_flags)
string(REPLACE " " ";" module_cxx_flags "${module_cxx_flags}")
target_compile_options(${MODULE_TARGET} PRIVATE ${module_cxx_flags})
endif()
if(module_cxx_flags_debug)
string(REPLACE " " ";" module_cxx_flags_debug "${module_cxx_flags_debug}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Debug>:${module_cxx_flags_debug}>)
endif()
if(module_cxx_flags_release)
string(REPLACE " " ";" module_cxx_flags_release "${module_cxx_flags_release}")
target_compile_options(${MODULE_TARGET} PRIVATE $<$<CONFIG:Release>:${module_cxx_flags_release}>)
endif()
endif()
set_property(TARGET ${MODULE_TARGET} PROPERTY US_MODULE_NAME ${_us_module_name})
# Add additional library search directories to a global property which
# can be evaluated by other CMake macros, e.g. our install scripts.
if(MODULE_ADDITIONAL_LIBS)
target_link_libraries(${MODULE_TARGET} PRIVATE ${MODULE_ADDITIONAL_LIBS})
get_property(_mitk_additional_library_search_paths GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS)
foreach(_lib_filepath ${MODULE_ADDITIONAL_LIBS})
get_filename_component(_search_path "${_lib_filepath}" PATH)
if(_search_path)
list(APPEND _mitk_additional_library_search_paths "${_search_path}")
endif()
endforeach()
if(_mitk_additional_library_search_paths)
list(REMOVE_DUPLICATES _mitk_additional_library_search_paths)
set_property(GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS ${_mitk_additional_library_search_paths})
endif()
endif()
# add the target name to a global property which is used in the top-level
# CMakeLists.txt file to export the target
set_property(GLOBAL APPEND PROPERTY MITK_MODULE_TARGETS ${MODULE_TARGET})
if(MODULE_AUTOLOAD_WITH)
# for auto-loaded modules, adapt the output directory
add_dependencies(${_module_autoload_meta_target} ${MODULE_TARGET})
if(WIN32)
set(_module_output_prop RUNTIME_OUTPUT_DIRECTORY)
else()
set(_module_output_prop LIBRARY_OUTPUT_DIRECTORY)
endif()
set(_module_output_dir ${CMAKE_${_module_output_prop}}/${MODULE_AUTOLOAD_WITH})
get_target_property(_module_is_imported ${MODULE_AUTOLOAD_WITH} IMPORTED)
if(NOT _module_is_imported)
# if the auto-loading module is not imported, get its location
# and put the auto-load module relative to it.
get_target_property(_module_output_dir ${MODULE_AUTOLOAD_WITH} ${_module_output_prop})
set_target_properties(${MODULE_TARGET} PROPERTIES
${_module_output_prop} ${_module_output_dir}/${MODULE_AUTOLOAD_WITH})
else()
set_target_properties(${MODULE_TARGET} PROPERTIES
${_module_output_prop} ${CMAKE_${_module_output_prop}}/${MODULE_AUTOLOAD_WITH})
endif()
set_target_properties(${MODULE_TARGET} PROPERTIES
MITK_AUTOLOAD_DIRECTORY ${MODULE_AUTOLOAD_WITH})
# add the auto-load module name as a property
set_property(TARGET ${MODULE_AUTOLOAD_WITH} APPEND PROPERTY MITK_AUTOLOAD_TARGETS ${MODULE_TARGET})
endif()
if(binary_res_files)
usFunctionAddResources(TARGET ${MODULE_TARGET}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${res_dir}
FILES ${binary_res_files})
endif()
if(source_res_files)
usFunctionAddResources(TARGET ${MODULE_TARGET}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${res_dir}
FILES ${source_res_files})
endif()
if(binary_res_files OR source_res_files)
usFunctionEmbedResources(TARGET ${MODULE_TARGET})
endif()
if(MODULE_DEPRECATED_SINCE)
set_property(TARGET ${MODULE_TARGET} PROPERTY MITK_MODULE_DEPRECATED_SINCE ${MODULE_DEPRECATED_SINCE})
endif()
# create export macros
if (NOT MODULE_EXECUTABLE)
set(_export_macro_name )
if(MITK_LEGACY_EXPORT_MACRO_NAME)
set(_export_macro_names
EXPORT_MACRO_NAME ${MODULE_EXPORT_DEFINE}
NO_EXPORT_MACRO_NAME ${MODULE_NAME}_NO_EXPORT
DEPRECATED_MACRO_NAME ${MODULE_NAME}_DEPRECATED
NO_DEPRECATED_MACRO_NAME ${MODULE_NAME}_NO_DEPRECATED
)
endif()
generate_export_header(${MODULE_NAME}
${_export_macro_names}
EXPORT_FILE_NAME ${MODULE_NAME}Exports.h
)
endif()
target_include_directories(${MODULE_TARGET} PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
endif()
# ---------------------------------------------------------------
# Properties for both header-only and compiled modules
if(MODULE_HEADERS_ONLY)
set(_module_property_type INTERFACE)
else()
set(_module_property_type PUBLIC)
endif()
if(MODULE_TARGET_DEPENDS)
- add_dependencies(${MODULE_TARGET} ${MODULE_TARGET_DEPENDS})
+ target_link_libraries(${MODULE_TARGET} ${MODULE_TARGET_DEPENDS})
endif()
set(DEPENDS "${MODULE_DEPENDS}")
if(NOT MODULE_NO_INIT AND NOT MODULE_HEADERS_ONLY)
# Add a CppMicroServices dependency implicitly, since it is
# needed for the generated "module initialization" code.
set(DEPENDS "CppMicroServices;${DEPENDS}")
endif()
if(DEPENDS OR MODULE_PACKAGE_DEPENDS)
mitk_use_modules(TARGET ${MODULE_TARGET}
MODULES ${DEPENDS}
PACKAGES ${MODULE_PACKAGE_DEPENDS}
)
endif()
if(NOT MODULE_C_MODULE)
target_compile_features(${MODULE_TARGET} ${_module_property_type} ${MITK_CXX_FEATURES})
endif()
# add include directories
if(MODULE_INTERNAL_INCLUDE_DIRS)
target_include_directories(${MODULE_TARGET} PRIVATE ${MODULE_INTERNAL_INCLUDE_DIRS})
endif()
if(NOT MODULE_NO_DEFAULT_INCLUDE_DIRS)
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/include)
target_include_directories(${MODULE_TARGET} ${_module_property_type} include)
else()
target_include_directories(${MODULE_TARGET} ${_module_property_type} .)
endif()
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src)
target_include_directories(${MODULE_TARGET} PRIVATE src)
endif()
endif()
target_include_directories(${MODULE_TARGET} ${_module_property_type} ${MODULE_INCLUDE_DIRS})
endif()
# -----------------------------------------------------------------
# Record missing dependency information
if(_MISSING_DEP)
if(MODULE_DESCRIPTION)
set(MODULE_DESCRIPTION "${MODULE_DESCRIPTION} (missing dependencies: ${_MISSING_DEP})")
else()
set(MODULE_DESCRIPTION "(missing dependencies: ${_MISSING_DEP})")
endif()
endif()
if(NOT MODULE_NO_FEATURE_INFO)
add_feature_info(${MODULE_NAME} MODULE_IS_ENABLED "${MODULE_DESCRIPTION}")
endif()
set(MODULE_NAME ${MODULE_NAME} PARENT_SCOPE)
set(MODULE_TARGET ${MODULE_TARGET} PARENT_SCOPE)
set(MODULE_IS_ENABLED ${MODULE_IS_ENABLED} PARENT_SCOPE)
endfunction()
diff --git a/CMake/mitkFunctionCreatePlugin.cmake b/CMake/mitkFunctionCreatePlugin.cmake
index d73c102897..d0da785c81 100644
--- a/CMake/mitkFunctionCreatePlugin.cmake
+++ b/CMake/mitkFunctionCreatePlugin.cmake
@@ -1,350 +1,356 @@
#! \brief Creates a MITK CTK plugin.
#!
#! This function should be called from the plugins CMakeLists.txt file.
#! The target name is available after the macro call as ${PLUGIN_TARGET}
#! to add additional libraries in your CMakeLists.txt. Include paths and link
#! libraries are set depending on the value of the Required-Plugins header
#! in your manifest_headers.cmake file.
#!
#! This function internally calls ctkMacroBuildPlugin() and adds support
#! for Qt Help files and installers.
#!
#! Options:
#! \param TEST_PLUGIN Mark this plug-in as a testing plug-in.
#! \param NO_INSTALL Don't install this plug-in.
#!
#! Parameters:
#!
#! \param EXPORT_DIRECTIVE (required) The export directive to use in the generated
#! <plugin_target>_Exports.h file.
#!
#! Multi-value parameters (all optional):
#!
#! \param EXPORTED_INCLUDE_SUFFIXES A list of sub-directories which should
#! be added to the current source directory. The resulting directories
#! will be available in the set of include directories of depending plug-ins.
#! \param MODULE_DEPENDS (optional) A list of Modules this plug-in depends on.
#! \param PACKAGE_DEPENDS (optional) A list of external packages this plug-in depends on.
+#! \param TARGET_DEPENDS (optional) A list of CMake targets this plug-in depends on.
#! \param DOXYGEN_TAGFILES (optional) Which external tag files should be available for the plugin documentation
#! \param MOC_OPTIONS (optional) Additional options to pass to the Qt MOC compiler
#! \param WARNINGS_NO_ERRORS (optional) Do not handle compiler warnings as errors
function(mitk_create_plugin)
# options
set(arg_options
TEST_PLUGIN # Mark this plug-in as a testing plug-in
NO_INSTALL # Don't install this plug-in
NO_QHP_TRANSFORM
WARNINGS_NO_ERRORS
)
# single value arguments
set(arg_single
EXPORT_DIRECTIVE # (required) TODO: could be generated via CMake as it is done for MITK modules already
)
# multiple value arguments
set(arg_multiple
EXPORTED_INCLUDE_SUFFIXES # (optional) additional public include directories
MODULE_DEPENDS # (optional)
PACKAGE_DEPENDS
+ TARGET_DEPENDS
DOXYGEN_TAGFILES
MOC_OPTIONS
SUBPROJECTS # deprecated
)
cmake_parse_arguments(_PLUGIN "${arg_options}" "${arg_single}" "${arg_multiple}" ${ARGN})
if(_PLUGIN_TEST_PLUGIN)
set(_PLUGIN_NO_INSTALL 1)
set(is_test_plugin "TEST_PLUGIN")
else()
set(is_test_plugin)
endif()
set(_PLUGIN_MOC_OPTIONS "-DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED ${_PLUGIN_MOC_OPTIONS}")
set(PLUGIN_TARGET ${PROJECT_NAME})
mitk_check_module_dependencies(MODULES ${_PLUGIN_MODULE_DEPENDS}
PACKAGES ${_PLUGIN_PACKAGE_DEPENDS}
MISSING_DEPENDENCIES_VAR _missing_deps
MODULE_DEPENDENCIES_VAR _module_deps
PACKAGE_DEPENDENCIES_VAR _package_deps)
if(_missing_deps)
if(NOT MITK_BUILD_ALL_PLUGINS)
message(SEND_ERROR "${PROJECT_NAME} is missing requirements and won't be built. Missing: ${_missing_deps}")
else()
message(STATUS "${PROJECT_NAME} is missing requirements and won't be built. Missing: ${_missing_deps}")
endif()
return()
endif()
foreach(_module_dep ${_PLUGIN_MODULE_DEPENDS})
if(TARGET ${_module_dep})
get_target_property(AUTLOAD_DEP ${_module_dep} MITK_AUTOLOAD_DIRECTORY)
if (AUTLOAD_DEP)
message(SEND_ERROR "Plugin \"${PROJECT_NAME}\" has an invalid dependency on autoload module \"${_module_dep}\". Check MITK_CREATE_PLUGIN usage for \"${PROJECT_NAME}\".")
endif()
endif()
endforeach()
# -------------- All dependencies are resolved ------------------
message(STATUS "Creating CTK plugin ${PROJECT_NAME}")
include(files.cmake)
set(_PLUGIN_CPP_FILES ${CPP_FILES})
set(_PLUGIN_MOC_H_FILES ${MOC_H_FILES})
set(_PLUGIN_UI_FILES ${UI_FILES})
set(_PLUGIN_CACHED_RESOURCE_FILES ${CACHED_RESOURCE_FILES})
set(_PLUGIN_TRANSLATION_FILES ${TRANSLATION_FILES})
set(_PLUGIN_QRC_FILES ${QRC_FILES})
set(_PLUGIN_H_FILES ${H_FILES})
set(_PLUGIN_TXX_FILES ${TXX_FILES})
set(_PLUGIN_DOX_FILES ${DOX_FILES})
set(_PLUGIN_CMAKE_FILES ${CMAKE_FILES} files.cmake)
set(_PLUGIN_FILE_DEPENDENCIES ${FILE_DEPENDENCIES})
if(CTK_PLUGINS_OUTPUT_DIR)
set(_output_dir "${CTK_PLUGINS_OUTPUT_DIR}")
else()
set(_output_dir "")
endif()
# Compute the plugin dependencies
ctkFunctionGetTargetLibraries(_PLUGIN_target_libraries "")
#------------------------------------------------------------#
#------------------ Qt Help support -------------------------#
set(PLUGIN_GENERATED_QCH_FILES )
if(BLUEBERRY_USE_QT_HELP AND
EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/documentation/UserManual")
set(PLUGIN_DOXYGEN_INPUT_DIR "${CMAKE_CURRENT_SOURCE_DIR}/documentation/UserManual")
set(PLUGIN_DOXYGEN_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/documentation/UserManual")
# Create a list of Doxygen tag files from the plug-in dependencies
set(PLUGIN_DOXYGEN_TAGFILES)
foreach(_dep_target ${_PLUGIN_target_libraries})
string(REPLACE _ . _dep ${_dep_target})
get_target_property(_is_imported ${_dep_target} IMPORTED)
if(_is_imported)
get_target_property(_import_loc_debug ${_dep_target} IMPORTED_LOCATION_DEBUG)
get_target_property(_import_loc_release ${_dep_target} IMPORTED_LOCATION_RELEASE)
# There is not necessarily a debug and release build
if(_import_loc_release)
set(_import_loc ${_import_loc_release})
else()
set(_import_loc ${_import_loc_debug})
endif()
get_filename_component(_target_filename "${_import_loc}" NAME)
# on windows there might be a Debug or Release subdirectory
string(REGEX REPLACE "/bin/plugins/(Debug/|Release/)?${_target_filename}" "/Plugins/${_dep}/documentation/UserManual" plugin_tag_dir "${_import_loc}" )
else()
set(plugin_tag_dir "${CMAKE_BINARY_DIR}/Plugins/${_dep}/documentation/UserManual")
endif()
set(_tag_file "${plugin_tag_dir}/${_dep_target}.tag")
if(EXISTS ${_tag_file})
set(PLUGIN_DOXYGEN_TAGFILES "${PLUGIN_DOXYGEN_TAGFILES} \"${_tag_file}=qthelp://${_dep}/bundle/\"")
endif()
endforeach()
if(_PLUGIN_DOXYGEN_TAGFILES)
set(PLUGIN_DOXYGEN_TAGFILES "${PLUGIN_DOXYGEN_TAGFILES} ${_PLUGIN_DOXYGEN_TAGFILES}")
endif()
#message("PLUGIN_DOXYGEN_TAGFILES: ${PLUGIN_DOXYGEN_TAGFILES}")
if(_PLUGIN_NO_QHP_TRANSFORM)
set(_use_qhp_xsl 0)
else()
set(_use_qhp_xsl 1)
endif()
_FUNCTION_CREATE_CTK_QT_COMPRESSED_HELP(PLUGIN_GENERATED_QCH_FILES ${_use_qhp_xsl})
list(APPEND _PLUGIN_CACHED_RESOURCE_FILES ${PLUGIN_GENERATED_QCH_FILES})
endif()
#------------------------------------------------------------#
#------------------ Create Plug-in --------------------------#
mitkFunctionOrganizeSources(
SOURCE ${_PLUGIN_CPP_FILES}
HEADER ${_PLUGIN_H_FILES}
TXX ${_PLUGIN_TXX_FILES}
DOC ${_PLUGIN_DOX_FILES}
UI ${_PLUGIN_UI_FILES}
QRC ${_PLUGIN_QRC_FILES} ${_PLUGIN_CACHED_RESOURCE_FILES}
META ${_PLUGIN_META_FILES}
MOC ${MY_MOC_CPP}
GEN_UI ${MY_UI_CPP}
GEN_QRC ${MY_QRC_SRCS}
)
ctkMacroBuildPlugin(
NAME ${PLUGIN_TARGET}
EXPORT_DIRECTIVE ${_PLUGIN_EXPORT_DIRECTIVE}
SRCS ${_PLUGIN_CPP_FILES} ${_PLUGIN_H_FILES} ${CORRESPONDING__H_FILES} ${GLOBBED__H_FILES}
MOC_SRCS ${_PLUGIN_MOC_H_FILES}
MOC_OPTIONS ${_PLUGIN_MOC_OPTIONS}
UI_FORMS ${_PLUGIN_UI_FILES}
EXPORTED_INCLUDE_SUFFIXES ${_PLUGIN_EXPORTED_INCLUDE_SUFFIXES}
RESOURCES ${_PLUGIN_QRC_FILES}
TARGET_LIBRARIES ${_PLUGIN_target_libraries}
CACHED_RESOURCEFILES ${_PLUGIN_CACHED_RESOURCE_FILES}
TRANSLATIONS ${_PLUGIN_TRANSLATION_FILES}
OUTPUT_DIR ${_output_dir}
NO_INSTALL # we install the plug-in ourselves
${is_test_plugin}
)
mitk_use_modules(TARGET ${PLUGIN_TARGET}
MODULES ${_PLUGIN_MODULE_DEPENDS}
PACKAGES ${_PLUGIN_PACKAGE_DEPENDS}
)
+ if(_PLUGIN_TARGET_DEPENDS)
+ target_link_libraries(${PLUGIN_TARGET} ${_PLUGIN_TARGET_DEPENDS})
+ endif()
+
set_property(TARGET ${PLUGIN_TARGET} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=${PLUGIN_TARGET})
set_property(TARGET ${PLUGIN_TARGET} PROPERTY US_MODULE_NAME ${PLUGIN_TARGET})
if(NOT CMAKE_CURRENT_SOURCE_DIR MATCHES "^${CMAKE_SOURCE_DIR}.*")
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
if(CMAKE_CURRENT_SOURCE_DIR MATCHES "^${MITK_EXTENSION_DIR}.*")
get_filename_component(MITK_EXTENSION_ROOT_FOLDER "${MITK_EXTENSION_DIR}" NAME)
set_property(TARGET ${PLUGIN_TARGET} PROPERTY FOLDER "${MITK_EXTENSION_ROOT_FOLDER}/Plugins")
break()
endif()
endforeach()
else()
set_property(TARGET ${PLUGIN_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Plugins")
endif()
set(plugin_c_flags)
set(plugin_cxx_flags)
if(NOT _PLUGIN_WARNINGS_NO_ERRORS)
if(MSVC_VERSION)
mitkFunctionCheckCAndCXXCompilerFlags("/WX" plugin_c_flags plugin_cxx_flags)
else()
mitkFunctionCheckCAndCXXCompilerFlags(-Werror plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=c++0x-static-nonintegral-init" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=static-member-init" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=unknown-warning" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=gnu" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=cast-function-type" plugin_c_flags plugin_cxx_flags)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=inconsistent-missing-override" plugin_c_flags plugin_cxx_flags)
endif()
endif()
if(plugin_c_flags)
string(REPLACE " " ";" plugin_c_flags "${plugin_c_flags}")
target_compile_options(${PLUGIN_TARGET} PRIVATE ${plugin_c_flags})
endif()
if(plugin_cxx_flags)
string(REPLACE " " ";" plugin_cxx_flags "${plugin_cxx_flags}")
target_compile_options(${PLUGIN_TARGET} PRIVATE ${plugin_cxx_flags})
endif()
if(_PLUGIN_TEST_PLUGIN)
find_package(CppUnit REQUIRED)
target_include_directories(${PLUGIN_TARGET} PRIVATE ${CppUnit_INCLUDE_DIRS})
target_link_libraries(${PLUGIN_TARGET} PRIVATE ${CppUnit_LIBRARIES})
endif()
if(mbilog_FOUND)
target_link_libraries(${PLUGIN_TARGET} PRIVATE mbilog)
endif()
set(_PLUGIN_META_FILES "${CMAKE_CURRENT_SOURCE_DIR}/manifest_headers.cmake")
if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/plugin.xml")
list(APPEND _PLUGIN_META_FILES "${CMAKE_CURRENT_SOURCE_DIR}/plugin.xml")
endif()
set(PLUGIN_TARGET ${PLUGIN_TARGET} PARENT_SCOPE)
#------------------------------------------------------------#
#------------------ Installer support -----------------------#
if(NOT _PLUGIN_NO_INSTALL)
set(install_directories "")
if(NOT MACOSX_BUNDLE_NAMES)
set(install_directories bin/plugins)
else(NOT MACOSX_BUNDLE_NAMES)
foreach(bundle_name ${MACOSX_BUNDLE_NAMES})
list(APPEND install_directories ${bundle_name}.app/Contents/MacOS/plugins)
endforeach(bundle_name)
endif(NOT MACOSX_BUNDLE_NAMES)
foreach(install_subdir ${install_directories})
mitkFunctionInstallCTKPlugin(TARGETS ${PLUGIN_TARGET}
DESTINATION ${install_subdir})
endforeach()
set(_autoload_targets )
foreach(_dependency ${_module_deps})
get_target_property(_dep_autoloads ${_dependency} MITK_AUTOLOAD_TARGETS)
if (_dep_autoloads)
list(APPEND _autoload_targets ${_dep_autoloads})
endif()
endforeach()
# The MITK_AUTOLOAD_TARGETS property is used in the mitkFunctionInstallAutoLoadModules
# macro which expects a list of plug-in targets.
if (_autoload_targets)
list(REMOVE_DUPLICATES _autoload_targets)
set_target_properties(${PLUGIN_TARGET} PROPERTIES MITK_AUTOLOAD_TARGETS "${_autoload_targets}")
endif()
endif()
endfunction()
function(_FUNCTION_CREATE_CTK_QT_COMPRESSED_HELP qch_file use_xsl)
set(_manifest_path "${CMAKE_CURRENT_SOURCE_DIR}/manifest_headers.cmake")
if(NOT EXISTS ${_manifest_path})
message(FATAL_ERROR "${_manifest_path} not found")
endif()
include(${_manifest_path})
string(REPLACE "_" "." Plugin-SymbolicName "${PLUGIN_TARGET}")
configure_file(${MITK_SOURCE_DIR}/Documentation/doxygen_plugin_manual.conf.in
${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf
)
set(_qhp_xsl_file "${MITK_SOURCE_DIR}/Documentation/qhp_toc.xsl")
set(_generated_qhp_file "${PLUGIN_DOXYGEN_OUTPUT_DIR}/html/index.qhp")
set(_transformed_qhp_file "${PLUGIN_DOXYGEN_OUTPUT_DIR}/html/${PLUGIN_TARGET}.qhp")
set(${qch_file} "${CMAKE_CURRENT_BINARY_DIR}/resources/${PLUGIN_TARGET}.qch")
set(_xsl_command )
if(use_xsl)
set(_xsl_command COMMAND ${QT_XMLPATTERNS_EXECUTABLE} ${_qhp_xsl_file} ${_generated_qhp_file} -output ${_transformed_qhp_file})
endif()
file(GLOB _file_dependencies "${PLUGIN_DOXYGEN_INPUT_DIR}/*")
add_custom_command(OUTPUT ${${qch_file}}
# Generate a Qt help project (index.qhp) with doxygen
COMMAND ${DOXYGEN_EXECUTABLE} ${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf
# Use a XSL transformation to get rid of the top-level entry
${_xsl_command}
# Generate the final Qt compressed help file (.qch)
COMMAND ${QT_HELPGENERATOR_EXECUTABLE} ${_transformed_qhp_file} -o ${${qch_file}}
DEPENDS ${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf ${_file_dependencies}
)
#set_source_files_properties(${qch_file} PROPERTIES GENERATED 1)
set(${qch_file} ${${qch_file}} PARENT_SCOPE)
endfunction()
function(MACRO_CREATE_MITK_CTK_PLUGIN)
message(SEND_ERROR "The function MACRO_CREATE_MITK_CTK_PLUGIN was renamed to mitk_create_plugin in MITK 2015.05.")
endfunction()
diff --git a/CMake/mitkFunctionUseModules.cmake b/CMake/mitkFunctionUseModules.cmake
index 0654f319be..173e0a5a95 100644
--- a/CMake/mitkFunctionUseModules.cmake
+++ b/CMake/mitkFunctionUseModules.cmake
@@ -1,173 +1,163 @@
function(_mitk_parse_package_args)
set(package_list ${ARGN})
set(PUBLIC_PACKAGE_NAMES )
set(PRIVATE_PACKAGE_NAMES )
set(INTERFACE_PACKAGE_NAMES )
set(_package_visibility PRIVATE)
foreach(_package ${package_list})
if(_package STREQUAL "PUBLIC" OR _package STREQUAL "PRIVATE" OR _package STREQUAL "INTERFACE")
set(_package_visibility ${_package})
else()
list(APPEND packages ${_package})
set(_package_name )
set(_package_components_list )
string(REPLACE "|" ";" _package_list ${_package})
if("${_package_list}" STREQUAL "${_package}")
set(_package_name ${_package})
else()
list(GET _package_list 0 _package_name)
list(GET _package_list 1 _package_components)
string(REPLACE "+" ";" _package_components_list "${_package_components}")
if(NOT _package_name OR NOT _package_components)
message(SEND_ERROR "PACKAGE argument syntax wrong. ${_package} is not of the form PACKAGE[|COMPONENT1[+COMPONENT2]...]")
endif()
endif()
list(APPEND ${_package_visibility}_PACKAGE_NAMES ${_package_name})
list(APPEND ${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS ${_package_components_list})
endif()
endforeach()
# remove duplicates and set package components in parent scope
foreach(_package_visibility PUBLIC PRIVATE INTERFACE)
foreach(_package_name ${${_package_visibility}_PACKAGE_NAMES})
if(${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS)
list(REMOVE_DUPLICATES ${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS)
endif()
set(${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS ${${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS} PARENT_SCOPE)
endforeach()
endforeach()
set(PUBLIC_PACKAGE_NAMES ${PUBLIC_PACKAGE_NAMES} PARENT_SCOPE)
set(PRIVATE_PACKAGE_NAMES ${PRIVATE_PACKAGE_NAMES} PARENT_SCOPE)
set(INTERFACE_PACKAGE_NAMES ${INTERFACE_PACKAGE_NAMES} PARENT_SCOPE)
set(PACKAGE_NAMES ${PUBLIC_PACKAGE_NAMES} ${PRIVATE_PACKAGE_NAMES} ${INTERFACE_PACKAGE_NAMES} PARENT_SCOPE)
endfunction()
function(_include_package_config pkg_config_file)
# wrap the inclusion of the MITK_<pkg>_Config.cmake file in a
# function to create a scope for its variables; this allows
# multiple inclusions of the file in the parent scope
include(${pkg_config_file})
set(ALL_INCLUDE_DIRECTORIES ${ALL_INCLUDE_DIRECTORIES} PARENT_SCOPE)
set(ALL_LIBRARIES ${ALL_LIBRARIES} PARENT_SCOPE)
set(ALL_COMPILE_DEFINITIONS ${ALL_COMPILE_DEFINITIONS} PARENT_SCOPE)
set(ALL_COMPILE_OPTIONS ${ALL_COMPILE_OPTIONS} PARENT_SCOPE)
endfunction()
#! This CMake function sets up the necessary include directories,
#! linker dependencies, and compile flags for a given target which
#! depends on a set of MITK modules or packages.
#!
#! A package argument is of the form
#!
#! [PUBLIC|PRIVATE|INTERFACE] PACKAGE[|COMPONENT1[+COMPONENT2]...]
#!
#! where PACKAGE is the package name (e.g. VTK) and components are
#! the names of required package components or libraries.
#!
#! If a dependency is not available, an error is thrown.
function(mitk_use_modules)
set(_macro_params
TARGET # The target name (required)
)
set(_macro_multiparams
MODULES # MITK modules which the given TARGET uses
PACKAGES # MITK packages which the given TARGET uses
)
set(_macro_options )
cmake_parse_arguments(USE "${_macro_options}" "${_macro_params}" "${_macro_multiparams}" ${ARGN})
# Sanity checks
if(NOT USE_TARGET)
message(SEND_ERROR "Required TARGET argument missing.")
elseif(NOT TARGET ${USE_TARGET})
message(SEND_ERROR "The given TARGET argument ${USE_TARGET} is not a valid target")
endif()
set(depends ${USE_MODULES})
set(package_depends ${USE_PACKAGES})
if(depends)
# Iterate over all module dependencies
foreach(dependency ${depends})
if(TARGET ${dependency} AND NOT MODULE_IS_DEPRECATED)
get_target_property(_is_interface_lib ${dependency} TYPE)
if(NOT _is_interface_lib)
get_target_property(_dependency_deprecated_since ${dependency} MITK_MODULE_DEPRECATED_SINCE)
if(_dependency_deprecated_since)
message(WARNING "Module ${dependency} is deprecated since ${_dependency_deprecated_since}")
endif()
endif()
endif()
endforeach()
target_link_libraries(${USE_TARGET} PUBLIC ${depends})
endif()
# Parse package dependencies
if(package_depends)
_mitk_parse_package_args(${package_depends})
# Some package config files like MITK_Qt5_Config.cmake rely on a
# properly set "MODULE_NAME" variable for the current target.
set(MODULE_NAME ${USE_TARGET})
# Read all package information
foreach(_package_visibility INTERFACE PUBLIC PRIVATE)
foreach(_package ${${_package_visibility}_PACKAGE_NAMES})
set(ALL_INCLUDE_DIRECTORIES)
set(ALL_LIBRARIES)
set(ALL_COMPILE_DEFINITIONS)
set(ALL_COMPILE_OPTIONS)
set(${_package}_REQUIRED_COMPONENTS_BY_MODULE ${${_package_visibility}_${_package}_REQUIRED_COMPONENTS})
set(_package_found 0)
foreach(dir ${MODULES_PACKAGE_DEPENDS_DIRS})
if((NOT DEFINED MITK_USE_${_package} OR MITK_USE_${_package}) AND EXISTS "${dir}/MITK_${_package}_Config.cmake")
_include_package_config("${dir}/MITK_${_package}_Config.cmake")
set(_package_found 1)
break()
endif()
endforeach()
if(_package_found)
if(ALL_INCLUDE_DIRECTORIES)
list(REMOVE_DUPLICATES ALL_INCLUDE_DIRECTORIES)
target_include_directories(${USE_TARGET} SYSTEM ${_package_visibility} ${ALL_INCLUDE_DIRECTORIES})
endif()
if(ALL_LIBRARIES)
# Don't remove "duplicats" because ALL_LIBRARIES may be of the form:
# "general;bla;debug;blad;general;foo;debug;food"
target_link_libraries(${USE_TARGET} ${_package_visibility} ${ALL_LIBRARIES})
endif()
if(ALL_COMPILE_DEFINITIONS)
list(REMOVE_DUPLICATES ALL_COMPILE_DEFINITIONS)
# Compile definitions are always added "PRIVATE" to avoid multiple definitions
# on the command line due to transitive and direct dependencies adding the
# same definitions.
target_compile_definitions(${USE_TARGET} PRIVATE ${ALL_COMPILE_DEFINITIONS})
endif()
if(ALL_COMPILE_OPTIONS)
list(REMOVE_DUPLICATES ALL_COMPILE_OPTIONS)
target_compile_options(${USE_TARGET} ${_package_visibility} ${ALL_COMPILE_OPTIONS})
endif()
- if("VTK" STREQUAL _package)
- # VTK module autoinit
- unset(_vtk_modules)
- foreach(_vtk_module ${VTK_REQUIRED_COMPONENTS_BY_MODULE})
- list(APPEND _vtk_modules "VTK::${_vtk_module}")
- endforeach()
- if(_vtk_modules)
- vtk_module_autoinit(TARGETS ${USE_TARGET} MODULES ${_vtk_modules})
- endif()
- endif()
else()
message(SEND_ERROR "Missing package: ${_package}")
endif()
endforeach()
endforeach()
endif()
endfunction()
diff --git a/CMake/mitkInstallRules.cmake b/CMake/mitkInstallRules.cmake
index 5ce1789fdc..c9ae3f0b51 100644
--- a/CMake/mitkInstallRules.cmake
+++ b/CMake/mitkInstallRules.cmake
@@ -1,170 +1,172 @@
# Install MITK icon and logo
MITK_INSTALL(FILES
"${MITK_SOURCE_DIR}/mitk.ico"
"${MITK_SOURCE_DIR}/mitk.bmp")
# Helper vars
if(WIN32)
set(_prefix "")
set(_ext ".dll")
elseif(UNIX)
set(_prefix "lib")
if(APPLE)
set(_ext ".dylib")
else()
set(_ext ".so")
endif()
endif()
# Install MITK executables including auto-load modules
get_property(_mitk_executable_targets GLOBAL PROPERTY MITK_EXECUTABLE_TARGETS)
if(_mitk_executable_targets)
get_property(_mitk_module_targets GLOBAL PROPERTY MITK_MODULE_TARGETS)
foreach(_mitk_module_target ${_mitk_module_targets})
if(TARGET ${_mitk_module_target})
get_target_property(_mitk_autoload_targets ${_mitk_module_target} MITK_AUTOLOAD_TARGETS)
if (_mitk_autoload_targets)
foreach(_mitk_autoload_target ${_mitk_autoload_targets})
get_target_property(_mitk_autoload_directory ${_mitk_autoload_target} MITK_AUTOLOAD_DIRECTORY)
if (_mitk_autoload_directory)
if(WIN32)
get_target_property(_target_location ${_mitk_autoload_target} RUNTIME_OUTPUT_DIRECTORY)
else()
get_target_property(_target_location ${_mitk_autoload_target} LIBRARY_OUTPUT_DIRECTORY)
endif()
if(NOT CMAKE_CFG_INTDIR STREQUAL ".")
set(_target_location "${_target_location}/Release")
endif()
set(_mitk_autoload_target_filename "${_prefix}${_mitk_autoload_target}${_ext}")
set(_mitk_autoload_target_filepath "${_target_location}/${_mitk_autoload_target_filename}")
set(_install_DESTINATION "${_mitk_autoload_directory}")
MITK_INSTALL(FILES ${_mitk_autoload_target_filepath})
if(UNIX AND NOT APPLE)
install(CODE "file(RPATH_REMOVE FILE \"\${CMAKE_INSTALL_PREFIX}/bin/${_mitk_autoload_directory}/${_mitk_autoload_target_filename}\")")
endif()
endif()
endforeach()
endif()
endif()
endforeach()
set(_install_DESTINATION "")
foreach(_mitk_executable_target ${_mitk_executable_targets})
get_target_property(_no_install ${_mitk_executable_target} NO_INSTALL)
if(_no_install)
continue()
endif()
MITK_INSTALL_TARGETS(EXECUTABLES ${_mitk_executable_target} GLOB_PLUGINS)
if(UNIX AND NOT APPLE)
- install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${_mitk_executable_target}.sh)
+ install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME "${_mitk_executable_target}.sh")
+ elseif(WIN32)
+ install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.bat" DESTINATION "." RENAME "${_mitk_executable_target}.bat")
endif()
endforeach()
endif()
# Install PythonQt
if(MITK_USE_Python3 AND PythonQt_DIR)
set(_python_qt_lib "${PythonQt_DIR}/")
if(WIN32)
set(_python_qt_lib "${_python_qt_lib}bin")
else()
set(_python_qt_lib "${_python_qt_lib}lib")
endif()
set(_python_qt_lib "${_python_qt_lib}/${_prefix}PythonQt${_ext}")
MITK_INSTALL(FILES ${_python_qt_lib})
endif()
# Install Qt plugins
if(MITK_USE_Qt5)
get_property(_qmake_location TARGET ${Qt5Core_QMAKE_EXECUTABLE} PROPERTY IMPORT_LOCATION)
get_filename_component(_qmake_path ${_qmake_location} DIRECTORY)
set(_install_DESTINATION "plugins/sqldrivers")
MITK_INSTALL(FILES "${_qmake_path}/../plugins/sqldrivers/${_prefix}qsqlite${_ext}")
set(_install_DESTINATION "plugins/imageformats")
MITK_INSTALL(FILES "${_qmake_path}/../plugins/imageformats/${_prefix}qsvg${_ext}")
set(_install_DESTINATION "plugins/iconengines")
MITK_INSTALL(FILES "${_qmake_path}/../plugins/iconengines/${_prefix}qsvgicon${_ext}")
# Install platform-specific Qt plugins
set(_install_DESTINATION "plugins/platforms")
if(WIN32)
MITK_INSTALL(FILES "${_qmake_path}/../plugins/platforms/qwindows.dll")
elseif(APPLE)
MITK_INSTALL(FILES "${_qmake_path}/../plugins/platforms/libqcocoa.dylib")
elseif(UNIX)
MITK_INSTALL(FILES "${_qmake_path}/../plugins/platforms/libqxcb.so")
set(_install_DESTINATION "plugins/xcbglintegrations")
MITK_INSTALL(FILES "${_qmake_path}/../plugins/xcbglintegrations/libqxcb-glx-integration.so")
endif()
# Install platform-specific Qt styles
set(_install_DESTINATION "plugins/styles")
if(WIN32)
MITK_INSTALL(FILES "${_qmake_path}/../plugins/styles/qwindowsvistastyle.dll")
elseif(APPLE)
MITK_INSTALL(FILES "${_qmake_path}/../plugins/styles/libqmacstyle.dylib")
endif()
# Install Qt WebEngine
if(APPLE)
set(_install_DESTINATION "../Frameworks/QtWebEngineCore.framework")
get_filename_component(_real_path "${_qmake_path}/../lib/QtWebEngineCore.framework/Helpers" REALPATH)
MITK_INSTALL(DIRECTORY ${_real_path} USE_SOURCE_PERMISSIONS)
# Translations are included in the Resources directory of
# QtWebEngineCore.framework and are installed by default.
else()
set(_install_DESTINATION "")
if(WIN32)
MITK_INSTALL(PROGRAMS "${_qmake_path}/QtWebEngineProcess.exe")
elseif(UNIX)
MITK_INSTALL(PROGRAMS "${_qmake_path}/../libexec/QtWebEngineProcess")
endif()
# make sure resources and translations exist and try system location as well
if(EXISTS "${_qmake_path}/../resources")
MITK_INSTALL(DIRECTORY "${_qmake_path}/../resources")
elseif(EXISTS "/usr/share/qt5/resources")
MITK_INSTALL(DIRECTORY "/usr/share/qt5/resources")
else()
message(WARNING "No webengine resources found!")
endif()
set(_install_DESTINATION "translations")
if(EXISTS "${_qmake_path}/../translations/qtwebengine_locales")
MITK_INSTALL(DIRECTORY "${_qmake_path}/../translations/qtwebengine_locales")
elseif(EXISTS "/usr/share/qt5/translations/qtwebengine_locales")
MITK_INSTALL(DIRECTORY "/usr/share/qt5/translations/qtwebengine_locales")
else()
message(WARNING "No webengine translations found!")
endif()
endif()
endif()
set(_install_DESTINATION "")
# Install MatchPoint binaries that are not auto-detected
if(MITK_USE_MatchPoint)
MITK_INSTALL(DIRECTORY "${MITK_EXTERNAL_PROJECT_PREFIX}/bin/" FILES_MATCHING PATTERN "MapUtilities*")
MITK_INSTALL(DIRECTORY "${MITK_EXTERNAL_PROJECT_PREFIX}/bin/" FILES_MATCHING PATTERN "MapAlgorithms*")
endif()
# IMPORTANT: Restore default install destination! Do not edit this file beyond this line!
set(_install_DESTINATION "")
diff --git a/CMake/mitkMacroCreateModuleTests.cmake b/CMake/mitkMacroCreateModuleTests.cmake
index 3dc3e7aa4f..f6f8a94b00 100644
--- a/CMake/mitkMacroCreateModuleTests.cmake
+++ b/CMake/mitkMacroCreateModuleTests.cmake
@@ -1,106 +1,107 @@
#
# Create tests and testdriver for this module
#
# Usage: MITK_CREATE_MODULE_TESTS( [EXTRA_DRIVER_INIT init_code] )
#
# EXTRA_DRIVER_INIT is inserted as c++ code in the testdriver and will be executed before each test
#
macro(MITK_CREATE_MODULE_TESTS)
cmake_parse_arguments(MODULE_TEST
- "US_MODULE;NO_INIT" "EXTRA_DRIVER_INIT;EXTRA_DRIVER_INCLUDE" "EXTRA_DEPENDS;DEPENDS;PACKAGE_DEPENDS" ${ARGN})
+ "US_MODULE;NO_INIT" "EXTRA_DRIVER_INIT;EXTRA_DRIVER_INCLUDE" "EXTRA_DEPENDS;DEPENDS;PACKAGE_DEPENDS;TARGET_DEPENDS" ${ARGN})
if(BUILD_TESTING AND MODULE_IS_ENABLED)
include(files.cmake)
include_directories(.)
set(TESTDRIVER ${MODULE_NAME}TestDriver)
set(MODULE_TEST_EXTRA_DRIVER_INIT "${MODULE_TEST_EXTRA_DRIVER_INIT}")
if(MITK_XVFB_TESTING)
set(xvfb_run ${MITK_XVFB_TESTING_COMMAND})
else()
set(xvfb_run )
endif()
if(MODULE_TEST_US_MODULE)
message(WARNING "The US_MODULE argument is deprecated and should be removed")
endif()
if(MODULE_TEST_US_MODULE AND MODULE_TEST_NO_INIT)
message(WARNING "Conflicting arguments US_MODULE and NO_INIT: NO_INIT wins.")
endif()
set(_no_init)
if(MODULE_TEST_NO_INIT)
set(_no_init NO_INIT)
endif()
set(MITK_MODULE_NAME_REGEX_MATCH )
set(MITK_MODULE_NAME_REGEX_NOT_MATCH )
set(_testdriver_file_list ${CMAKE_CURRENT_BINARY_DIR}/testdriver_files.cmake)
configure_file(${MITK_CMAKE_DIR}/mitkTestDriverFiles.cmake.in ${_testdriver_file_list} @ONLY)
mitk_create_executable(${TESTDRIVER}
DEPENDS ${MODULE_NAME} ${MODULE_TEST_DEPENDS} ${MODULE_TEST_EXTRA_DEPENDS} MitkTestingHelper
PACKAGE_DEPENDS ${MODULE_TEST_PACKAGE_DEPENDS}
+ TARGET_DEPENDS ${MODULE_TEST_TARGET_DEPENDS}
FILES_CMAKE ${_testdriver_file_list}
NO_FEATURE_INFO
NO_BATCH_FILE
NO_INSTALL
${_no_init})
set_property(TARGET ${EXECUTABLE_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Modules/Tests")
#
# Now tell CMake which tests should be run. This is done automatically
# for all tests in ${KITNAME}_TESTS and ${KITNAME}_IMAGE_TESTS. The IMAGE_TESTS
# are run for each image in the TESTIMAGES list.
#
include(files.cmake)
foreach(test ${MODULE_TESTS} ${MODULE_RENDERING_TESTS})
get_filename_component(TName ${test} NAME_WE)
add_test(NAME ${TName} COMMAND ${xvfb_run} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} ${TName})
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_RELEASE release RELEASE)
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH_DEBUG debug DEBUG)
set(test_env_path ${MITK_RUNTIME_PATH_RELEASE} ${MITK_RUNTIME_PATH_DEBUG} $ENV{PATH})
list(REMOVE_DUPLICATES test_env_path)
string (REGEX REPLACE "\;" "\\\;" test_env_path "${test_env_path}")
set_property(TEST ${TName} PROPERTY ENVIRONMENT "PATH=${test_env_path}" APPEND)
set_property(TEST ${TName} PROPERTY SKIP_RETURN_CODE 77)
endforeach()
foreach(test ${MODULE_RENDERING_TESTS})
get_filename_component(TName ${test} NAME_WE)
set_property(TEST ${TName} APPEND PROPERTY LABELS "Rendering Tests")
set_property(TEST ${TName} PROPERTY RUN_SERIAL TRUE)
endforeach()
set(TEST_TYPES IMAGE SURFACE POINTSET) # add other file types here
foreach(test_type ${TEST_TYPES})
foreach(test_data ${MODULE_TEST${test_type}} ${ADDITIONAL_TEST_${test_type}})
if(EXISTS ${test_data})
set(TEST_DATA_FULL_PATH ${test_data})
else()
# todo: maybe search other paths as well
# yes, please in mitk/Testing/Data, too
set(TEST_DATA_FULL_PATH ${MITK_DATA_DIR}/${test_data})
endif()
if(EXISTS ${TEST_DATA_FULL_PATH})
foreach( test ${MODULE_${test_type}_TESTS})
get_filename_component(TName ${test} NAME_WE)
get_filename_component(DName ${TEST_DATA_FULL_PATH} NAME)
add_test(NAME ${TName}_${DName} COMMAND ${xvfb_run} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${TESTDRIVER} ${TName} ${TEST_DATA_FULL_PATH})
set_property(TEST ${TName}_${DName} PROPERTY ENVIRONMENT "PATH=${test_env_path}" APPEND)
set_property(TEST ${TName}_${DName} PROPERTY SKIP_RETURN_CODE 77)
endforeach()
else()
message("!!!!! No such file: ${TEST_DATA_FULL_PATH} !!!!!")
endif()
endforeach()
endforeach()
endif()
endmacro()
diff --git a/CMake/mitkSetupCPack.cmake b/CMake/mitkSetupCPack.cmake
index 1663a79fb3..6a95fec76a 100644
--- a/CMake/mitkSetupCPack.cmake
+++ b/CMake/mitkSetupCPack.cmake
@@ -1,142 +1,97 @@
#
# First, set the generator variable
#
if(NOT CPACK_GENERATOR)
if(WIN32)
find_program(NSIS_MAKENSIS NAMES makensis
PATHS [HKEY_LOCAL_MACHINE\\SOFTWARE\\NSIS]
DOC "Where is makensis.exe located"
)
- if(NOT NSIS_MAKENSIS)
- set(CPACK_GENERATOR ZIP)
- else()
- set(CPACK_GENERATOR "NSIS;ZIP")
+ set(CPACK_GENERATOR ZIP)
- endif(NOT NSIS_MAKENSIS)
+ if(NSIS_MAKENSIS)
+ set(MITK_CREATE_NSIS_INSTALLER ON CACHE BOOL "Create NSIS installer in addition to ZIP archive")
+ mark_as_advanced(MITK_CREATE_NSIS_INSTALLER)
+ if(MITK_CREATE_NSIS_INSTALLER)
+ list(APPEND CPACK_GENERATOR NSIS)
+ endif()
+ endif()
else()
if(APPLE)
set(CPACK_GENERATOR DragNDrop)
else()
set(CPACK_GENERATOR TGZ)
endif()
endif()
-endif(NOT CPACK_GENERATOR)
-
-# Set Redistributable information for windows
-if(${CMAKE_SYSTEM_NAME} MATCHES Windows)
- include(mitkFunctionGetMSVCVersion)
- mitkFunctionGetMSVCVersion()
- set(CPACK_VISUAL_STUDIO_VERSION_MAJOR "${VISUAL_STUDIO_VERSION_MAJOR}")
- set(CPACK_VISUAL_STUDIO_PRODUCT_NAME "${VISUAL_STUDIO_PRODUCT_NAME}")
- set(CPACK_LIBRARY_ARCHITECTURE "${CMAKE_LIBRARY_ARCHITECTURE}")
-
- # Visual Studio 2017 already comes with redistributable installers.
- # Try to find the right one.
-
- set(vswhere "$ENV{PROGRAMFILES\(X86\)}\\Microsoft Visual Studio\\Installer\\vswhere.exe")
-
- if(EXISTS ${vswhere})
- execute_process(COMMAND ${vswhere} -latest -property installationPath
- OUTPUT_VARIABLE installationPath
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- file(TO_CMAKE_PATH "${installationPath}" installationPath)
- set(redistPath "${installationPath}/VC/Redist/MSVC")
- file(GLOB redistPath "${installationPath}/VC/Redist/MSVC/*")
- list(LENGTH redistPath length)
- if(length EQUAL 1)
- if(CMAKE_SIZEOF_VOID_P EQUAL 8)
- set(redistPath "${redistPath}/vc_redist.x64.exe")
- else()
- set(redistPath "${redistPath}/vc_redist.x86.exe")
- endif()
- if(EXISTS ${redistPath})
- set(CMAKE_${CPACK_VISUAL_STUDIO_PRODUCT_NAME}_REDISTRIBUTABLE ${redistPath} CACHE FILEPATH "Path to the appropriate Microsoft Visual Studio Redistributable")
- endif()
- endif()
- endif()
-
- if(NOT DEFINED CMAKE_${CPACK_VISUAL_STUDIO_PRODUCT_NAME}_REDISTRIBUTABLE)
- set(CMAKE_${CPACK_VISUAL_STUDIO_PRODUCT_NAME}_REDISTRIBUTABLE "" CACHE FILEPATH "Path to the appropriate Microsoft Visual Studio Redistributable")
- endif()
-endif()
-
-if(EXISTS ${CMAKE_${CPACK_VISUAL_STUDIO_PRODUCT_NAME}_REDISTRIBUTABLE} )
- install(PROGRAMS ${CMAKE_${CPACK_VISUAL_STUDIO_PRODUCT_NAME}_REDISTRIBUTABLE}
- DESTINATION thirdpartyinstallers)
-
- get_filename_component(CPACK_REDISTRIBUTABLE_FILE_NAME ${CMAKE_${CPACK_VISUAL_STUDIO_PRODUCT_NAME}_REDISTRIBUTABLE} NAME )
endif()
# On windows set default install directory appropriately for 32 and 64 bit
# installers if not already set
if(WIN32 AND NOT CPACK_NSIS_INSTALL_ROOT)
if(CMAKE_CL_64)
set(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES64")
else()
set(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
endif()
endif()
# By default, do not warn when built on machines using only VS Express
-if(NOT DEFINED CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS)
- set(CMAKE_INSTALL_SYSTEM_RUNTIME_LIBS_NO_WARNINGS ON)
+if(MITK_USE_OpenMP)
+ set(CMAKE_INSTALL_OPENMP_LIBRARIES ON)
endif()
# include required mfc libraries
include(InstallRequiredSystemLibraries)
set(CPACK_PACKAGE_NAME "MITK")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Medical Imaging Interaction Toolkit")
set(CPACK_PACKAGE_VENDOR "German Cancer Research Center (DKFZ)")
set(CPACK_PACKAGE_DESCRIPTION_FILE "${MITK_SOURCE_DIR}/LICENSE")
set(CPACK_RESOURCE_FILE_LICENSE "${MITK_SOURCE_DIR}/LICENSE")
string(REPLACE "/" "_" CPACK_PACKAGE_VERSION_MAJOR "${MITK_REVISION_DESC}")
# tell cpack to strip all debug symbols from all files
set(CPACK_STRIP_FILES ON)
# set version
if(NOT CPACK_PACKAGE_VERSION_MAJOR)
set(CPACK_PACKAGE_VERSION_MAJOR ${MITK_VERSION_MAJOR})
set(CPACK_PACKAGE_VERSION_MINOR ${MITK_VERSION_MINOR})
set(CPACK_PACKAGE_VERSION_PATCH ${MITK_VERSION_PATCH})
set(CPACK_PACKAGE_VERSION "${MITK_VERSION_MAJOR}.${MITK_VERSION_MINOR}.${MITK_VERSION_PATCH}")
else()
set(CPACK_PACKAGE_VERSION ${CPACK_PACKAGE_VERSION_MAJOR})
endif()
# determine possible system specific extension
set(CPACK_PACKAGE_ARCH "unkown-architecture")
if(${CMAKE_SYSTEM_NAME} MATCHES Windows)
if(CMAKE_CL_64)
set(CPACK_PACKAGE_ARCH "windows-x86_64")
elseif(WIN32)
set(CPACK_PACKAGE_ARCH "windows-x86")
endif()
endif()
if(${CMAKE_SYSTEM_NAME} MATCHES Linux)
if(${CMAKE_SYSTEM_PROCESSOR} MATCHES i686)
set(CPACK_PACKAGE_ARCH "linux-x86")
elseif(${CMAKE_SYSTEM_PROCESSOR} MATCHES x86_64)
if(${CMAKE_CXX_FLAGS} MATCHES " -m32 ")
set(CPACK_PACKAGE_ARCH "linux-x86")
else()
set(CPACK_PACKAGE_ARCH "linux-x86_64")
endif()
else()
set(CPACK_PACKAGE_ARCH "linux")
endif()
endif()
if(${CMAKE_SYSTEM_NAME} MATCHES Darwin)
set(CPACK_PACKAGE_ARCH "macos-x86_64")
endif()
set(CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_PACKAGE_ARCH}")
-
-
-
diff --git a/CMakeExternals/Boost.cmake b/CMakeExternals/Boost.cmake
index a2921b9714..392f597f9f 100644
--- a/CMakeExternals/Boost.cmake
+++ b/CMakeExternals/Boost.cmake
@@ -1,335 +1,333 @@
#-----------------------------------------------------------------------------
# Boost
#-----------------------------------------------------------------------------
include(mitkFunctionGetMSVCVersion)
#[[ Sanity checks ]]
if(DEFINED BOOST_ROOT AND NOT EXISTS ${BOOST_ROOT})
message(FATAL_ERROR "BOOST_ROOT variable is defined but corresponds to non-existing directory")
endif()
string(REPLACE "^^" ";" MITK_USE_Boost_LIBRARIES "${MITK_USE_Boost_LIBRARIES}")
set(proj Boost)
set(proj_DEPENDENCIES )
set(Boost_DEPENDS ${proj})
if(NOT DEFINED BOOST_ROOT AND NOT MITK_USE_SYSTEM_Boost)
#[[ Reset variables. ]]
set(patch_cmd "")
set(configure_cmd "")
set(install_cmd "")
set(BOOST_ROOT ${ep_prefix})
if(WIN32)
set(BOOST_LIBRARYDIR "${BOOST_ROOT}/lib")
endif()
#[[ If you update Boost, make sure that the FindBoost module of the minimum
required version of CMake supports the new version of Boost.
In case you are using a higher version of CMake, download at least the
source code of the minimum required version of CMake to look into the
right version of the FindBoost module:
<CMAKE_INSTALL_DIR>/share/cmake-<VERSION>/Modules/FindBoost.cmake
Search for a list called _Boost_KNOWN_VERSIONS. If the new version is
not included in this list, you have three options:
* Update the minimum required version of CMake. This may require
adaptions of other parts of our CMake scripts and has the most
impact on other MITK developers. Yet this is the safest and
cleanest option.
* Set Boost_ADDITIONAL_VERSIONS (see the documentation of the
FindBoost module). As Boost libraries and dependencies between
them are hard-coded in the FindBoost module only for known versions,
this may cause trouble for other MITK developers relying on new
components of Boost or components with changed dependencies.
* Copy a newer version of the FindBoost module into our CMake
directory. Our CMake directory has a higher precedence than the
default CMake module directory. Doublecheck if the minimum required
version of CMake is able to process the newer version of the
FindBoost module. Also, DO NOT FORGET to mention this option right
above the call of cmake_minimum_required() in the top-level
CMakeLists.txt file AND in this file right above the set(url)
command below so if we update the minimum required version of CMake
or use another option in the future, we do not forget to remove our
copy of the FindBoost module again. ]]
- set(url "${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/boost_1_70_0.tar.gz")
- set(md5 fea771fe8176828fabf9c09242ee8c26)
+ set(url "${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/boost_1_74_0.tar.gz")
+ set(md5 3c8fb92ce08b9ad5a5f0b35731ac2c8e)
if(MITK_USE_Boost_LIBRARIES)
#[[ Boost has a two-step build process. In the first step, a bootstrap
script is called to build b2, an executable that is used to actually
build Boost in the second step.
The bootstrap script expects a toolset (compiler) argument that is
used to build the b2 executable. The scripts and their expected
argument format differ between Windows and Unix. ]]
if(WIN32)
mitkFunctionGetMSVCVersion()
if(VISUAL_STUDIO_VERSION_MINOR EQUAL 0)
#[[ Use just the major version in the toolset name. ]]
set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR})
elseif(VISUAL_STUDIO_VERSION_MAJOR EQUAL 14 AND VISUAL_STUDIO_VERSION_MINOR LESS 20)
#[[ Assume Visual Studio 2017. ]]
set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR}1)
elseif(VISUAL_STUDIO_VERSION_MAJOR EQUAL 14 AND VISUAL_STUDIO_VERSION_MINOR LESS 30)
#[[ Assume Visual Studio 2019. ]]
set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR}2)
else()
#[[ Fallback to the generic case. Be prepared to add another elseif
branch above for future versions of Visual Studio. ]]
set(bootstrap_args vc${VISUAL_STUDIO_VERSION_MAJOR})
endif()
else()
#[[ We support GCC and Clang on Unix. On macOS, the toolset must be set
- to darwin. The actual compiler for all of these toolkits is set
+ to clang. The actual compiler for all of these toolkits is set
further below, after the bootstrap script but before b2. ]]
- if(APPLE)
- set(toolset darwin)
- elseif(CMAKE_CXX_COMPILER_ID STREQUAL GNU)
+ if(CMAKE_CXX_COMPILER_ID STREQUAL GNU)
set(toolset gcc)
- elseif(CMAKE_CXX_COMPILER_ID STREQUAL Clang)
+ elseif(CMAKE_CXX_COMPILER_ID STREQUAL Clang OR APPLE)
set(toolset clang)
endif()
if(toolset)
set(bootstrap_args --with-toolset=${toolset})
endif()
#[[ At least give it a shot if the toolset is something else and let
the bootstrap script decide on the toolset by not passing any
argument. ]]
endif()
#[[ The call of b2 is more complex. b2 arguments are grouped into options
and properties. Options follow the standard format for arguments while
properties are plain key-value pairs. ]]
set(b2_options
--build-dir=<BINARY_DIR>
--stagedir=<INSTALL_DIR>
--ignore-site-config #[[ Build independent of any site.config file ]]
-q #[[ Stop at first error ]]
)
if(APPLE AND CMAKE_OSX_SYSROOT)
#[[ Specify the macOS platform SDK to be used. ]]
list(APPEND b2_options --sysroot=${CMAKE_OSX_SYSROOT})
endif()
foreach(lib ${MITK_USE_Boost_LIBRARIES})
list(APPEND b2_options --with-${lib})
endforeach()
set(b2_properties
threading=multi
runtime-link=shared
"cxxflags=${MITK_CXX14_FLAG} ${CMAKE_CXX_FLAGS}"
)
if(CMAKE_SIZEOF_VOID_P EQUAL 8)
list(APPEND b2_properties address-model=64)
else()
list(APPEND b2_properties address-model=32)
endif()
if(BUILD_SHARED_LIBS)
list(APPEND b2_properties link=shared)
else()
list(APPEND b2_properties link=static)
endif()
list(APPEND b2_properties "\
$<$<CONFIG:Debug>:variant=debug>\
$<$<CONFIG:Release>:variant=release>\
$<$<CONFIG:MinSizeRel>:variant=release>\
$<$<CONFIG:RelWithDebInfo>:variant=release>")
if(WIN32)
set(bootstrap_cmd if not exist b2.exe \( call bootstrap.bat ${bootstrap_args} \))
set(b2_cmd b2 ${b2_options} ${b2_properties} stage)
else()
set(bootstrap_cmd #[[ test -e ./b2 || ]] ./bootstrap.sh ${bootstrap_args})
set(b2_cmd ./b2 ${b2_options} ${b2_properties} stage)
#[[ We already told Boost if we want to use GCC or Clang but so far we
were not able to specify the exact same compiler we set in CMake
when configuring the MITK superbuild for the first time.
For example, this can be different from the system default
when multiple versions of the same compiler are installed
at the same time.
The bootstrap script creates a configuration file for b2 that should
be modified if necessary before b2 is called.
We look for a line like
using gcc ;
and replace it with something more specific like
using gcc : : /usr/bin/gcc-7.3 ;
We use the stream editor sed for the replacement but as macOS is
based on BSD Unix, we use the limited but portable BSD syntax
instead of the more powerful GNU syntax. We also use | instead of
the more commonly used / separator for sed because the replacement
contains slashes. ]]
if(toolset)
set(configure_cmd sed -i.backup "\
s|\
using[[:space:]][[:space:]]*${toolset}[[:space:]]*$<SEMICOLON>|\
using ${toolset} : : ${CMAKE_CXX_COMPILER} $<SEMICOLON>|\
g"
<SOURCE_DIR>/project-config.jam
)
endif()
endif()
endif()
if(WIN32)
set(dummy_cmd cd .)
else()
set(dummy_cmd true) #[[ "cd ." does not work reliably ]]
endif()
if(NOT patch_cmd)
set(patch_cmd ${dummy_cmd}) #[[ Do nothing ]]
endif()
if(NOT configure_cmd)
set(configure_cmd ${dummy_cmd}) #[[ Do nothing ]]
endif()
if(WIN32)
set(install_cmd
if not exist $<SHELL_PATH:${ep_prefix}/include/boost/config.hpp>
\( ${CMAKE_COMMAND} -E copy_directory <SOURCE_DIR>/boost <INSTALL_DIR>/include/boost \)
)
else()
set(install_cmd
# test -e <INSTALL_DIR>/include/boost/config.hpp ||
${CMAKE_COMMAND} -E copy_directory <SOURCE_DIR>/boost <INSTALL_DIR>/include/boost
)
endif()
ExternalProject_Add(${proj}
URL ${url}
URL_MD5 ${md5}
PATCH_COMMAND ${patch_cmd}
CONFIGURE_COMMAND ${configure_cmd}
BUILD_COMMAND ""
INSTALL_COMMAND ${install_cmd}
)
ExternalProject_Add_Step(${proj} bootstrap
COMMAND ${bootstrap_cmd}
DEPENDEES patch
DEPENDERS configure
WORKING_DIRECTORY <SOURCE_DIR>
)
ExternalProject_Add_Step(${proj} b2
COMMAND ${b2_cmd}
DEPENDEES bootstrap
DEPENDERS build
WORKING_DIRECTORY <SOURCE_DIR>
)
if(WIN32)
#[[ Reuse already extracted files. ]]
set(stamp_dir ${ep_prefix}/src/Boost-stamp)
configure_file(
${CMAKE_CURRENT_LIST_DIR}/extract-Boost.replacement.cmake
${stamp_dir}/extract-Boost.replacement.cmake
COPYONLY)
ExternalProject_Add_Step(${proj} pre_download
COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-pre_download.cmake
DEPENDEES mkdir
DEPENDERS download
WORKING_DIRECTORY ${stamp_dir}
)
endif()
set(install_manifest_dependees install)
if(MITK_USE_Boost_LIBRARIES)
if(WIN32)
#[[ Move DLLs from lib to bin directory. ]]
ExternalProject_Add_Step(${proj} post_install
COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-post_install-WIN32.cmake
DEPENDEES install
WORKING_DIRECTORY <INSTALL_DIR>/lib
)
set(install_manifest_dependees post_install)
elseif(APPLE)
#[[ Boost does not follow the common practice of either using rpath or
absolute paths for referencing dependencies. We have to use the
install_name_tool to fix this. ]]
ExternalProject_Add_Step(${proj} post_install
COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-post_install-APPLE.cmake
DEPENDEES install
WORKING_DIRECTORY <INSTALL_DIR>/lib
)
set(install_manifest_dependees post_install)
endif()
endif()
ExternalProject_Add_Step(${proj} install_manifest
COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_LIST_DIR}/Boost-install_manifest.cmake
DEPENDEES ${install_manifest_dependees}
WORKING_DIRECTORY ${ep_prefix}
)
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
diff --git a/CMakeExternals/CTK.cmake b/CMakeExternals/CTK.cmake
index 095ab60876..ed64006736 100644
--- a/CMakeExternals/CTK.cmake
+++ b/CMakeExternals/CTK.cmake
@@ -1,100 +1,100 @@
#-----------------------------------------------------------------------------
# CTK
#-----------------------------------------------------------------------------
if(MITK_USE_CTK)
# Sanity checks
if(DEFINED CTK_DIR AND NOT EXISTS ${CTK_DIR})
message(FATAL_ERROR "CTK_DIR variable is defined but corresponds to non-existing directory")
endif()
set(proj CTK)
set(proj_DEPENDENCIES DCMTK)
set(CTK_DEPENDS ${proj})
if(NOT DEFINED CTK_DIR)
- set(revision_tag "78341aba")
+ set(revision_tag "7210c5bc")
set(ctk_optional_cache_args )
if(MITK_USE_Python3)
list(APPEND ctk_optional_cache_args
-DCTK_LIB_Scripting/Python/Widgets:BOOL=ON
-DCTK_ENABLE_Python_Wrapping:BOOL=OFF
-DCTK_APP_ctkSimplePythonShell:BOOL=OFF
"-DPYTHON_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIRS}"
"-DPYTHON_LIBRARY:FILEPATH=${Python3_LIBRARY_RELEASE}"
)
else()
list(APPEND ctk_optional_cache_args
-DCTK_LIB_Scripting/Python/Widgets:BOOL=OFF
-DCTK_ENABLE_Python_Wrapping:BOOL=OFF
-DCTK_APP_ctkSimplePythonShell:BOOL=OFF
-DDCMTK_CMAKE_DEBUG_POSTFIX:STRING=d
)
endif()
if(CTEST_USE_LAUNCHERS)
list(APPEND ctk_optional_cache_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
FOREACH(type RUNTIME ARCHIVE LIBRARY)
IF(DEFINED CTK_PLUGIN_${type}_OUTPUT_DIRECTORY)
LIST(APPEND mitk_optional_cache_args -DCTK_PLUGIN_${type}_OUTPUT_DIRECTORY:PATH=${CTK_PLUGIN_${type}_OUTPUT_DIRECTORY})
ENDIF()
ENDFOREACH()
mitk_query_custom_ep_vars()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
GIT_REPOSITORY https://github.com/commontk/CTK
GIT_TAG ${revision_tag}
UPDATE_COMMAND ""
INSTALL_COMMAND ""
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${ctk_optional_cache_args}
# The CTK PluginFramework cannot cope with
# a non-empty CMAKE_DEBUG_POSTFIX for the plugin
# libraries yet.
-DCMAKE_DEBUG_POSTFIX:STRING=
-DCTK_QT_VERSION:STRING=5
-DQt5_DIR=${Qt5_DIR}
-DGIT_EXECUTABLE:FILEPATH=${GIT_EXECUTABLE}
-DCTK_BUILD_QTDESIGNER_PLUGINS:BOOL=ON
-DCTK_LIB_CommandLineModules/Backend/LocalProcess:BOOL=ON
-DCTK_LIB_CommandLineModules/Frontend/QtGui:BOOL=ON
-DCTK_LIB_PluginFramework:BOOL=ON
-DCTK_LIB_DICOM/Widgets:BOOL=ON
-DCTK_LIB_XNAT/Core:BOOL=ON
-DCTK_PLUGIN_org.commontk.eventadmin:BOOL=ON
-DCTK_PLUGIN_org.commontk.configadmin:BOOL=ON
-DCTK_USE_GIT_PROTOCOL:BOOL=OFF
-DDCMTK_DIR:PATH=${DCMTK_DIR}
-DPythonQt_URL:STRING=${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/PythonQt_fae23012.tar.gz
${${proj}_CUSTOM_CMAKE_ARGS}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
DEPENDS ${proj_DEPENDENCIES}
)
ExternalProject_Get_Property(${proj} binary_dir)
set(CTK_DIR ${binary_dir})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
endif()
diff --git a/CMakeExternals/CppUnit-1.12.1.patch b/CMakeExternals/CppUnit-1.12.1.patch
deleted file mode 100644
index 03830eeea5..0000000000
--- a/CMakeExternals/CppUnit-1.12.1.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff -ru cppunit-1.12.1/include/cppunit/extensions/HelperMacros.h CppUnit/include/cppunit/extensions/HelperMacros.h
---- cppunit-1.12.1/include/cppunit/extensions/HelperMacros.h 2004-03-13 13:52:56.000000000 +0100
-+++ CppUnit/include/cppunit/extensions/HelperMacros.h 2018-03-02 13:18:25.487754669 +0100
-@@ -169,7 +169,7 @@
- static CPPUNIT_NS::TestSuite *suite() \
- { \
- const CPPUNIT_NS::TestNamer &namer = getTestNamer__(); \
-- std::auto_ptr<CPPUNIT_NS::TestSuite> suite( \
-+ std::unique_ptr<CPPUNIT_NS::TestSuite> suite( \
- new CPPUNIT_NS::TestSuite( namer.getFixtureName() )); \
- CPPUNIT_NS::ConcretTestFixtureFactory<TestFixtureType> factory; \
- CPPUNIT_NS::TestSuiteBuilderContextBase context( *suite.get(), \
-diff -ru cppunit-1.12.1/src/cppunit/TypeInfoHelper.cpp CppUnit/src/cppunit/TypeInfoHelper.cpp
---- cppunit-1.12.1/src/cppunit/TypeInfoHelper.cpp 2004-02-18 21:45:44.000000000 +0100
-+++ CppUnit/src/cppunit/TypeInfoHelper.cpp 2018-03-02 13:16:03.100753385 +0100
-@@ -7,6 +7,7 @@
-
- #if CPPUNIT_HAVE_GCC_ABI_DEMANGLE
- #include <cxxabi.h>
-+#include <stdlib.h>
- #endif
diff --git a/CMakeExternals/CppUnit.cmake b/CMakeExternals/CppUnit.cmake
index 085e5f3597..7ebf18c970 100644
--- a/CMakeExternals/CppUnit.cmake
+++ b/CMakeExternals/CppUnit.cmake
@@ -1,50 +1,49 @@
#-----------------------------------------------------------------------------
# CppUnit
#-----------------------------------------------------------------------------
# Sanity checks
if(DEFINED CppUnit_DIR AND NOT EXISTS ${CppUnit_DIR})
message(FATAL_ERROR "CppUnit_DIR variable is defined but corresponds to non-existing directory")
endif()
set(proj CppUnit)
set(proj_DEPENDENCIES )
set(${proj}_DEPENDS ${proj})
if(NOT DEFINED CppUnit_DIR)
set(additional_args )
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
- URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/cppunit-1.12.1.tar.gz
- URL_MD5 bd30e9cf5523cdfc019b94f5e1d7fd19
+ URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/cppunit-1.15.1.tar.gz
+ URL_MD5 9dc669e6145cadd9674873e24943e6dd
PATCH_COMMAND
- ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/CppUnit-1.12.1.patch
COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_LIST_DIR}/${proj}config.h.cmake <SOURCE_DIR>/config/config.h.cmake
COMMAND ${CMAKE_COMMAND} -Dproj=${proj} -Dproj_target:STRING=cppunit -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_args}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
DEPENDS ${proj_DEPENDENCIES}
)
set(${proj}_DIR ${ep_prefix}/lib/cmake/CppUnit)
mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
diff --git a/CMakeExternals/CppUnitCMakeLists.txt b/CMakeExternals/CppUnitCMakeLists.txt
index 993cc852cd..14c7590705 100644
--- a/CMakeExternals/CppUnitCMakeLists.txt
+++ b/CMakeExternals/CppUnitCMakeLists.txt
@@ -1,229 +1,228 @@
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.18)
project(CppUnit)
set(${PROJECT_NAME}_MAJOR_VERSION 1)
-set(${PROJECT_NAME}_MINOR_VERSION 12)
+set(${PROJECT_NAME}_MINOR_VERSION 15)
set(${PROJECT_NAME}_PATCH_VERSION 1)
set(${PROJECT_NAME}_VERSION ${${PROJECT_NAME}_MAJOR_VERSION}.${${PROJECT_NAME}_MINOR_VERSION}.${${PROJECT_NAME}_PATCH_VERSION})
# UNICODE support
# See Visual C Unicode Programming Summary
# http://msdn.microsoft.com/en-us/library/dybsewaf%28VS.100%29.aspx
#add_definitions(-DUNICODE -D_UNICODE)
# Generates include/cppunit/config-auto.h
# This is originally done by autoconf
include(CheckIncludeFile)
include(CheckIncludeFileCXX)
include(CheckCXXSourceCompiles)
include(CheckCSourceCompiles)
include(CheckLibraryExists)
include(CheckFunctionExists)
#Not used == not seen in any *.h *.cpp files
#Not used FUNC_STRING_COMPARE_STRING_FIRST
check_include_file_cxx(sstream CPPUNIT_HAVE_SSTREAM)
check_include_file_cxx(strstream CPPUNIT_HAVE_STRSTREAM)
set (CMAKE_REQUIRED_DEFINITIONS -DHAVE_STRSTREAM=CPPUNIT_HAVE_STRSTREAM)
check_cxx_source_compiles(
"#ifdef HAVE_STRSTREAM
#include <strstream>
#else
#include <strstream.h>
#endif
int main() {
std::ostrstream message;
message << \"Hello\";
return 0;
}" CPPUNIT_HAVE_CLASS_STRSTREAM)
check_include_file_cxx(cmath CPPUNIT_HAVE_CMATH)
#Not used, dld library is obsolete anyway HAVE_DLD
#Not used HAVE_DLERROR
check_include_file(dlfcn.h CPPUNIT_HAVE_DLFCN_H)
check_c_source_compiles(
"#include <math.h>
int main() {
return finite(3);
}" CPPUNIT_HAVE_FINITE)
check_c_source_compiles(
"#include <math.h>
int main() {
return _finite(3);
}" CPPUNIT_HAVE__FINITE)
check_include_file_cxx(cxxabi.h CPPUNIT_HAVE_GCC_ABI_DEMANGLE)
#Not used HAVE_INTTYPES_H
check_c_source_compiles(
"#include <math.h>
int main() {
return isfinite(3);
}" CPPUNIT_HAVE_ISFINITE)
check_library_exists(dl dlopen "" CPPUNIT_HAVE_LIBDL)
#Not used HAVE_MEMORY_H
check_cxx_source_compiles(
"namespace Outer {
namespace Inner {
int i = 0;
}
}
using namespace Outer::Inner;
int main() {
return i;
}" CPPUNIT_HAVE_NAMESPACES)
check_cxx_source_compiles(
"#include <typeinfo>
class Base {
public:
Base() {}
virtual int f() { return 0; }
};
class Derived : public Base {
public:
Derived() {}
virtual int f() { return 1; }
};
int main() {
Derived d;
Base * ptr = &d;
return typeid(*ptr) == typeid(Derived);
}" CPPUNIT_HAVE_RTTI)
check_library_exists(dl shl_load "" CPPUNIT_HAVE_SHL_LOAD)
#Not used HAVE_STDINT_H
#Not used HAVE_STDLIB_H
#Not used HAVE_STRINGS_H
#Not used HAVE_STRING_H
#Not used HAVE_SYS_STAT_H
#Not used HAVE_SYS_TYPES_H
#Not used HAVE_UNISTD_H
#Not used PACKAGE
#Not used PACKAGE_BUGREPORT
#Not used PACKAGE_NAME
#Not used PACKAGE_STRING
#Not used PACKAGE_TARNAME
#Not used PACKAGE_VERSION
#Not used STDC_HEADERS
check_include_file_cxx(typeinfo CPPUNIT_USE_TYPEINFO_NAME)
#CPPUNIT_VERSION ok
configure_file(config/config.h.cmake ${CMAKE_CURRENT_SOURCE_DIR}/include/cppunit/config-auto.h)
##
set(cppunit_SRCS
src/cppunit/AdditionalMessage.cpp
src/cppunit/Asserter.cpp
- src/cppunit/BeOsDynamicLibraryManager.cpp
src/cppunit/BriefTestProgressListener.cpp
src/cppunit/CompilerOutputter.cpp
src/cppunit/DefaultProtector.h
src/cppunit/DefaultProtector.cpp
src/cppunit/DynamicLibraryManager.cpp
src/cppunit/DynamicLibraryManagerException.cpp
src/cppunit/Exception.cpp
src/cppunit/Message.cpp
src/cppunit/PlugInManager.cpp
src/cppunit/PlugInParameters.cpp
src/cppunit/Protector.cpp
src/cppunit/ProtectorChain.h
src/cppunit/ProtectorContext.h
src/cppunit/ProtectorChain.cpp
src/cppunit/RepeatedTest.cpp
src/cppunit/ShlDynamicLibraryManager.cpp
src/cppunit/SourceLine.cpp
src/cppunit/StringTools.cpp
src/cppunit/SynchronizedObject.cpp
src/cppunit/Test.cpp
src/cppunit/TestAssert.cpp
src/cppunit/TestCase.cpp
src/cppunit/TestCaseDecorator.cpp
src/cppunit/TestComposite.cpp
src/cppunit/TestDecorator.cpp
src/cppunit/TestFactoryRegistry.cpp
src/cppunit/TestFailure.cpp
src/cppunit/TestLeaf.cpp
src/cppunit/TestNamer.cpp
src/cppunit/TestPath.cpp
src/cppunit/TestPlugInDefaultImpl.cpp
src/cppunit/TestResult.cpp
src/cppunit/TestResultCollector.cpp
src/cppunit/TestRunner.cpp
src/cppunit/TestSetUp.cpp
src/cppunit/TestSuccessListener.cpp
src/cppunit/TestSuite.cpp
src/cppunit/TestSuiteBuilderContext.cpp
src/cppunit/TextOutputter.cpp
src/cppunit/TextTestProgressListener.cpp
src/cppunit/TextTestResult.cpp
src/cppunit/TextTestRunner.cpp
src/cppunit/TypeInfoHelper.cpp
src/cppunit/UnixDynamicLibraryManager.cpp
src/cppunit/Win32DynamicLibraryManager.cpp
src/cppunit/XmlDocument.cpp
src/cppunit/XmlElement.cpp
src/cppunit/XmlOutputter.cpp
src/cppunit/XmlOutputterHook.cpp
)
add_library(cppunit SHARED ${cppunit_SRCS})
target_include_directories(cppunit
PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
"$<INSTALL_INTERFACE:include>"
)
target_compile_definitions(cppunit PRIVATE CPPUNIT_BUILD_DLL)
set_target_properties(cppunit PROPERTIES
VERSION ${${PROJECT_NAME}_VERSION}
SOVERSION ${${PROJECT_NAME}_VERSION}
)
set(${PROJECT_NAME}_LIBRARIES cppunit)
# Install support
install(TARGETS ${${PROJECT_NAME}_LIBRARIES} EXPORT ${PROJECT_NAME}_TARGETS
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib
RUNTIME DESTINATION bin
)
install(DIRECTORY include/cppunit
DESTINATION include
)
# Config files
configure_file(
${PROJECT_NAME}Config.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
@ONLY
)
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}ConfigVersion.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
@ONLY
)
export(EXPORT ${PROJECT_NAME}_TARGETS
FILE ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Targets.cmake
)
set(config_package_location lib/cmake/${PROJECT_NAME})
install(EXPORT ${PROJECT_NAME}_TARGETS
FILE ${PROJECT_NAME}Targets.cmake
DESTINATION ${config_package_location}
)
install(FILES
"${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake"
DESTINATION ${config_package_location}
)
diff --git a/CMakeExternals/DCMQI.cmake b/CMakeExternals/DCMQI.cmake
index 6ed5173b5e..f0cbb3ee51 100644
--- a/CMakeExternals/DCMQI.cmake
+++ b/CMakeExternals/DCMQI.cmake
@@ -1,65 +1,65 @@
#-----------------------------------------------------------------------------
# DCMQI
#-----------------------------------------------------------------------------
if(MITK_USE_DCMQI)
# Sanity checks
if(DEFINED DCMQI_DIR AND NOT EXISTS ${DCMQI_DIR})
message(FATAL_ERROR "DCMQI_DIR variable is defined but corresponds to non-existing directory")
endif()
set(proj DCMQI)
set(proj_DEPENDENCIES DCMTK ITK)
set(DCMQI_DEPENDS ${proj})
if(NOT DEFINED DCMQI_DIR)
set(additional_cmake_args)
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_cmake_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
mitk_query_custom_ep_vars()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
GIT_REPOSITORY https://github.com/qiicr/dcmqi.git
- GIT_TAG ea4f0809c8ba771e262a69b5f81d547a3945b264
+ GIT_TAG 99192b76
UPDATE_COMMAND ""
INSTALL_COMMAND ""
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_cmake_args}
#-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
-DBUILD_SHARED_LIBS:BOOL=ON
-DDCMQI_BUILD_APPS:BOOL=OFF
-DDCMTK_DIR:PATH=${DCMTK_DIR}
-DITK_DIR:PATH=${ITK_DIR}
-DITK_NO_IO_FACTORY_REGISTER_MANAGER:BOOL=ON
-DDCMQI_SUPERBUILD:BOOL=OFF
-DDCMQI_CMAKE_CXX_STANDARD:STRING=14
${${proj}_CUSTOM_CMAKE_ARGS}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
DEPENDS ${proj_DEPENDENCIES}
)
ExternalProject_Get_Property(${proj} binary_dir)
set(DCMQI_DIR ${binary_dir})
#set(${proj}_DIR ${ep_prefix})
#message(${proj}_DIR: ${${proj}_DIR})
#mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
endif()
diff --git a/CMakeExternals/DCMTK.cmake b/CMakeExternals/DCMTK.cmake
index 92b6faa32a..4429abba21 100644
--- a/CMakeExternals/DCMTK.cmake
+++ b/CMakeExternals/DCMTK.cmake
@@ -1,69 +1,70 @@
#-----------------------------------------------------------------------------
# DCMTK
#-----------------------------------------------------------------------------
if(MITK_USE_DCMTK)
# Sanity checks
if(DEFINED DCMTK_DIR AND NOT EXISTS ${DCMTK_DIR})
message(FATAL_ERROR "DCMTK_DIR variable is defined but corresponds to non-existing directory")
endif()
set(proj DCMTK)
set(proj_DEPENDENCIES )
set(DCMTK_DEPENDS ${proj})
if(NOT DEFINED DCMTK_DIR)
if(DCMTK_DICOM_ROOT_ID)
set(DCMTK_CXX_FLAGS "${DCMTK_CXX_FLAGS} -DSITE_UID_ROOT=\\\"${DCMTK_DICOM_ROOT_ID}\\\"")
set(DCMTK_C_FLAGS "${DCMTK_CXX_FLAGS} -DSITE_UID_ROOT=\\\"${DCMTK_DICOM_ROOT_ID}\\\"")
endif()
set(additional_args )
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
mitk_query_custom_ep_vars()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/dcmtk-3.6.5.tar.gz
URL_MD5 e19707f64ee5695c496b9c1e48e39d07
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_args}
"-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} ${DCMTK_CXX_FLAGS}"
"-DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS} ${DCMTK_C_FLAGS}"
+ -DDCMTK_ENABLE_BUILTIN_DICTIONARY:BOOL=ON
-DDCMTK_ENABLE_CXX11:BOOL=ON
-DDCMTK_ENABLE_STL:BOOL=ON
-DDCMTK_WITH_DOXYGEN:BOOL=OFF
-DDCMTK_WITH_ZLIB:BOOL=OFF # see bug #9894
-DDCMTK_WITH_OPENSSL:BOOL=OFF # see bug #9894
-DDCMTK_WITH_PNG:BOOL=OFF # see bug #9894
-DDCMTK_WITH_TIFF:BOOL=OFF # see bug #9894
-DDCMTK_WITH_XML:BOOL=OFF # see bug #9894
-DDCMTK_WITH_ICONV:BOOL=OFF # see bug #9894
-DDCMTK_WITH_ICU:BOOL=OFF # see T26438
${${proj}_CUSTOM_CMAKE_ARGS}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
DEPENDS ${proj_DEPENDENCIES}
)
set(DCMTK_DIR ${ep_prefix})
mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
endif()
diff --git a/CMakeExternals/ExternalProjectList.cmake b/CMakeExternals/ExternalProjectList.cmake
index ab452fc867..7eeb49a07a 100644
--- a/CMakeExternals/ExternalProjectList.cmake
+++ b/CMakeExternals/ExternalProjectList.cmake
@@ -1,26 +1,31 @@
mitkFunctionAddExternalProject(NAME Poco ON COMPONENTS Foundation Net Util XML Zip)
mitkFunctionAddExternalProject(NAME DCMTK ON DOC "EXPERIMENTAL, superbuild only: Use DCMTK in MITK")
mitkFunctionAddExternalProject(NAME OpenIGTLink OFF)
-mitkFunctionAddExternalProject(NAME tinyxml ON ADVANCED)
+mitkFunctionAddExternalProject(NAME tinyxml2 ON ADVANCED)
mitkFunctionAddExternalProject(NAME GDCM ON ADVANCED)
mitkFunctionAddExternalProject(NAME Eigen ON ADVANCED DOC "Use the Eigen library")
mitkFunctionAddExternalProject(NAME ANN ON ADVANCED DOC "Use Approximate Nearest Neighbor Library")
mitkFunctionAddExternalProject(NAME CppUnit ON ADVANCED DOC "Use CppUnit for unit tests")
-mitkFunctionAddExternalProject(NAME PCRE OFF ADVANCED NO_PACKAGE)
mitkFunctionAddExternalProject(NAME HDF5 ON ADVANCED)
-mitkFunctionAddExternalProject(NAME SWIG OFF ADVANCED NO_PACKAGE DEPENDS PCRE)
mitkFunctionAddExternalProject(NAME OpenCV OFF)
mitkFunctionAddExternalProject(NAME Vigra OFF DEPENDS HDF5)
mitkFunctionAddExternalProject(NAME ITK ON NO_CACHE DEPENDS HDF5)
mitkFunctionAddExternalProject(NAME VTK ON NO_CACHE)
mitkFunctionAddExternalProject(NAME Boost ON NO_CACHE)
mitkFunctionAddExternalProject(NAME ZLIB OFF ADVANCED)
mitkFunctionAddExternalProject(NAME cpprestsdk OFF DEPENDS Boost ZLIB ADVANCED)
mitkFunctionAddExternalProject(NAME OpenMesh OFF)
mitkFunctionAddExternalProject(NAME CTK ON DEPENDS Qt5 DCMTK DOC "Use CTK in MITK")
mitkFunctionAddExternalProject(NAME DCMQI ON DEPENDS DCMTK ITK DOC "Use dcmqi in MITK")
mitkFunctionAddExternalProject(NAME MatchPoint OFF ADVANCED DEPENDS ITK DOC "Use the MatchPoint translation image registration library")
if(MITK_USE_Qt5)
mitkFunctionAddExternalProject(NAME Qwt ON ADVANCED DEPENDS Qt5)
endif()
+
+if(UNIX)
+ mitkFunctionAddExternalProject(NAME PCRE OFF ADVANCED NO_PACKAGE)
+ mitkFunctionAddExternalProject(NAME SWIG OFF ADVANCED NO_PACKAGE DEPENDS PCRE)
+else()
+ mitkFunctionAddExternalProject(NAME SWIG OFF ADVANCED NO_PACKAGE)
+endif()
diff --git a/CMakeExternals/GDCM.cmake b/CMakeExternals/GDCM.cmake
index a8d1577792..0d384ba1e8 100644
--- a/CMakeExternals/GDCM.cmake
+++ b/CMakeExternals/GDCM.cmake
@@ -1,71 +1,71 @@
#-----------------------------------------------------------------------------
# GDCM
#-----------------------------------------------------------------------------
# Sanity checks
if(DEFINED GDCM_DIR AND NOT EXISTS ${GDCM_DIR})
message(FATAL_ERROR "GDCM_DIR variable is defined but corresponds to non-existing directory")
endif()
# Check if an external ITK build tree was specified.
# If yes, use the GDCM from ITK, otherwise ITK will complain
if(ITK_DIR)
find_package(ITK)
if(ITK_GDCM_DIR)
set(GDCM_DIR ${ITK_GDCM_DIR})
endif()
endif()
set(proj GDCM)
set(proj_DEPENDENCIES )
set(GDCM_DEPENDS ${proj})
if(NOT DEFINED GDCM_DIR)
set(additional_args )
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
# On Mac some assertions fail that prevent reading certain DICOM files. Bug #19995
if(APPLE)
list(APPEND additional_args
"-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG} -DNDEBUG"
)
endif()
mitk_query_custom_ep_vars()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
- URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/gdcm-3.0.4.tar.gz
- URL_MD5 f12dbded708356d5fa0b5ed37ccdb66e
+ URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/gdcm-3.0.8.tar.gz
+ URL_MD5 29e0e60b04183e3eb9c18ad093156b2c
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_args}
-DGDCM_BUILD_SHARED_LIBS:BOOL=ON
-DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=OFF
${${proj}_CUSTOM_CMAKE_ARGS}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
DEPENDS ${proj_DEPENDENCIES}
)
set(GDCM_DIR ${ep_prefix})
mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
find_package(GDCM)
endif()
diff --git a/CMakeExternals/ITK-4.13.3.patch b/CMakeExternals/ITK-4.13.3.patch
new file mode 100644
index 0000000000..d1d3ece7f7
--- /dev/null
+++ b/CMakeExternals/ITK-4.13.3.patch
@@ -0,0 +1,40 @@
+diff --git a/Modules/Core/Common/include/itkBoundingBox.h b/Modules/Core/Common/include/itkBoundingBox.h
+index 36b03aaa7f..64205acfab 100644
+--- a/Modules/Core/Common/include/itkBoundingBox.h
++++ b/Modules/Core/Common/include/itkBoundingBox.h
+@@ -87,7 +87,7 @@ public:
+ itkTypeMacro(BoundingBox, Object);
+
+ /** Method for creation through the object factory. */
+- itkNewMacro(Self);
++ itkFactorylessNewMacro(Self);
+
+ /** Hold on to the type information specified by the template parameters. */
+ typedef TPointIdentifier PointIdentifier;
+diff --git a/Modules/Core/Common/include/itkVectorContainer.h b/Modules/Core/Common/include/itkVectorContainer.h
+index 72293c4ce8..e6366c66b5 100644
+--- a/Modules/Core/Common/include/itkVectorContainer.h
++++ b/Modules/Core/Common/include/itkVectorContainer.h
+@@ -92,7 +92,7 @@ public:
+ typedef VectorType STLContainerType;
+
+ /** Method for creation through the object factory. */
+- itkNewMacro(Self);
++ itkFactorylessNewMacro(Self);
+
+ /** Standard part of every itk Object. */
+ itkTypeMacro(VectorContainer, Object);
+diff --git a/Modules/Core/Transform/include/itkScalableAffineTransform.h b/Modules/Core/Transform/include/itkScalableAffineTransform.h
+index 4e830476a2..b5efeb95a4 100644
+--- a/Modules/Core/Transform/include/itkScalableAffineTransform.h
++++ b/Modules/Core/Transform/include/itkScalableAffineTransform.h
+@@ -47,7 +47,8 @@ public:
+ itkTypeMacro(ScalableAffineTransform, AffineTransform);
+
+ /** New macro for creation of through a Smart Pointer */
+- itkNewMacro(Self);
++ itkFactorylessNewMacro(Self);
++ itkCloneMacro(Self);
+
+ /** Dimension of the domain space. */
+ itkStaticConstMacro(InputSpaceDimension, unsigned int, NDimensions);
diff --git a/CMakeExternals/ITK.cmake b/CMakeExternals/ITK.cmake
index 6217b38384..973e57229d 100644
--- a/CMakeExternals/ITK.cmake
+++ b/CMakeExternals/ITK.cmake
@@ -1,85 +1,84 @@
#-----------------------------------------------------------------------------
# ITK
#-----------------------------------------------------------------------------
# Sanity checks
if(DEFINED ITK_DIR AND NOT EXISTS ${ITK_DIR})
message(FATAL_ERROR "ITK_DIR variable is defined but corresponds to non-existing directory")
endif()
set(proj ITK)
set(proj_DEPENDENCIES GDCM)
if(MITK_USE_OpenCV)
list(APPEND proj_DEPENDENCIES OpenCV)
endif()
if(MITK_USE_HDF5)
list(APPEND proj_DEPENDENCIES HDF5)
endif()
set(ITK_DEPENDS ${proj})
if(NOT DEFINED ITK_DIR)
set(additional_cmake_args -DUSE_WRAP_ITK:BOOL=OFF)
if(MITK_USE_OpenCV)
list(APPEND additional_cmake_args
-DModule_ITKVideoBridgeOpenCV:BOOL=ON
-DOpenCV_DIR:PATH=${OpenCV_DIR}
)
endif()
# Keep the behaviour of ITK 4.3 which by default turned on ITK Review
# see MITK bug #17338
list(APPEND additional_cmake_args
-DModule_ITKReview:BOOL=ON
- # for 4.7, the OpenJPEG is needed by review but the variable must be set
- -DModule_ITKOpenJPEG:BOOL=ON
- # Added Module for Wavelets
+ -DModule_ITKOpenJPEG:BOOL=ON # for 4.7, the OpenJPEG is needed by review but the variable must be set
-DModule_IsotropicWavelets:BOOL=ON
)
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_cmake_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
mitk_query_custom_ep_vars()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
UPDATE_COMMAND ""
- # ITK 4.13 release branch snapshot
- URL https://github.com/InsightSoftwareConsortium/ITK/archive/e53d1d94.tar.gz
- URL_MD5 977f77cb299cf3d722d13dd5408bcde5
+ URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/InsightToolkit-4.13.3.tar.gz
+ URL_MD5 d1c10c8288b47577d718a71190444815
+ PATCH_COMMAND
+ ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/ITK-4.13.3.patch
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_cmake_args}
-DBUILD_EXAMPLES:BOOL=OFF
-DITK_USE_SYSTEM_GDCM:BOOL=ON
-DGDCM_DIR:PATH=${GDCM_DIR}
-DITK_USE_SYSTEM_HDF5:BOOL=ON
-DHDF5_DIR:PATH=${HDF5_DIR}
${${proj}_CUSTOM_CMAKE_ARGS}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
DEPENDS ${proj_DEPENDENCIES}
)
set(ITK_DIR ${ep_prefix})
mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
diff --git a/CMakeExternals/Qwt-6.1.0.patch b/CMakeExternals/Qwt-6.1.0.patch
deleted file mode 100644
index 51124e995c..0000000000
--- a/CMakeExternals/Qwt-6.1.0.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -urNb qwt-6.1.0/src/qwt_transform.cpp Qwt-src/src/qwt_transform.cpp
---- qwt-6.1.0/src/qwt_transform.cpp 2013-05-30 17:18:27.000000000 +0200
-+++ Qwt-src/src/qwt_transform.cpp 2015-01-13 20:39:27.533871912 +0100
-@@ -15,10 +15,10 @@
- #endif
-
- //! Smallest allowed value for logarithmic scales: 1.0e-150
--QT_STATIC_CONST_IMPL double QwtLogTransform::LogMin = 1.0e-150;
-+const double QwtLogTransform::LogMin = 1.0e-150;
-
- //! Largest allowed value for logarithmic scales: 1.0e150
--QT_STATIC_CONST_IMPL double QwtLogTransform::LogMax = 1.0e150;
-+const double QwtLogTransform::LogMax = 1.0e150;
-
- //! Constructor
- QwtTransform::QwtTransform()
-diff -urNb qwt-6.1.0/src/qwt_transform.h Qwt-src/src/qwt_transform.h
---- qwt-6.1.0/src/qwt_transform.h 2013-05-30 17:18:25.000000000 +0200
-+++ Qwt-src/src/qwt_transform.h 2015-01-13 20:39:27.533871912 +0100
-@@ -107,8 +107,8 @@
-
- virtual QwtTransform *copy() const;
-
-- QT_STATIC_CONST double LogMin;
-- QT_STATIC_CONST double LogMax;
-+ static const double LogMin;
-+ static const double LogMax;
- };
-
- /*!
diff --git a/CMakeExternals/Qwt.cmake b/CMakeExternals/Qwt.cmake
index b397f9e042..e14f51089a 100644
--- a/CMakeExternals/Qwt.cmake
+++ b/CMakeExternals/Qwt.cmake
@@ -1,62 +1,61 @@
#-----------------------------------------------------------------------------
# Qwt
#-----------------------------------------------------------------------------
if(MITK_USE_Qwt)
# Sanity checks
if(DEFINED Qwt_DIR AND NOT EXISTS ${Qwt_DIR})
message(FATAL_ERROR "Qwt_DIR variable is defined but corresponds to non-existing directory")
endif()
set(proj Qwt)
set(proj_DEPENDENCIES )
set(${proj}_DEPENDS ${proj})
if(NOT DEFINED ${proj}_DIR)
set(patch_cmd ${CMAKE_COMMAND} -Dproj:STRING=${proj} -Dproj_target:STRING=qwt -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake)
set(qt54patch_cmd ${CMAKE_COMMAND} -DTEMPLATE_FILE:FILEPATH=${MITK_SOURCE_DIR}/CMakeExternals/EmptyFileForPatching.dummy -P ${MITK_SOURCE_DIR}/CMakeExternals/PatchQwt-6.1.0.cmake)
set(additional_cmake_args
"-DQt5Svg_DIR:PATH=${Qt5Svg_DIR}"
"-DQt5OpenGL_DIR:PATH=${Qt5OpenGL_DIR}"
"-DQt5PrintSupport_DIR:PATH=${Qt5PrintSupport_DIR}"
"-DQt5Concurrent_DIR:PATH=${Qt5Concurrent_DIR}"
"-DQt5Designer_DIR:PATH=${Qt5_DIR}Designer"
)
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_cmake_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
- URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/qwt-6.1.0.tar.bz2
- URL_MD5 aef0437b37f191067a6a9dc01c30ba64
- PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/Qwt-6.1.0.patch
- COMMAND ${CMAKE_COMMAND} -Dproj=${proj} -Dproj_target:STRING=qwt -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake
+ URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/qwt-6.1.5.tar.bz2
+ URL_MD5 d65582f99312796ed42c3be3208ed3db
+ PATCH_COMMAND ${CMAKE_COMMAND} -Dproj=${proj} -Dproj_target:STRING=qwt -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_cmake_args}
${qt_project_args}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
DEPENDS ${proj_DEPENDENCIES}
)
set(${proj}_DIR ${ep_prefix})
mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
endif()
diff --git a/CMakeExternals/QwtCMakeLists.txt b/CMakeExternals/QwtCMakeLists.txt
index 50bd9c2805..5c91a4acac 100644
--- a/CMakeExternals/QwtCMakeLists.txt
+++ b/CMakeExternals/QwtCMakeLists.txt
@@ -1,264 +1,264 @@
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.18)
project(Qwt)
set(${PROJECT_NAME}_MAJOR_VERSION 6)
set(${PROJECT_NAME}_MINOR_VERSION 1)
set(${PROJECT_NAME}_PATCH_VERSION 0)
set(${PROJECT_NAME}_VERSION ${${PROJECT_NAME}_MAJOR_VERSION}.${${PROJECT_NAME}_MINOR_VERSION}.${${PROJECT_NAME}_PATCH_VERSION})
set(QWT_MOC_HEADERS
# General
qwt_dyngrid_layout.h
qwt_magnifier.h
qwt_panner.h
qwt_picker.h
qwt_text_label.h
# QwtPlot
qwt_abstract_legend.h
qwt_legend.h
qwt_legend_label.h
qwt_plot.h
qwt_plot_renderer.h
qwt_plot_canvas.h
qwt_plot_panner.h
qwt_plot_picker.h
qwt_plot_zoomer.h
qwt_plot_magnifier.h
qwt_sampling_thread.h
qwt_scale_widget.h
# QwtOpenGL
qwt_plot_glcanvas.h
# QwtWidgets
qwt_abstract_slider.h
qwt_abstract_scale.h
qwt_analog_clock.h
qwt_compass.h
qwt_counter.h
qwt_dial.h
qwt_knob.h
qwt_slider.h
qwt_thermo.h
qwt_wheel.h
)
set(QWT_SOURCES
# General
qwt_abstract_scale_draw.cpp
qwt_clipper.cpp
qwt_color_map.cpp
qwt_column_symbol.cpp
qwt_date.cpp
qwt_date_scale_draw.cpp
qwt_date_scale_engine.cpp
qwt_dyngrid_layout.cpp
qwt_event_pattern.cpp
qwt_graphic.cpp
qwt_interval.cpp
qwt_interval_symbol.cpp
qwt_math.cpp
qwt_magnifier.cpp
qwt_null_paintdevice.cpp
qwt_painter.cpp
qwt_painter_command.cpp
qwt_panner.cpp
qwt_picker.cpp
qwt_picker_machine.cpp
qwt_pixel_matrix.cpp
qwt_point_3d.cpp
qwt_point_polar.cpp
qwt_round_scale_draw.cpp
qwt_scale_div.cpp
qwt_scale_draw.cpp
qwt_scale_map.cpp
qwt_spline.cpp
qwt_scale_engine.cpp
qwt_symbol.cpp
qwt_system_clock.cpp
qwt_text_engine.cpp
qwt_text_label.cpp
qwt_text.cpp
qwt_transform.cpp
qwt_widget_overlay.cpp
# QwtPlot
qwt_curve_fitter.cpp
qwt_abstract_legend.cpp
qwt_legend.cpp
qwt_legend_data.cpp
qwt_legend_label.cpp
qwt_plot.cpp
qwt_plot_renderer.cpp
qwt_plot_xml.cpp
qwt_plot_axis.cpp
qwt_plot_curve.cpp
qwt_plot_dict.cpp
qwt_plot_directpainter.cpp
qwt_plot_grid.cpp
qwt_plot_histogram.cpp
qwt_plot_item.cpp
qwt_plot_abstract_barchart.cpp
qwt_plot_barchart.cpp
qwt_plot_multi_barchart.cpp
qwt_plot_intervalcurve.cpp
qwt_plot_zoneitem.cpp
qwt_plot_tradingcurve.cpp
qwt_plot_spectrogram.cpp
qwt_plot_spectrocurve.cpp
qwt_plot_scaleitem.cpp
qwt_plot_legenditem.cpp
qwt_plot_seriesitem.cpp
qwt_plot_shapeitem.cpp
qwt_plot_marker.cpp
qwt_plot_textlabel.cpp
qwt_plot_layout.cpp
qwt_plot_canvas.cpp
qwt_plot_panner.cpp
qwt_plot_rasteritem.cpp
qwt_plot_picker.cpp
qwt_plot_zoomer.cpp
qwt_plot_magnifier.cpp
qwt_plot_rescaler.cpp
qwt_point_mapper.cpp
qwt_raster_data.cpp
qwt_matrix_raster_data.cpp
qwt_sampling_thread.cpp
qwt_series_data.cpp
qwt_point_data.cpp
qwt_scale_widget.cpp
# QwtSvg
qwt_plot_svgitem.cpp
# QwtOpenGL
qwt_plot_glcanvas.cpp
# QwtWidgets
qwt_abstract_slider.cpp
qwt_abstract_scale.cpp
qwt_arrow_button.cpp
qwt_analog_clock.cpp
qwt_compass.cpp
qwt_compass_rose.cpp
qwt_counter.cpp
qwt_dial.cpp
qwt_dial_needle.cpp
qwt_knob.cpp
qwt_slider.cpp
qwt_thermo.cpp
qwt_wheel.cpp
)
set(_qwt_moc_headers )
foreach(_header ${QWT_MOC_HEADERS})
list(APPEND _qwt_moc_headers src/${_header})
endforeach()
set(_qwt_sources )
foreach(_source ${QWT_SOURCES})
list(APPEND _qwt_sources src/${_source})
endforeach()
find_package(Qt5Svg REQUIRED)
find_package(Qt5OpenGL REQUIRED)
find_package(Qt5PrintSupport REQUIRED)
find_package(Qt5Concurrent REQUIRED)
qt5_wrap_cpp(_qwt_sources ${_qwt_moc_headers})
add_library(qwt SHARED ${_qwt_sources})
target_link_libraries(qwt PUBLIC Qt5::Svg Qt5::OpenGL Qt5::PrintSupport Qt5::Concurrent)
target_compile_definitions(qwt PUBLIC QWT_DLL PRIVATE QWT_MAKEDLL)
set_target_properties(qwt PROPERTIES
SOVERSION ${${PROJECT_NAME}_VERSION}
)
# Build the designer plug-in
option(QWT_BUILD_DESIGNER_PLUGIN "Build the Qt Designer plugin" ON)
if (QWT_BUILD_DESIGNER_PLUGIN)
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src)
set(_qwt_designer_sources
designer/qwt_designer_plotdialog.cpp
designer/qwt_designer_plugin.cpp
)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/plugins/designer)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/plugins/designer)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/plugins/designer)
find_package(Qt5Designer REQUIRED)
include_directories(${Qt5Designer_INCLUDE_DIRS})
qt5_wrap_cpp(_qwt_designer_sources
designer/qwt_designer_plugin.h
designer/qwt_designer_plotdialog.h
)
qt5_add_resources(_qwt_designer_sources designer/qwt_designer_plugin.qrc)
add_library(qwt_designer_plugin SHARED ${_qwt_designer_sources})
target_link_libraries(qwt_designer_plugin qwt Qt5::Designer)
set_target_properties(qwt_designer_plugin PROPERTIES
SOVERSION ${${PROJECT_NAME}_VERSION}
COMPILE_DEFINITIONS QWT_DLL)
endif()
set(${PROJECT_NAME}_LIBRARIES qwt)
# Install support
if (QWT_BUILD_DESIGNER_PLUGIN)
install(TARGETS qwt_designer_plugin
RUNTIME DESTINATION plugins/designer
LIBRARY DESTINATION plugins/designer
)
endif()
install(TARGETS ${${PROJECT_NAME}_LIBRARIES} EXPORT ${PROJECT_NAME}_TARGETS
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib
RUNTIME DESTINATION bin
INCLUDES DESTINATION include/${PROJECT_NAME}
)
install(DIRECTORY src/
DESTINATION include/${PROJECT_NAME}
FILES_MATCHING PATTERN "*.h"
)
# Config files
configure_file(
${PROJECT_NAME}Config.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
@ONLY
)
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}ConfigVersion.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
@ONLY
)
export(EXPORT ${PROJECT_NAME}_TARGETS
FILE ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Targets.cmake
)
set(config_package_location lib/cmake/${PROJECT_NAME})
install(EXPORT ${PROJECT_NAME}_TARGETS
FILE ${PROJECT_NAME}Targets.cmake
DESTINATION ${config_package_location}
)
install(FILES
"${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake"
DESTINATION ${config_package_location}
)
diff --git a/CMakeExternals/SWIG.cmake b/CMakeExternals/SWIG.cmake
index 0c008b722e..eccbfd6aae 100644
--- a/CMakeExternals/SWIG.cmake
+++ b/CMakeExternals/SWIG.cmake
@@ -1,71 +1,72 @@
#------------------------------------------------------------
# SWIG (Simple Wrapper Interface Generator)
#-----------------------------------------------------------
if(MITK_USE_SWIG)
if(DEFINED SWIG_DIR AND NOT EXISTS ${SWIG_DIR})
message(FATAL_ERROR "SWIG_DIR variable is defined but corresponds to non-existing directory")
endif()
set(SWIG_TARGET_VERSION 3.0.2)
set(proj SWIG)
- set(proj_DEPENDENCIES PCRE)
+ if(WIN32)
+ set(proj_DEPENDENCIES)
+ else()
+ set(proj_DEPENDENCIES PCRE)
+ endif()
set(SWIG_DEPENDS ${proj})
if(NOT SWIG_DIR)
# We don't "install" SWIG in the common install prefix,
# since it is only used as a tool during the MITK super-build
# to generate the Python wrappings for some projects.
# binary SWIG for windows
if(WIN32)
set(swig_source_dir ${CMAKE_CURRENT_BINARY_DIR}/swigwin-${SWIG_TARGET_VERSION})
# swig.exe available as pre-built binary on Windows:
ExternalProject_Add(${proj}
URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/swigwin-${SWIG_TARGET_VERSION}.zip
URL_MD5 "3f18de4fc09ab9abb0d3be37c11fbc8f"
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ""
)
ExternalProject_Get_Property(${proj} source_dir)
set(SWIG_DIR ${source_dir})
set(SWIG_EXECUTABLE ${source_dir}/swig.exe)
else()
-
- list(APPEND SWIG_DEPENDENCIES PCRE)
-
# swig uses bison find it by cmake and pass it down
find_package(BISON)
set(BISON_FLAGS "" CACHE STRING "Flags used by bison")
mark_as_advanced( BISON_FLAGS)
ExternalProject_add(${proj}
LIST_SEPARATOR ${sep}
URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/swig-${SWIG_TARGET_VERSION}.tar.gz
# Custom install dir for SWIG
INSTALL_DIR ${ep_prefix}/src/${proj}-install
URL_MD5 "62f9b0d010cef36a13a010dc530d0d41"
CONFIGURE_COMMAND <SOURCE_DIR>/./configure
CC=${CMAKE_C_COMPILER}${CMAKE_C_COMPILER_ARG1}
LDFLAGS=${CMAKE_LINKER_FLAGS} ${CMAKE_LINKER_FLAGS_RELEASE}
CXX=${CMAKE_CXX_COMPILER}${CMAKE_CXX_COMPILER_ARG1}
"--prefix=<INSTALL_DIR>"
"--with-pcre-prefix=${PCRE_DIR}"
--without-octave
"--with-python=${Python3_EXECUTABLE}"
DEPENDS ${proj_DEPENDENCIES}
)
ExternalProject_Get_Property(${proj} install_dir)
set(SWIG_DIR ${install_dir}/share/swig/${SWIG_TARGET_VERSION})
set(SWIG_EXECUTABLE ${install_dir}/bin/swig)
endif()
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
endif()
diff --git a/CMakeExternals/VTK-9.0.0.patch b/CMakeExternals/VTK-9.0.0.patch
new file mode 100644
index 0000000000..a468c8fff2
--- /dev/null
+++ b/CMakeExternals/VTK-9.0.0.patch
@@ -0,0 +1,15 @@
+diff --git a/Rendering/FreeType/vtkFreeTypeTools.cxx b/Rendering/FreeType/vtkFreeTypeTools.cxx
+index c54289dc60..03b899c4da 100644
+--- a/Rendering/FreeType/vtkFreeTypeTools.cxx
++++ b/Rendering/FreeType/vtkFreeTypeTools.cxx
+@@ -378,8 +378,7 @@ FTC_CMapCache* vtkFreeTypeTools::GetCMapCache()
+ }
+
+ //----------------------------------------------------------------------------
+-FT_CALLBACK_DEF(FT_Error)
+-vtkFreeTypeToolsFaceRequester(
++static FT_Error vtkFreeTypeToolsFaceRequester(
+ FTC_FaceID face_id, FT_Library lib, FT_Pointer request_data, FT_Face* face)
+ {
+ #if VTK_FTFC_DEBUG_CD
+
diff --git a/CMakeExternals/VTK.cmake b/CMakeExternals/VTK.cmake
index 36c53a21b2..96341d9d64 100644
--- a/CMakeExternals/VTK.cmake
+++ b/CMakeExternals/VTK.cmake
@@ -1,86 +1,88 @@
#-----------------------------------------------------------------------------
# VTK
#-----------------------------------------------------------------------------
# Sanity checks
if(DEFINED VTK_DIR AND NOT EXISTS ${VTK_DIR})
message(FATAL_ERROR "VTK_DIR variable is defined but corresponds to non-existing directory")
endif()
set(proj VTK)
set(proj_DEPENDENCIES )
set(VTK_DEPENDS ${proj})
if(MITK_USE_HDF5)
list(APPEND proj_DEPENDENCIES HDF5)
endif()
if(NOT DEFINED VTK_DIR)
set(additional_cmake_args )
if(WIN32)
list(APPEND additional_cmake_args
-DCMAKE_CXX_MP_FLAG:BOOL=ON
)
else()
list(APPEND additional_cmake_args
-DVTK_MODULE_USE_EXTERNAL_VTK_freetype:BOOL=ON
)
endif()
# Optionally enable memory leak checks for any objects derived from vtkObject. This
# will force unit tests to fail if they have any of these memory leaks.
option(MITK_VTK_DEBUG_LEAKS OFF)
mark_as_advanced(MITK_VTK_DEBUG_LEAKS)
list(APPEND additional_cmake_args
-DVTK_DEBUG_LEAKS:BOOL=${MITK_VTK_DEBUG_LEAKS}
)
if(MITK_USE_Qt5)
list(APPEND additional_cmake_args
-DVTK_GROUP_ENABLE_Qt:STRING=YES
-DQt5_DIR:PATH=${Qt5_DIR}
)
endif()
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_cmake_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
mitk_query_custom_ep_vars()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/VTK-9.0.0.tar.gz
URL_MD5 fa61cd36491d89a17edab18522bdda49
+ PATCH_COMMAND
+ ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/VTK-9.0.0.patch
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
-DVTK_ENABLE_WRAPPING:BOOL=OFF
-DVTK_LEGACY_REMOVE:BOOL=ON
-DVTK_MODULE_ENABLE_VTK_TestingRendering:STRING=YES
-DVTK_MODULE_ENABLE_VTK_RenderingContextOpenGL2:STRING=YES
-DVTK_MODULE_ENABLE_VTK_RenderingVolumeOpenGL2:STRING=YES
${additional_cmake_args}
${${proj}_CUSTOM_CMAKE_ARGS}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
${${proj}_CUSTOM_CMAKE_CACHE_ARGS}
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS}
DEPENDS ${proj_DEPENDENCIES}
)
set(VTK_DIR ${ep_prefix})
mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
diff --git a/CMakeExternals/cpprestsdk.cmake b/CMakeExternals/cpprestsdk.cmake
index c48dccc0cf..93644937b8 100644
--- a/CMakeExternals/cpprestsdk.cmake
+++ b/CMakeExternals/cpprestsdk.cmake
@@ -1,40 +1,39 @@
set(proj cpprestsdk)
set(proj_DEPENDENCIES Boost ZLIB)
if(MITK_USE_${proj})
set(${proj}_DEPENDS ${proj})
if(DEFINED ${proj}_DIR AND NOT EXISTS ${${proj}_DIR})
message(FATAL_ERROR "${proj}_DIR variable is defined but corresponds to non-existing directory!")
endif()
if(NOT DEFINED ${proj}_DIR)
set(cmake_cache_args
${ep_common_cache_args}
-DBUILD_SAMPLES:BOOL=OFF
-DBUILD_TESTS:BOOL=OFF
-DWERROR:BOOL=OFF
)
if(OPENSSL_ROOT_DIR)
list(APPEND cmake_cache_args
-DOPENSSL_ROOT_DIR:PATH=${OPENSSL_ROOT_DIR}
)
endif()
ExternalProject_Add(${proj}
- URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/cpprestsdk-2.10.10.tar.gz
- URL_MD5 705c4bd79158433309b21251a4936b18
- PATCH_COMMAND ${PATCH_COMMAND} -d "Release/libs/websocketpp" -N -p1 -i "${CMAKE_CURRENT_LIST_DIR}/${proj}.patch"
+ GIT_REPOSITORY https://github.com/microsoft/cpprestsdk.git
+ GIT_TAG v2.10.16
SOURCE_SUBDIR Release
CMAKE_ARGS ${ep_common_args}
CMAKE_CACHE_ARGS ${cmake_cache_args}
CMAKE_CACHE_DEFAULT_ARGS ${ep_common_cache_default_args}
DEPENDS ${proj_DEPENDENCIES}
)
set(${proj}_DIR ${ep_prefix})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
endif()
diff --git a/CMakeExternals/cpprestsdk.patch b/CMakeExternals/cpprestsdk.patch
deleted file mode 100644
index c6e9591407..0000000000
--- a/CMakeExternals/cpprestsdk.patch
+++ /dev/null
@@ -1,139 +0,0 @@
-From c769c9238ad62178f506038178714a1c35aa2769 Mon Sep 17 00:00:00 2001
-From: Stefan Floeren <42731906+stefan-floeren@users.noreply.github.com>
-Date: Tue, 16 Apr 2019 08:38:01 +0200
-Subject: [PATCH 1/2] Replace make_shared with new in some cases
-
-Replace make_shared for asio types that take a lib::ref as a parameter.
-This should fix the ASIO change (boostorg/asio@59066d8) for 1.70,
-while keeping it backwards compatible to older boost versions.
----
- websocketpp/transport/asio/connection.hpp | 7 ++++---
- websocketpp/transport/asio/endpoint.hpp | 3 +--
- websocketpp/transport/asio/security/none.hpp | 3 +--
- websocketpp/transport/asio/security/tls.hpp | 3 +--
- 4 files changed, 7 insertions(+), 9 deletions(-)
-
-diff --git a/websocketpp/transport/asio/connection.hpp b/websocketpp/transport/asio/connection.hpp
-index 60f88a79..1ccda8f3 100644
---- a/websocketpp/transport/asio/connection.hpp
-+++ b/websocketpp/transport/asio/connection.hpp
-@@ -311,9 +311,10 @@ class connection : public config::socket_type::socket_con_type {
- * needed.
- */
- timer_ptr set_timer(long duration, timer_handler callback) {
-- timer_ptr new_timer = lib::make_shared<lib::asio::steady_timer>(
-- lib::ref(*m_io_service),
-- lib::asio::milliseconds(duration)
-+ timer_ptr new_timer(
-+ new lib::asio::steady_timer(
-+ *m_io_service,
-+ lib::asio::milliseconds(duration))
- );
-
- if (config::enable_multithreading) {
-diff --git a/websocketpp/transport/asio/endpoint.hpp b/websocketpp/transport/asio/endpoint.hpp
-index ddab2c74..4b719a97 100644
---- a/websocketpp/transport/asio/endpoint.hpp
-+++ b/websocketpp/transport/asio/endpoint.hpp
-@@ -195,8 +195,7 @@ class endpoint : public config::socket_type {
-
- m_io_service = ptr;
- m_external_io_service = true;
-- m_acceptor = lib::make_shared<lib::asio::ip::tcp::acceptor>(
-- lib::ref(*m_io_service));
-+ m_acceptor.reset(new lib::asio::ip::tcp::acceptor(*m_io_service));
-
- m_state = READY;
- ec = lib::error_code();
-diff --git a/websocketpp/transport/asio/security/none.hpp b/websocketpp/transport/asio/security/none.hpp
-index 5c8293db..6c7d3524 100644
---- a/websocketpp/transport/asio/security/none.hpp
-+++ b/websocketpp/transport/asio/security/none.hpp
-@@ -168,8 +168,7 @@ class connection : public lib::enable_shared_from_this<connection> {
- return socket::make_error_code(socket::error::invalid_state);
- }
-
-- m_socket = lib::make_shared<lib::asio::ip::tcp::socket>(
-- lib::ref(*service));
-+ m_socket.reset(new lib::asio::ip::tcp::socket(*service));
-
- if (m_socket_init_handler) {
- m_socket_init_handler(m_hdl, *m_socket);
-diff --git a/websocketpp/transport/asio/security/tls.hpp b/websocketpp/transport/asio/security/tls.hpp
-index c76fd9aa..04ac3790 100644
---- a/websocketpp/transport/asio/security/tls.hpp
-+++ b/websocketpp/transport/asio/security/tls.hpp
-@@ -193,8 +193,7 @@ class connection : public lib::enable_shared_from_this<connection> {
- if (!m_context) {
- return socket::make_error_code(socket::error::invalid_tls_context);
- }
-- m_socket = lib::make_shared<socket_type>(
-- _WEBSOCKETPP_REF(*service),lib::ref(*m_context));
-+ m_socket.reset(new socket_type(*service, *m_context));
-
- if (m_socket_init_handler) {
- m_socket_init_handler(m_hdl, get_socket());
-
-From f810ca2e800e9b55be41c5911cf1d1185fcd516b Mon Sep 17 00:00:00 2001
-From: Stefan Floeren <42731906+stefan-floeren@users.noreply.github.com>
-Date: Wed, 17 Apr 2019 10:06:18 +0000
-Subject: [PATCH 2/2] Fix missed entries; fix testing
-
----
- CMakeLists.txt | 2 +-
- websocketpp/transport/asio/connection.hpp | 3 +--
- websocketpp/transport/asio/endpoint.hpp | 7 ++-----
- 3 files changed, 4 insertions(+), 8 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 2786aba9..951de975 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -202,7 +202,7 @@ if (BUILD_TESTS OR BUILD_EXAMPLES)
- endif ()
-
- if (NOT Boost_USE_STATIC_LIBS)
-- add_definitions (/DBOOST_TEST_DYN_LINK)
-+ add_definitions (-DBOOST_TEST_DYN_LINK)
- endif ()
-
- set (Boost_FIND_REQUIRED TRUE)
-diff --git a/websocketpp/transport/asio/connection.hpp b/websocketpp/transport/asio/connection.hpp
-index 1ccda8f3..57dda74a 100644
---- a/websocketpp/transport/asio/connection.hpp
-+++ b/websocketpp/transport/asio/connection.hpp
-@@ -462,8 +462,7 @@ class connection : public config::socket_type::socket_con_type {
- m_io_service = io_service;
-
- if (config::enable_multithreading) {
-- m_strand = lib::make_shared<lib::asio::io_service::strand>(
-- lib::ref(*io_service));
-+ m_strand.reset(new lib::asio::io_service::strand(*io_service));
- }
-
- lib::error_code ec = socket_con_type::init_asio(io_service, m_strand,
-diff --git a/websocketpp/transport/asio/endpoint.hpp b/websocketpp/transport/asio/endpoint.hpp
-index 4b719a97..94509adb 100644
---- a/websocketpp/transport/asio/endpoint.hpp
-+++ b/websocketpp/transport/asio/endpoint.hpp
-@@ -687,9 +687,7 @@ class endpoint : public config::socket_type {
- * @since 0.3.0
- */
- void start_perpetual() {
-- m_work = lib::make_shared<lib::asio::io_service::work>(
-- lib::ref(*m_io_service)
-- );
-+ m_work.reset(new lib::asio::io_service::work(*m_io_service));
- }
-
- /// Clears the endpoint's perpetual flag, allowing it to exit when empty
-@@ -853,8 +851,7 @@ class endpoint : public config::socket_type {
-
- // Create a resolver
- if (!m_resolver) {
-- m_resolver = lib::make_shared<lib::asio::ip::tcp::resolver>(
-- lib::ref(*m_io_service));
-+ m_resolver.reset(new lib::asio::ip::tcp::resolver(*m_io_service));
- }
-
- tcon->set_uri(u);
diff --git a/CMakeExternals/tinyxml-2.6.2.patch b/CMakeExternals/tinyxml-2.6.2.patch
deleted file mode 100644
index 4a601bb1e5..0000000000
--- a/CMakeExternals/tinyxml-2.6.2.patch
+++ /dev/null
@@ -1,266 +0,0 @@
-diff -burN tinyxml/tinyxml.cpp tinyxml-src/tinyxml.cpp
---- tinyxml/tinyxml.cpp 2011-05-15 04:24:57.000000000 +0200
-+++ tinyxml-src/tinyxml.cpp 2015-01-14 15:19:38.685333149 +0100
-@@ -34,6 +34,9 @@
- FILE* TiXmlFOpen( const char* filename, const char* mode );
-
- bool TiXmlBase::condenseWhiteSpace = true;
-+static unsigned int required_decimal_places = 14+1; // Need 14 for mitk default accuracy plus 1 to make sure we're within tolerance.
-+
-+
-
- // Microsoft compiler security
- FILE* TiXmlFOpen( const char* filename, const char* mode )
-@@ -757,21 +760,21 @@
- #endif
-
-
--void TiXmlElement::SetDoubleAttribute( const char * name, double val )
-+void TiXmlElement::SetDoubleAttribute( const char * name, double val, const unsigned int requiredDecimalPlaces )
- {
- TiXmlAttribute* attrib = attributeSet.FindOrCreate( name );
- if ( attrib ) {
-- attrib->SetDoubleValue( val );
-+ attrib->SetDoubleValue( val, requiredDecimalPlaces );
- }
- }
-
-
- #ifdef TIXML_USE_STL
--void TiXmlElement::SetDoubleAttribute( const std::string& name, double val )
-+void TiXmlElement::SetDoubleAttribute( const std::string& name, double val, const unsigned int requiredDecimalPlaces )
- {
- TiXmlAttribute* attrib = attributeSet.FindOrCreate( name );
- if ( attrib ) {
-- attrib->SetDoubleValue( val );
-+ attrib->SetDoubleValue( val, requiredDecimalPlaces );
- }
- }
- #endif
-@@ -1242,33 +1245,73 @@
-
- int TiXmlAttribute::QueryDoubleValue( double* dval ) const
- {
-+ //save old locale
-+ char * oldLocale;
-+ oldLocale = setlocale( LC_ALL, 0 );
-+
-+ //set new locale
-+ setlocale( LC_ALL, "C" );
- if ( TIXML_SSCANF( value.c_str(), "%lf", dval ) == 1 )
-+ {
-+ //restore locale
-+ setlocale( LC_ALL, oldLocale );
- return TIXML_SUCCESS;
-+ }
-+ //restore locale
-+ setlocale( LC_ALL, oldLocale );
- return TIXML_WRONG_TYPE;
- }
-
- void TiXmlAttribute::SetIntValue( int _value )
- {
- char buf [64];
-- #if defined(TIXML_SNPRINTF)
-+#if defined(TIXML_SNPRINTF)
- TIXML_SNPRINTF(buf, sizeof(buf), "%d", _value);
-- #else
-+#else
- sprintf (buf, "%d", _value);
-- #endif
-+#endif
- SetValue (buf);
- }
-
--void TiXmlAttribute::SetDoubleValue( double _value )
-+
-+
-+
-+void TiXmlAttribute::SetDoubleValue( double _value, const unsigned int requiredDecimalPlaces )
- {
-+#if defined(TIXML_USE_STL)
-+ std::ostringstream ss;
-+ //save old locale
-+ char * oldLocale;
-+ oldLocale = setlocale( LC_ALL, 0 );
-+
-+ //set new locale
-+ setlocale( LC_ALL, "C" );
-+ ss.precision(TiXmlBase::Precision(_value, requiredDecimalPlaces));
-+ ss << _value;
-+ SetValue( ss.str() );
-+ //restore locale
-+ setlocale( LC_ALL, oldLocale );
-+#else
- char buf [256];
-- #if defined(TIXML_SNPRINTF)
-- TIXML_SNPRINTF( buf, sizeof(buf), "%g", _value);
-- #else
-- sprintf (buf, "%g", _value);
-- #endif
-+
-+ //save old locale
-+ char * oldLocale;
-+ oldLocale = setlocale( LC_ALL, 0 );
-+
-+ //set new locale
-+ setlocale( LC_ALL, "C" );
-+#if defined(TIXML_SNPRINTF)
-+ TIXML_SNPRINTF( buf, sizeof(buf), TiXmlBase::Format(_value, requiredDecimalPlaces).c_str(), _value);
-+#else
-+ sprintf (buf, TiXmlBase::Format(_value, requiredDecimalPlaces).c_str(), _value);
-+#endif
- SetValue (buf);
-+ //restore locale
-+ setlocale( LC_ALL, oldLocale );
-+#endif
- }
-
-+
- int TiXmlAttribute::IntValue() const
- {
- return atoi (value.c_str ());
-@@ -1276,7 +1319,15 @@
-
- double TiXmlAttribute::DoubleValue() const
- {
-+#if defined(TIXML_USE_STL)
-+ std::istringstream ss(value);
-+ ss.imbue(std::locale("C"));
-+ double dval;
-+ ss >> dval;
-+ return dval;
-+#else
- return atof (value.c_str ());
-+#endif
- }
-
-
-@@ -1884,3 +1935,36 @@
- return true;
- }
-
-+unsigned int TiXmlBase::Precision( const double value, const unsigned int requiredDecimalPlaces ) const
-+{
-+ unsigned int lhs = 0;
-+ unsigned int one_for_plus_minus_sign = 1;
-+
-+ lhs = 0;
-+ double temp(value);
-+ while (temp >= 1.0)
-+ {
-+ lhs++;
-+ temp /= 10.0;
-+ }
-+
-+ return( lhs + requiredDecimalPlaces + one_for_plus_minus_sign );
-+}
-+
-+/**
-+ Return the printf format string that will ensure that the double value
-+ passed in will be stored with 'required_decimal_places' worth of decimal
-+ points as well as enough digits for the left hand side of the decimal point.
-+ */
-+TIXML_STRING TiXmlBase::Format( const double value, const unsigned int requiredDecimalPlaces ) const
-+{
-+ char buf[ 32 ];
-+
-+#if defined(TIXML_SNPRINTF)
-+ TIXML_SNPRINTF( buf, sizeof(buf), "%%%d.%dlf", Precision(value, requiredDecimalPlaces), requiredDecimalPlaces);
-+#else
-+ sprintf( buf, "%%%d.%dlf", Precision(value, requiredDecimalPlaces), requiredDecimalPlaces);
-+#endif
-+
-+ return(TIXML_STRING(buf));
-+}
-diff -burN tinyxml/tinyxml.h tinyxml-src/tinyxml.h
---- tinyxml/tinyxml.h 2011-05-15 04:24:57.000000000 +0200
-+++ tinyxml-src/tinyxml.h 2015-01-14 15:19:38.686333149 +0100
-@@ -20,12 +20,24 @@
-
- 3. This notice may not be removed or altered from any source
- distribution.
--*/
-+ */
-
-
- #ifndef TINYXML_INCLUDED
- #define TINYXML_INCLUDED
-
-+#ifndef TIXML_USE_STL
-+ #define TIXML_USE_STL
-+#endif
-+
-+#ifndef TIXML_USE_STL
-+#define TIXML_USE_STL
-+#endif
-+
-+#ifndef TIXML_USE_STL
-+#define TIXML_USE_STL
-+#endif
-+
- #ifdef _MSC_VER
- #pragma warning( push )
- #pragma warning( disable : 4530 )
-@@ -93,9 +105,11 @@
- const int TIXML_MINOR_VERSION = 6;
- const int TIXML_PATCH_VERSION = 2;
-
-+#define DEFAULT_REQUIRED_DECIMAL_PLACES 14
-+
- /* Internal structure for tracking location of items
- in the XML file.
--*/
-+ */
- struct TiXmlCursor
- {
- TiXmlCursor() { Clear(); }
-@@ -283,6 +297,10 @@
- TIXML_ERROR_STRING_COUNT
- };
-
-+ unsigned int Precision( const double value, const unsigned int requiredDecimalPlaces ) const ;
-+
-+ TIXML_STRING Format( const double value, const unsigned int requiredDecimalPlaces ) const;
-+
- protected:
-
- static const char* SkipWhiteSpace( const char*, TiXmlEncoding encoding );
-@@ -836,14 +854,14 @@
- void SetValue( const char* _value ) { value = _value; } ///< Set the value.
-
- void SetIntValue( int _value ); ///< Set the value from an integer.
-- void SetDoubleValue( double _value ); ///< Set the value from a double.
-+ void SetDoubleValue( double _value, const unsigned int requiredDecimalPlaces = DEFAULT_REQUIRED_DECIMAL_PLACES ); ///< Set the value from a double.
-
-- #ifdef TIXML_USE_STL
-+#ifdef TIXML_USE_STL
- /// STL std::string form.
- void SetName( const std::string& _name ) { name = _name; }
- /// STL std::string form.
- void SetValue( const std::string& _value ) { value = _value; }
-- #endif
-+#endif
-
- /// Get the next sibling attribute in the DOM. Returns null at end.
- const TiXmlAttribute* Next() const;
-@@ -1061,8 +1079,8 @@
- ///< STL std::string form.
- void SetAttribute( const std::string& name, int _value );
- ///< STL std::string form.
-- void SetDoubleAttribute( const std::string& name, double value );
-- #endif
-+ void SetDoubleAttribute( const std::string& name, double value, const unsigned int requiredDecimalPlaces = DEFAULT_REQUIRED_DECIMAL_PLACES );
-+#endif
-
- /** Sets an attribute of name to a given value. The attribute
- will be created if it does not exist, or changed if it does.
-@@ -1072,7 +1090,7 @@
- /** Sets an attribute of name to a given value. The attribute
- will be created if it does not exist, or changed if it does.
- */
-- void SetDoubleAttribute( const char * name, double value );
-+ void SetDoubleAttribute( const char * name, double value, const unsigned int requiredDecimalPlaces = DEFAULT_REQUIRED_DECIMAL_PLACES );
-
- /** Deletes an attribute with the given name.
- */
diff --git a/CMakeExternals/tinyxml.cmake b/CMakeExternals/tinyxml2.cmake
similarity index 65%
rename from CMakeExternals/tinyxml.cmake
rename to CMakeExternals/tinyxml2.cmake
index 74391bee27..8b24f8c184 100644
--- a/CMakeExternals/tinyxml.cmake
+++ b/CMakeExternals/tinyxml2.cmake
@@ -1,52 +1,52 @@
#-----------------------------------------------------------------------------
-# tinyxml
+# tinyxml2
#-----------------------------------------------------------------------------
# Sanity checks
-if(DEFINED tinyxml_DIR AND NOT EXISTS ${tinyxml_DIR})
- message(FATAL_ERROR "tinyxml_DIR variable is defined but corresponds to non-existing directory")
+if(DEFINED tinyxml2_DIR AND NOT EXISTS ${tinyxml2_DIR})
+ message(FATAL_ERROR "tinyxml2_DIR variable is defined but corresponds to non-existing directory")
endif()
-set(proj tinyxml)
+set(proj tinyxml2)
set(proj_DEPENDENCIES )
set(${proj}_DEPENDS ${proj})
-if(NOT DEFINED tinyxml_DIR)
+if(NOT DEFINED tinyxml2_DIR)
set(additional_cmake_args )
if(WIN32)
set(additional_cmake_args -DBUILD_SHARED_LIBS:BOOL=OFF)
endif()
if(CTEST_USE_LAUNCHERS)
list(APPEND additional_cmake_args
"-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake"
)
endif()
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
- URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/tinyxml_2_6_2.tar.gz
- URL_MD5 c1b864c96804a10526540c664ade67f0
- PATCH_COMMAND ${PATCH_COMMAND} -N -p1 -i ${CMAKE_CURRENT_LIST_DIR}/tinyxml-2.6.2.patch
- COMMAND ${CMAKE_COMMAND} -Dproj=${proj} -Dproj_target:STRING=tinyxml -P ${CMAKE_CURRENT_LIST_DIR}/GenerateDefaultCMakeBuildSystem.cmake
+ URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/tinyxml2-8.0.0.tar.gz
+ URL_MD5 5dc535c8b34ee621fe2128f072d275b5
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_ARGS
${ep_common_args}
${additional_cmake_args}
CMAKE_CACHE_ARGS
${ep_common_cache_args}
+ -DBUILD_TESTING:BOOL=OFF
+ -DBUILD_TESTS:BOOL=OFF
CMAKE_CACHE_DEFAULT_ARGS
${ep_common_cache_default_args}
DEPENDS ${proj_DEPENDENCIES}
)
set(${proj}_DIR ${ep_prefix})
mitkFunctionInstallExternalCMakeProject(${proj})
else()
mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}")
endif()
diff --git a/CMakeExternals/tinyxmlCMakeLists.txt b/CMakeExternals/tinyxmlCMakeLists.txt
deleted file mode 100644
index d19c0dfb25..0000000000
--- a/CMakeExternals/tinyxmlCMakeLists.txt
+++ /dev/null
@@ -1,66 +0,0 @@
-cmake_minimum_required(VERSION 2.8.4)
-
-project(tinyxml)
-
-set(${PROJECT_NAME}_MAJOR_VERSION 2)
-set(${PROJECT_NAME}_MINOR_VERSION 6)
-set(${PROJECT_NAME}_PATCH_VERSION 2)
-set(${PROJECT_NAME}_VERSION ${${PROJECT_NAME}_MAJOR_VERSION}.${${PROJECT_NAME}_MINOR_VERSION}.${${PROJECT_NAME}_PATCH_VERSION})
-
-
-set(tinyxml_HEADERS
- tinystr.h
- tinyxml.h
-)
-
-set(tinyxml_SOURCES
- tinyxml.cpp
- tinyxmlparser.cpp
- tinyxmlerror.cpp
- tinystr.cpp
-)
-
-add_library(tinyxml ${tinyxml_HEADERS} ${tinyxml_SOURCES})
-set_target_properties(tinyxml PROPERTIES
- SOVERSION ${${PROJECT_NAME}_VERSION})
-
-set(${PROJECT_NAME}_LIBRARIES tinyxml)
-
-# Install support
-
-install(TARGETS ${${PROJECT_NAME}_LIBRARIES} EXPORT ${PROJECT_NAME}_TARGETS
- LIBRARY DESTINATION lib
- ARCHIVE DESTINATION lib
- RUNTIME DESTINATION bin
- INCLUDES DESTINATION include/${PROJECT_NAME}
-)
-install(FILES ${tinyxml_HEADERS}
- DESTINATION include/${PROJECT_NAME}
-)
-
-# Config files
-configure_file(
- ${PROJECT_NAME}Config.cmake.in
- ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake
- @ONLY
-)
-configure_file(
- ${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}ConfigVersion.cmake.in
- ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
- @ONLY
-)
-
-export(EXPORT ${PROJECT_NAME}_TARGETS
- FILE ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Targets.cmake
-)
-
-set(config_package_location lib/cmake/${PROJECT_NAME})
-install(EXPORT ${PROJECT_NAME}_TARGETS
- FILE ${PROJECT_NAME}Targets.cmake
- DESTINATION ${config_package_location}
-)
-install(FILES
- "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
- "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake"
- DESTINATION ${config_package_location}
-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 1cd4bc6dd5..9dbf9c2326 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,1418 +1,1422 @@
-set(MITK_CMAKE_MINIMUM_REQUIRED_VERSION 3.14.5)
+set(MITK_CMAKE_MINIMUM_REQUIRED_VERSION 3.18)
cmake_minimum_required(VERSION ${MITK_CMAKE_MINIMUM_REQUIRED_VERSION})
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.19 AND CMAKE_VERSION VERSION_LESS 3.19.2)
+ message(FATAL_ERROR "\
+CMake v${CMAKE_VERSION} is defective [1]. \
+Please either downgrade to v3.18 or upgrade to at least v3.19.2.\n\
+[1] https://gitlab.kitware.com/cmake/cmake/-/issues/21529")
+endif()
+
#-----------------------------------------------------------------------------
-# See https://cmake.org/cmake/help/v3.14/manual/cmake-policies.7.html for details
+# Policies
#-----------------------------------------------------------------------------
-set(project_policies )
-foreach(policy ${project_policies})
- if(POLICY ${policy})
- cmake_policy(SET ${policy} NEW)
- endif()
-endforeach()
+#[[ T28060
+
+ https://cmake.org/cmake/help/v3.18/policy/CMP0091.html
+ https://cmake.org/cmake/help/v3.18/variable/CMAKE_MSVC_RUNTIME_LIBRARY.html
+
+ We pass CMP0091 to all external projects as command-line argument:
+ -DCMAKE_POLICY_DEFAULT_CMP0091:STRING=OLD
+ ]]
+cmake_policy(SET CMP0091 OLD)
#-----------------------------------------------------------------------------
# Superbuild Option - Enabled by default
#-----------------------------------------------------------------------------
option(MITK_USE_SUPERBUILD "Build MITK and the projects it depends on via SuperBuild.cmake." ON)
if(MITK_USE_SUPERBUILD)
project(MITK-superbuild)
set(MITK_SOURCE_DIR ${PROJECT_SOURCE_DIR})
set(MITK_BINARY_DIR ${PROJECT_BINARY_DIR})
else()
project(MITK VERSION 2018.04.99)
include_directories(SYSTEM ${MITK_SUPERBUILD_BINARY_DIR})
endif()
#-----------------------------------------------------------------------------
# MITK Extension Feature
#-----------------------------------------------------------------------------
set(MITK_EXTENSION_DIRS "" CACHE STRING "")
unset(MITK_ABSOLUTE_EXTENSION_DIRS)
foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS})
get_filename_component(MITK_ABSOLUTE_EXTENSION_DIR "${MITK_EXTENSION_DIR}" ABSOLUTE)
list(APPEND MITK_ABSOLUTE_EXTENSION_DIRS "${MITK_ABSOLUTE_EXTENSION_DIR}")
endforeach()
set(MITK_DIR_PLUS_EXTENSION_DIRS "${MITK_SOURCE_DIR}" ${MITK_ABSOLUTE_EXTENSION_DIRS})
#-----------------------------------------------------------------------------
# Update CMake module path
#-----------------------------------------------------------------------------
set(MITK_CMAKE_DIR ${MITK_SOURCE_DIR}/CMake)
set(CMAKE_MODULE_PATH ${MITK_CMAKE_DIR})
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
set(MITK_CMAKE_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMake")
if(EXISTS "${MITK_CMAKE_EXTENSION_DIR}")
list(APPEND CMAKE_MODULE_PATH "${MITK_CMAKE_EXTENSION_DIR}")
endif()
endforeach()
#-----------------------------------------------------------------------------
# CMake function(s) and macro(s)
#-----------------------------------------------------------------------------
# Standard CMake macros
include(FeatureSummary)
include(CTest)
include(CMakeParseArguments)
include(FindPackageHandleStandardArgs)
# MITK macros
include(mitkFunctionGetGccVersion)
include(mitkFunctionCheckCompilerFlags)
include(mitkFunctionSuppressWarnings) # includes several functions
include(mitkMacroEmptyExternalProject)
include(mitkFunctionEnableBuildConfiguration)
include(mitkFunctionWhitelists)
include(mitkFunctionAddExternalProject)
include(mitkFunctionAddLibrarySearchPaths)
SUPPRESS_VC_DEPRECATED_WARNINGS()
#-----------------------------------------------------------------------------
# Set a default build type if none was specified
#-----------------------------------------------------------------------------
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
message(STATUS "Setting build type to 'Debug' as none was specified.")
set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY
STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
endif()
#-----------------------------------------------------------------------------
# Check miminum macOS version
#-----------------------------------------------------------------------------
# The minimum supported macOS version is 10.13. If you use a version less than 10.13, there is no guarantee that the build still works.
if(APPLE)
exec_program(sw_vers ARGS -productVersion OUTPUT_VARIABLE macos_version)
if (macos_version VERSION_LESS "10.13")
message(WARNING "Detected macOS version \"${macos_version}\" is not supported anymore. Minimum required macOS version is at least 10.13.")
endif()
if (CMAKE_OSX_DEPLOYMENT_TARGET AND CMAKE_OSX_DEPLOYMENT_TARGET VERSION_LESS 10.13)
message(WARNING "Detected macOS deployment target \"${CMAKE_OSX_DEPLOYMENT_TARGET}\" is not supported anymore. Minimum required macOS version is at least 10.13.")
endif()
endif()
#-----------------------------------------------------------------------------
# Check miminum compiler versions
#-----------------------------------------------------------------------------
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
# require at least gcc 4.9 as provided by ppa:ubuntu-toolchain-r/test for Ubuntu 14.04
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9)
message(FATAL_ERROR "GCC version must be at least 4.9
If you are using Ubuntu 14.04, you can easily install gcc and g++ 4.9 (or any later version available) in addition to your version ${CMAKE_CXX_COMPILER_VERSION}:
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-4.9 g++-4.9
Make sure to explicitly specify these compilers when configuring MITK:
CMAKE_C_COMPILER:FILEPATH=/usr/bin/gcc-4.9
CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/g++-4.9
For more information on the proposed PPA see the Toolchain Updates section of https://wiki.ubuntu.com/ToolChain.")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
# require at least clang 3.4
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.4)
message(FATAL_ERROR "Clang version must be at least 3.4")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang")
# require at least clang 5.0
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
message(FATAL_ERROR "Apple Clang version must be at least 5.0")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
# require at least Visual Studio 2017
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19.10)
message(FATAL_ERROR "Microsoft Visual Studio 2017 or newer required")
endif()
else()
message(WARNING "You are using an unsupported compiler! Compilation has only been tested with Clang (Linux or Apple), GCC and MSVC.")
endif()
if(CMAKE_COMPILER_IS_GNUCXX)
mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION)
else()
set(GCC_VERSION 0)
endif()
set(MITK_CXX_STANDARD 14)
set(CMAKE_CXX_EXTENSIONS 0)
set(CMAKE_CXX_STANDARD ${MITK_CXX_STANDARD})
set(CMAKE_CXX_STANDARD_REQUIRED 1)
# This is necessary to avoid problems with compile feature checks.
# CMAKE_CXX_STANDARD seems to only set the -std=c++14 flag for targets.
# However, compile flag checks also need to be done with -std=c++14.
# The MITK_CXX14_FLAG variable is also used for external projects
# build during the MITK super-build.
mitkFunctionCheckCompilerFlags("-std=c++14" MITK_CXX14_FLAG)
#-----------------------------------------------------------------------------
# Warn if source or build path is too long
#-----------------------------------------------------------------------------
if(WIN32)
set(_src_dir_length_max 50)
set(_bin_dir_length_max 50)
if(MITK_USE_SUPERBUILD)
set(_src_dir_length_max 34) # _src_dir_length_max - strlen(ep/src/ITK-build)
set(_bin_dir_length_max 40) # _bin_dir_length_max - strlen(MITK-build)
endif()
string(LENGTH "${MITK_SOURCE_DIR}" _src_n)
string(LENGTH "${MITK_BINARY_DIR}" _bin_n)
# The warnings should be converted to errors
if(_src_n GREATER _src_dir_length_max)
message(WARNING "MITK source code directory path length is too long (${_src_n} > ${_src_dir_length_max})."
"Please move the MITK source code directory to a directory with a shorter path." )
endif()
if(_bin_n GREATER _bin_dir_length_max)
message(WARNING "MITK build directory path length is too long (${_bin_n} > ${_bin_dir_length_max})."
"Please move the MITK build directory to a directory with a shorter path." )
endif()
endif()
#-----------------------------------------------------------------------------
# Additional MITK Options (also shown during superbuild)
#-----------------------------------------------------------------------------
# -----------------------------------------
# General build options
option(BUILD_SHARED_LIBS "Build MITK with shared libraries" ON)
option(WITH_COVERAGE "Enable/Disable coverage" OFF)
option(BUILD_TESTING "Test the project" ON)
option(MITK_FAST_TESTING "Disable long-running tests like packaging" OFF)
option(MITK_XVFB_TESTING "Execute test drivers through xvfb-run" OFF)
option(MITK_BUILD_ALL_APPS "Build all MITK applications" OFF)
option(MITK_BUILD_EXAMPLES "Build the MITK Examples" OFF)
option(MITK_ENABLE_PIC_READER "Enable support for reading the DKFZ pic file format." ON)
mark_as_advanced(
MITK_XVFB_TESTING
MITK_FAST_TESTING
MITK_BUILD_ALL_APPS
MITK_ENABLE_PIC_READER
)
#-----------------------------------------------------------------------------
# Set UI testing flags
#-----------------------------------------------------------------------------
if(MITK_XVFB_TESTING)
set(MITK_XVFB_TESTING_COMMAND "xvfb-run" "--auto-servernum" CACHE STRING "Command and options to test through Xvfb")
mark_as_advanced(MITK_XVFB_TESTING_COMMAND)
endif(MITK_XVFB_TESTING)
# -----------------------------------------
# Other options
set(MITK_CUSTOM_REVISION_DESC "" CACHE STRING "Override MITK revision description")
mark_as_advanced(MITK_CUSTOM_REVISION_DESC)
set_property(GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS "")
include(CMakeExternals/ExternalProjectList.cmake)
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
set(MITK_CMAKE_EXTERNALS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMakeExternals")
if(EXISTS "${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake")
include("${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake")
endif()
endforeach()
# -----------------------------------------
# Other MITK_USE_* options not related to
# external projects build via the
# MITK superbuild
option(MITK_USE_BLUEBERRY "Build the BlueBerry platform" ON)
option(MITK_USE_OpenCL "Use OpenCL GPU-Computing library" OFF)
option(MITK_USE_OpenMP "Use OpenMP" OFF)
option(MITK_USE_Python3 "Use Python 3" OFF)
#-----------------------------------------------------------------------------
# Build configurations
#-----------------------------------------------------------------------------
set(_buildConfigs "Custom")
file(GLOB _buildConfigFiles CMake/BuildConfigurations/*.cmake)
foreach(_buildConfigFile ${_buildConfigFiles})
get_filename_component(_buildConfigFile ${_buildConfigFile} NAME_WE)
list(APPEND _buildConfigs ${_buildConfigFile})
endforeach()
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
file(GLOB _extBuildConfigFiles "${MITK_EXTENSION_DIR}/CMake/BuildConfigurations/*.cmake")
foreach(_extBuildConfigFile ${_extBuildConfigFiles})
get_filename_component(_extBuildConfigFile "${_extBuildConfigFile}" NAME_WE)
list(APPEND _buildConfigs "${_extBuildConfigFile}")
endforeach()
list(REMOVE_DUPLICATES _buildConfigs)
endforeach()
set(MITK_BUILD_CONFIGURATION "Custom" CACHE STRING "Use pre-defined MITK configurations")
set_property(CACHE MITK_BUILD_CONFIGURATION PROPERTY STRINGS ${_buildConfigs})
mitkFunctionEnableBuildConfiguration()
mitkFunctionCreateWhitelistPaths(MITK)
mitkFunctionFindWhitelists(MITK)
# -----------------------------------------
# Qt version related variables
option(MITK_USE_Qt5 "Use Qt 5 library" ON)
if(MITK_USE_Qt5)
if(WIN32)
set(MITK_QT5_MINIMUM_VERSION 5.12.9)
else()
set(MITK_QT5_MINIMUM_VERSION 5.12)
endif()
set(MITK_QT5_COMPONENTS Concurrent OpenGL PrintSupport Script Sql Svg Widgets Xml XmlPatterns WebEngineWidgets UiTools Help LinguistTools)
if(APPLE)
list(APPEND MITK_QT5_COMPONENTS DBus)
elseif(UNIX)
list(APPEND MITK_QT5_COMPONENTS X11Extras)
endif()
# Hint at default install locations of Qt
if(NOT Qt5_DIR)
if(MSVC)
set(_dir_candidates "C:/Qt")
if(CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)")
set(_compilers "msvc${CMAKE_MATCH_1}")
elseif(CMAKE_GENERATOR MATCHES "Ninja")
include(mitkFunctionGetMSVCVersion)
mitkFunctionGetMSVCVersion()
if(VISUAL_STUDIO_PRODUCT_NAME MATCHES "^Visual Studio ([0-9]+)")
set(_compilers "msvc${CMAKE_MATCH_1}")
endif()
endif()
if(_compilers MATCHES "[0-9]+")
if (CMAKE_MATCH_0 EQUAL 2019)
list(APPEND _compilers "msvc2017") # Binary compatible to 2019
endif()
endif()
else()
set(_dir_candidates ~/Qt)
if(APPLE)
set(_compilers clang)
else()
list(APPEND _dir_candidates /opt/Qt)
set(_compilers gcc)
endif()
endif()
if(CMAKE_SIZEOF_VOID_P EQUAL 8)
foreach(_compiler ${_compilers})
list(APPEND _compilers64 "${_compiler}_64")
endforeach()
set(_compilers ${_compilers64})
endif()
foreach(_dir_candidate ${_dir_candidates})
get_filename_component(_dir_candidate ${_dir_candidate} REALPATH)
foreach(_compiler ${_compilers})
set(_glob_expression "${_dir_candidate}/5.*/${_compiler}")
file(GLOB _hints ${_glob_expression})
list(SORT _hints)
list(APPEND MITK_QT5_HINTS ${_hints})
endforeach()
endforeach()
endif()
find_package(Qt5 ${MITK_QT5_MINIMUM_VERSION} COMPONENTS ${MITK_QT5_COMPONENTS} REQUIRED HINTS ${MITK_QT5_HINTS})
endif()
# -----------------------------------------
# Custom dependency logic
option(MITK_USE_SYSTEM_Boost "Use the system Boost" OFF)
set(MITK_USE_Boost_LIBRARIES "" CACHE STRING "A semi-colon separated list of required Boost libraries")
if(MITK_USE_cpprestsdk)
if(WIN32 AND Qt5_DIR)
set(_dir_candidate "${Qt5_DIR}/../../../../../Tools/OpenSSL/Win_x64")
get_filename_component(_dir_candidate ${_dir_candidate} ABSOLUTE)
if(EXISTS "${_dir_candidate}")
set(OPENSSL_ROOT_DIR "${_dir_candidate}")
endif()
endif()
find_package(OpenSSL QUIET)
if(NOT OpenSSL_FOUND)
set(openssl_message "Could not find OpenSSL (dependency of C++ REST SDK).\n")
if(UNIX)
if(APPLE)
set(openssl_message "${openssl_message}Please install it using your favorite package management "
"system (i.e. Homebrew or MacPorts).\n")
else()
set(openssl_message "${openssl_message}Please install the dev package of OpenSSL (i.e. libssl-dev).\n")
endif()
else()
set(openssl_message "${openssl_message}Please either install Win32 OpenSSL:\n"
" https://slproweb.com/products/Win32OpenSSL.html\n"
"Or use the Qt Maintenance tool to install:\n"
" Developer and Designer Tools > OpenSSL Toolkit > OpenSSL 64-bit binaries\n")
endif()
set(openssl_message "${openssl_message}If it still cannot be found, you can hint CMake to find OpenSSL by "
"adding/setting the OPENSSL_ROOT_DIR variable to the root directory of an "
"OpenSSL installation. Make sure to clear variables of partly found "
"versions of OpenSSL before, or they will be mixed up.")
message(FATAL_ERROR ${openssl_message})
endif()
list(APPEND MITK_USE_Boost_LIBRARIES date_time regex system)
if(UNIX)
list(APPEND MITK_USE_Boost_LIBRARIES atomic chrono filesystem random thread)
endif()
list(REMOVE_DUPLICATES MITK_USE_Boost_LIBRARIES)
set(MITK_USE_Boost_LIBRARIES ${MITK_USE_Boost_LIBRARIES} CACHE STRING "A semi-colon separated list of required Boost libraries" FORCE)
endif()
if(MITK_USE_Python3)
set(MITK_USE_ZLIB ON CACHE BOOL "" FORCE)
if(APPLE AND CMAKE_FRAMEWORK_PATH AND CMAKE_FRAMEWORK_PATH MATCHES "python3\\.?([0-9]+)")
find_package(Python3 3.${CMAKE_MATCH_1} EXACT REQUIRED COMPONENTS Interpreter Development NumPy)
else()
find_package(Python3 REQUIRED COMPONENTS Interpreter Development NumPy)
endif()
if(WIN32)
string(REPLACE "\\" "/" Python3_STDARCH "${Python3_STDARCH}")
string(REPLACE "\\" "/" Python3_STDLIB "${Python3_STDLIB}")
string(REPLACE "\\" "/" Python3_SITELIB "${Python3_SITELIB}")
endif()
endif()
if(BUILD_TESTING AND NOT MITK_USE_CppUnit)
message("> Forcing MITK_USE_CppUnit to ON because BUILD_TESTING=ON")
set(MITK_USE_CppUnit ON CACHE BOOL "Use CppUnit for unit tests" FORCE)
endif()
if(MITK_USE_BLUEBERRY)
option(MITK_BUILD_ALL_PLUGINS "Build all MITK plugins" OFF)
mark_as_advanced(MITK_BUILD_ALL_PLUGINS)
if(NOT MITK_USE_CTK)
message("> Forcing MITK_USE_CTK to ON because of MITK_USE_BLUEBERRY")
set(MITK_USE_CTK ON CACHE BOOL "Use CTK in MITK" FORCE)
endif()
endif()
#-----------------------------------------------------------------------------
# Pixel type multiplexing
#-----------------------------------------------------------------------------
# Customize the default pixel types for multiplex macros
set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES
"int, unsigned int, short, unsigned short, char, unsigned char"
CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros")
set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
"double, float"
CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros")
set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
"itk::RGBPixel<unsigned char>, itk::RGBAPixel<unsigned char>"
CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros")
set(MITK_ACCESSBYITK_DIMENSIONS
"2,3"
CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros")
mark_as_advanced(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES
MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
MITK_ACCESSBYITK_DIMENSIONS
)
# consistency checks
if(NOT MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES)
set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES
"int, unsigned int, short, unsigned short, char, unsigned char"
CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES)
set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES
"double, float"
CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES)
set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES
"itk::RGBPixel<unsigned char>, itk::RGBAPixel<unsigned char>"
CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES)
string(REPLACE "," ";" _integral_types ${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES})
string(REPLACE "," ";" _floating_types ${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES})
foreach(_scalar_type ${_integral_types} ${_floating_types})
set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES
"${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}itk::VariableLengthVector<${_scalar_type}>,")
endforeach()
string(LENGTH "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" _length)
math(EXPR _length "${_length} - 1")
string(SUBSTRING "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" 0 ${_length} MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES)
set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES ${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}
CACHE STRING "List of vector pixel types used in AccessByItk and InstantiateAccessFunction macros for itk::VectorImage types" FORCE)
endif()
if(NOT MITK_ACCESSBYITK_DIMENSIONS)
set(MITK_ACCESSBYITK_DIMENSIONS
"2,3"
CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros")
endif()
find_package(Git REQUIRED)
#-----------------------------------------------------------------------------
# Superbuild script
#-----------------------------------------------------------------------------
if(MITK_USE_SUPERBUILD)
include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
# Print configuration summary
message("\n\n")
feature_summary(
DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------"
WHAT ALL)
return()
endif()
#*****************************************************************************
#**************************** END OF SUPERBUILD ****************************
#*****************************************************************************
#-----------------------------------------------------------------------------
# Organize MITK targets in folders
#-----------------------------------------------------------------------------
set_property(GLOBAL PROPERTY USE_FOLDERS ON)
set(MITK_ROOT_FOLDER "MITK" CACHE STRING "")
mark_as_advanced(MITK_ROOT_FOLDER)
#-----------------------------------------------------------------------------
# CMake function(s) and macro(s)
#-----------------------------------------------------------------------------
include(WriteBasicConfigVersionFile)
include(CheckCXXSourceCompiles)
include(GenerateExportHeader)
include(mitkFunctionAddCustomModuleTest)
include(mitkFunctionCheckModuleDependencies)
include(mitkFunctionCompileSnippets)
include(mitkFunctionConfigureVisualStudioUserProjectFile)
include(mitkFunctionCreateBlueBerryApplication)
include(mitkFunctionCreateCommandLineApp)
include(mitkFunctionCreateModule)
include(mitkFunctionCreatePlugin)
include(mitkFunctionCreateProvisioningFile)
include(mitkFunctionGetLibrarySearchPaths)
include(mitkFunctionGetVersion)
include(mitkFunctionGetVersionDescription)
include(mitkFunctionInstallAutoLoadModules)
include(mitkFunctionInstallCTKPlugin)
include(mitkFunctionInstallProvisioningFiles)
include(mitkFunctionInstallThirdPartyCTKPlugins)
include(mitkFunctionOrganizeSources)
include(mitkFunctionUseModules)
if( ${MITK_USE_MatchPoint} )
include(mitkFunctionCreateMatchPointDeployedAlgorithm)
endif()
include(mitkMacroConfigureItkPixelTypes)
include(mitkMacroCreateExecutable)
include(mitkMacroCreateModuleTests)
include(mitkMacroGenerateToolsLibrary)
include(mitkMacroGetLinuxDistribution)
include(mitkMacroGetPMDPlatformString)
include(mitkMacroInstall)
include(mitkMacroInstallHelperApp)
include(mitkMacroInstallTargets)
include(mitkMacroMultiplexPicType)
# Deprecated
include(mitkMacroCreateCTKPlugin)
#-----------------------------------------------------------------------------
# Global CMake variables
#-----------------------------------------------------------------------------
# Required and enabled C++14 features for all MITK code.
# These are added as PUBLIC compile features to all MITK modules.
set(MITK_CXX_FEATURES
cxx_auto_type
cxx_decltype
cxx_enum_forward_declarations
cxx_extended_friend_declarations
cxx_extern_templates
cxx_final
cxx_lambdas
cxx_local_type_template_args
cxx_long_long_type
cxx_nullptr
cxx_override
cxx_range_for
cxx_right_angle_brackets
cxx_rvalue_references
cxx_static_assert
cxx_strong_enums
cxx_template_template_parameters
cxx_trailing_return_types
cxx_variadic_macros
)
if(NOT DEFINED CMAKE_DEBUG_POSTFIX)
# We can't do this yet because the CTK Plugin Framework
# cannot cope with a postfix yet.
#set(CMAKE_DEBUG_POSTFIX d)
endif()
#-----------------------------------------------------------------------------
# Output directories.
#-----------------------------------------------------------------------------
set(_default_LIBRARY_output_dir lib)
set(_default_RUNTIME_output_dir bin)
set(_default_ARCHIVE_output_dir lib)
foreach(type LIBRARY RUNTIME ARCHIVE)
# Make sure the directory exists
if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY
AND NOT EXISTS ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY})
message("Creating directory MITK_CMAKE_${type}_OUTPUT_DIRECTORY: ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}")
file(MAKE_DIRECTORY "${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}")
endif()
if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY)
set(CMAKE_${type}_OUTPUT_DIRECTORY ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY})
else()
set(CMAKE_${type}_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${_default_${type}_output_dir})
set(MITK_CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY})
endif()
set(CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY} CACHE INTERNAL "Output directory for ${type} files.")
mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY)
endforeach()
#-----------------------------------------------------------------------------
# Set MITK specific options and variables (NOT available during superbuild)
#-----------------------------------------------------------------------------
# Look for optional Doxygen package
find_package(Doxygen)
option(BLUEBERRY_DEBUG_SMARTPOINTER "Enable code for debugging smart pointers" OFF)
mark_as_advanced(BLUEBERRY_DEBUG_SMARTPOINTER)
# Ask the user to show the console window for applications
option(MITK_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting MITK GUI Applications" ON)
mark_as_advanced(MITK_SHOW_CONSOLE_WINDOW)
-# TODO: check if necessary
-option(USE_ITKZLIB "Use the ITK zlib for pic compression." ON)
-mark_as_advanced(USE_ITKZLIB)
-
if(NOT MITK_FAST_TESTING)
if(MITK_CTEST_SCRIPT_MODE STREQUAL "Continuous" OR MITK_CTEST_SCRIPT_MODE STREQUAL "Experimental")
set(MITK_FAST_TESTING ON)
endif()
endif()
if(NOT UNIX)
set(MITK_WIN32_FORCE_STATIC "STATIC" CACHE INTERNAL "Use this variable to always build static libraries on non-unix platforms")
endif()
if(MITK_BUILD_ALL_PLUGINS)
set(MITK_BUILD_ALL_PLUGINS_OPTION "FORCE_BUILD_ALL")
endif()
# Configure pixel types used for ITK image access multiplexing
mitkMacroConfigureItkPixelTypes()
# Configure module naming conventions
set(MITK_MODULE_NAME_REGEX_MATCH "^[A-Z].*$")
set(MITK_MODULE_NAME_REGEX_NOT_MATCH "^[Mm][Ii][Tt][Kk].*$")
set(MITK_DEFAULT_MODULE_NAME_PREFIX "Mitk")
set(MITK_MODULE_NAME_PREFIX ${MITK_DEFAULT_MODULE_NAME_PREFIX})
set(MITK_MODULE_NAME_DEFAULTS_TO_DIRECTORY_NAME 1)
#-----------------------------------------------------------------------------
# Get MITK version info
#-----------------------------------------------------------------------------
mitkFunctionGetVersion(${MITK_SOURCE_DIR} MITK)
mitkFunctionGetVersionDescription(${MITK_SOURCE_DIR} MITK)
# MITK_VERSION
set(MITK_VERSION_STRING "${MITK_VERSION_MAJOR}.${MITK_VERSION_MINOR}.${MITK_VERSION_PATCH}")
if(MITK_VERSION_PATCH STREQUAL "99")
set(MITK_VERSION_STRING "${MITK_VERSION_STRING}-${MITK_REVISION_SHORTID}")
endif()
#-----------------------------------------------------------------------------
# Installation preparation
#
# These should be set before any MITK install macros are used
#-----------------------------------------------------------------------------
# on macOS all BlueBerry plugins get copied into every
# application bundle (.app directory) specified here
if(MITK_USE_BLUEBERRY AND APPLE)
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications")
if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake")
set(MITK_APPS "")
include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake")
foreach(mitk_app ${MITK_APPS})
# extract option_name
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 1 option_name)
list(GET target_info_list 0 app_name)
# check if the application is enabled
if(${option_name} OR MITK_BUILD_ALL_APPS)
set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} Mitk${app_name})
endif()
endforeach()
endif()
endforeach()
endif()
#-----------------------------------------------------------------------------
# Set coverage Flags
#-----------------------------------------------------------------------------
if(WITH_COVERAGE)
if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG")
set(COVERAGE_CXX_FLAGS ${coverage_flags})
set(COVERAGE_C_FLAGS ${coverage_flags})
endif()
endif()
#-----------------------------------------------------------------------------
# MITK C/CXX Flags
#-----------------------------------------------------------------------------
set(MITK_C_FLAGS "${COVERAGE_C_FLAGS}")
set(MITK_C_FLAGS_DEBUG )
set(MITK_C_FLAGS_RELEASE )
set(MITK_CXX_FLAGS "${COVERAGE_CXX_FLAGS} ${MITK_CXX14_FLAG}")
set(MITK_CXX_FLAGS_DEBUG )
set(MITK_CXX_FLAGS_RELEASE )
set(MITK_EXE_LINKER_FLAGS )
set(MITK_SHARED_LINKER_FLAGS )
if(WIN32)
set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DPOCO_NO_UNWINDOWS -DWIN32_LEAN_AND_MEAN -DNOMINMAX")
mitkFunctionCheckCompilerFlags("/wd4005" MITK_CXX_FLAGS) # warning C4005: macro redefinition
mitkFunctionCheckCompilerFlags("/wd4231" MITK_CXX_FLAGS) # warning C4231: nonstandard extension used : 'extern' before template explicit instantiation
# the following line should be removed after fixing bug 17637
mitkFunctionCheckCompilerFlags("/wd4316" MITK_CXX_FLAGS) # warning C4316: object alignment on heap
mitkFunctionCheckCompilerFlags("/wd4180" MITK_CXX_FLAGS) # warning C4180: qualifier applied to function type has no meaning
mitkFunctionCheckCompilerFlags("/wd4251" MITK_CXX_FLAGS) # warning C4251: 'identifier' : class 'type' needs to have dll-interface to be used by clients of class 'type2'
endif()
if(APPLE)
set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DGL_SILENCE_DEPRECATION") # Apple deprecated OpenGL in macOS 10.14
endif()
if(NOT MSVC_VERSION)
foreach(_flag
-Wall
-Wextra
-Wpointer-arith
-Winvalid-pch
-Wcast-align
-Wwrite-strings
-Wno-error=gnu
-Wno-error=unknown-pragmas
# The strict-overflow warning is generated by ITK template code
-Wno-error=strict-overflow
-Woverloaded-virtual
-Wstrict-null-sentinel
#-Wold-style-cast
#-Wsign-promo
-Wno-error=deprecated-copy
-Wno-array-bounds
-fdiagnostics-show-option
)
mitkFunctionCheckCAndCXXCompilerFlags(${_flag} MITK_C_FLAGS MITK_CXX_FLAGS)
endforeach()
endif()
if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE)
mitkFunctionCheckCompilerFlags("-Wl,--no-undefined" MITK_SHARED_LINKER_FLAGS)
mitkFunctionCheckCompilerFlags("-Wl,--as-needed" MITK_SHARED_LINKER_FLAGS)
endif()
if(CMAKE_COMPILER_IS_GNUCXX)
mitkFunctionCheckCAndCXXCompilerFlags("-fstack-protector-all" MITK_C_FLAGS MITK_CXX_FLAGS)
set(MITK_CXX_FLAGS_RELEASE "-U_FORTIFY_SOURCES -D_FORTIFY_SOURCE=2 ${MITK_CXX_FLAGS_RELEASE}")
endif()
set(MITK_MODULE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS})
set(MITK_EXE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS})
#-----------------------------------------------------------------------------
# MITK Packages
#-----------------------------------------------------------------------------
set(MITK_MODULES_PACKAGE_DEPENDS_DIR ${MITK_SOURCE_DIR}/CMake/PackageDepends)
set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR})
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
set(MITK_PACKAGE_DEPENDS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMake/PackageDepends")
if(EXISTS "${MITK_PACKAGE_DEPENDS_EXTENSION_DIR}")
list(APPEND MODULES_PACKAGE_DEPENDS_DIRS "${MITK_PACKAGE_DEPENDS_EXTENSION_DIR}")
endif()
endforeach()
if(NOT MITK_USE_SYSTEM_Boost)
set(Boost_NO_SYSTEM_PATHS 1)
endif()
set(Boost_USE_MULTITHREADED 1)
set(Boost_USE_STATIC_LIBS 0)
set(Boost_USE_STATIC_RUNTIME 0)
-set(Boost_ADDITIONAL_VERSIONS 1.68 1.68.0)
+set(Boost_ADDITIONAL_VERSIONS 1.74 1.74.0)
# We need this later for a DCMTK workaround
set(_dcmtk_dir_orig ${DCMTK_DIR})
# This property is populated at the top half of this file
get_property(MITK_EXTERNAL_PROJECTS GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS)
foreach(ep ${MITK_EXTERNAL_PROJECTS})
get_property(_package GLOBAL PROPERTY MITK_${ep}_PACKAGE)
get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS)
if(MITK_USE_${ep} AND _package)
if(_components)
find_package(${_package} COMPONENTS ${_components} REQUIRED CONFIG)
else()
# Prefer config mode first because it finds external
# <proj>Config.cmake files pointed at by <proj>_DIR variables.
# Otherwise, existing Find<proj>.cmake files could fail.
if(DEFINED ${_package}_DIR)
#we store the information because it will be overwritten by find_package
#and would get lost for all EPs that use on Find<proj>.cmake instead of config
#files.
set(_temp_EP_${_package}_dir ${${_package}_DIR})
endif(DEFINED ${_package}_DIR)
find_package(${_package} QUIET CONFIG)
string(TOUPPER "${_package}" _package_uc)
if(NOT (${_package}_FOUND OR ${_package_uc}_FOUND))
if(DEFINED _temp_EP_${_package}_dir)
set(${_package}_DIR ${_temp_EP_${_package}_dir} CACHE PATH "externaly set dir of the package ${_package}" FORCE)
endif(DEFINED _temp_EP_${_package}_dir)
find_package(${_package} REQUIRED)
endif()
endif()
endif()
endforeach()
# Ensure that the MITK CMake module path comes first
set(CMAKE_MODULE_PATH
${MITK_CMAKE_DIR}
${CMAKE_MODULE_PATH}
)
if(MITK_USE_DCMTK)
# Due to the preferred CONFIG mode in find_package calls above,
# the DCMTKConfig.cmake file is read, which does not provide useful
# package information. We explictly need MODULE mode to find DCMTK.
if(${_dcmtk_dir_orig} MATCHES "${MITK_EXTERNAL_PROJECT_PREFIX}.*")
# Help our FindDCMTK.cmake script find our super-build DCMTK
set(DCMTK_DIR ${MITK_EXTERNAL_PROJECT_PREFIX})
else()
# Use the original value
set(DCMTK_DIR ${_dcmtk_dir_orig})
endif()
find_package(DCMTK REQUIRED MODULE)
endif()
if(MITK_USE_DCMQI)
# Due to the preferred CONFIG mode in find_package calls above,
# the DCMQIConfig.cmake file is read, which does not provide useful
# package information. We explictly need MODULE mode to find DCMQI.
# Help our FindDCMQI.cmake script find our super-build DCMQI
set(DCMQI_DIR ${MITK_EXTERNAL_PROJECT_PREFIX})
find_package(DCMQI REQUIRED)
endif()
-link_directories(${Boost_LIBRARY_DIRS})
-
if(MITK_USE_OpenIGTLink)
link_directories(${OpenIGTLink_LIBRARY_DIRS})
endif()
if(MITK_USE_OpenCL)
find_package(OpenCL REQUIRED)
endif()
if(MITK_USE_OpenMP)
find_package(OpenMP REQUIRED COMPONENTS CXX)
else()
find_package(OpenMP QUIET COMPONENTS CXX)
if(OpenMP_FOUND)
set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE)
elseif(APPLE AND OpenMP_libomp_LIBRARY AND NOT OpenMP_CXX_LIB_NAMES)
set(OpenMP_CXX_LIB_NAMES libomp CACHE STRING "" FORCE)
get_filename_component(openmp_lib_dir "${OpenMP_libomp_LIBRARY}" DIRECTORY)
set(openmp_include_dir "${openmp_lib_dir}/../include")
if(EXISTS "${openmp_include_dir}")
get_filename_component(openmp_include_dir "${openmp_include_dir}" REALPATH)
set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${openmp_include_dir}" CACHE STRING "" FORCE)
find_package(OpenMP QUIET COMPONENTS CXX)
if(OpenMP_FOUND)
set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE)
endif()
endif()
endif()
endif()
# Qt support
if(MITK_USE_Qt5)
find_package(Qt5Core ${MITK_QT5_MINIMUM_VERSION} REQUIRED) # at least Core required
get_target_property(_qmake_exec Qt5::qmake LOCATION)
execute_process(COMMAND ${_qmake_exec} -query QT_INSTALL_BINS
RESULT_VARIABLE _result
OUTPUT_VARIABLE QT_BINARY_DIR
ERROR_VARIABLE _error
)
string(STRIP "${QT_BINARY_DIR}" QT_BINARY_DIR)
if(_result OR NOT EXISTS "${QT_BINARY_DIR}")
message(FATAL_ERROR "Could not determine Qt binary directory: ${_result} ${QT_BINARY_DIR} ${_error}")
endif()
find_program(QT_HELPGENERATOR_EXECUTABLE
NAMES qhelpgenerator qhelpgenerator-qt5 qhelpgenerator5
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
find_program(QT_COLLECTIONGENERATOR_EXECUTABLE
NAMES qcollectiongenerator qcollectiongenerator-qt5 qcollectiongenerator5
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
find_program(QT_ASSISTANT_EXECUTABLE
NAMES assistant assistant-qt5 assistant5
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
find_program(QT_XMLPATTERNS_EXECUTABLE
NAMES xmlpatterns
PATHS ${QT_BINARY_DIR}
NO_DEFAULT_PATH
)
mark_as_advanced(QT_HELPGENERATOR_EXECUTABLE
QT_COLLECTIONGENERATOR_EXECUTABLE
QT_ASSISTANT_EXECUTABLE
QT_XMLPATTERNS_EXECUTABLE
)
if(MITK_USE_BLUEBERRY)
option(BLUEBERRY_USE_QT_HELP "Enable support for integrating plugin documentation into Qt Help" ${DOXYGEN_FOUND})
mark_as_advanced(BLUEBERRY_USE_QT_HELP)
# Sanity checks for in-application BlueBerry plug-in help generation
if(BLUEBERRY_USE_QT_HELP)
set(_force_blueberry_use_qt_help_to_off 0)
if(NOT DOXYGEN_FOUND)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen was not found.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(DOXYGEN_FOUND AND DOXYGEN_VERSION VERSION_LESS 1.8.7)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen version 1.8.7 or newer not found.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT QT_HELPGENERATOR_EXECUTABLE)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because QT_HELPGENERATOR_EXECUTABLE is empty.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT MITK_USE_Qt5)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because MITK_USE_Qt5 is OFF.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT QT_XMLPATTERNS_EXECUTABLE)
message("You have enabled Qt Help support, but QT_XMLPATTERNS_EXECUTABLE is empty")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(_force_blueberry_use_qt_help_to_off)
set(BLUEBERRY_USE_QT_HELP OFF CACHE BOOL "Enable support for integrating plugin documentation into Qt Help" FORCE)
endif()
endif()
if(BLUEBERRY_QT_HELP_REQUIRED AND NOT BLUEBERRY_USE_QT_HELP)
message(FATAL_ERROR "BLUEBERRY_USE_QT_HELP is required to be set to ON")
endif()
endif()
endif()
#-----------------------------------------------------------------------------
# Testing
#-----------------------------------------------------------------------------
if(BUILD_TESTING)
#[[ See T27701
# Initial cache for ProjectTemplate and PluginGenerator tests
configure_file(
CMake/mitkTestInitialCache.txt.in
${MITK_BINARY_DIR}/mitkTestInitialCache.txt
@ONLY
)]]
# Configuration for the CMake-generated test driver
set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include <stdexcept>")
set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "
try
{")
set(CMAKE_TESTDRIVER_AFTER_TESTMAIN "
}
catch (const std::exception& e)
{
fprintf(stderr, \"%s\\n\", e.what());
return EXIT_FAILURE;
}
catch (...)
{
printf(\"Exception caught in the test driver\\n\");
return EXIT_FAILURE;
}")
set(MITK_TEST_OUTPUT_DIR "${MITK_BINARY_DIR}/test_output")
if(NOT EXISTS ${MITK_TEST_OUTPUT_DIR})
file(MAKE_DIRECTORY ${MITK_TEST_OUTPUT_DIR})
endif()
# Test the package target
include(mitkPackageTest)
endif()
configure_file(mitkTestingConfig.h.in ${MITK_BINARY_DIR}/mitkTestingConfig.h)
#-----------------------------------------------------------------------------
# MITK_SUPERBUILD_BINARY_DIR
#-----------------------------------------------------------------------------
# If MITK_SUPERBUILD_BINARY_DIR isn't defined, it means MITK is *NOT* build using Superbuild.
# In that specific case, MITK_SUPERBUILD_BINARY_DIR should default to MITK_BINARY_DIR
if(NOT DEFINED MITK_SUPERBUILD_BINARY_DIR)
set(MITK_SUPERBUILD_BINARY_DIR ${MITK_BINARY_DIR})
endif()
#-----------------------------------------------------------------------------
# Set C/CXX and linker flags for MITK code
#-----------------------------------------------------------------------------
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MITK_CXX_FLAGS}")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${MITK_CXX_FLAGS_DEBUG}")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${MITK_CXX_FLAGS_RELEASE}")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MITK_C_FLAGS}")
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} ${MITK_C_FLAGS_DEBUG}")
set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} ${MITK_C_FLAGS_RELEASE}")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MITK_EXE_LINKER_FLAGS}")
set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${MITK_SHARED_LINKER_FLAGS}")
set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${MITK_MODULE_LINKER_FLAGS}")
#-----------------------------------------------------------------------------
# Add subdirectories
#-----------------------------------------------------------------------------
add_subdirectory(Utilities)
add_subdirectory(Modules)
include("${CMAKE_CURRENT_SOURCE_DIR}/Modules/ModuleList.cmake")
mitkFunctionWhitelistModules(MITK MITK_MODULES)
set(MITK_ROOT_FOLDER_BACKUP "${MITK_ROOT_FOLDER}")
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
get_filename_component(MITK_ROOT_FOLDER "${MITK_EXTENSION_DIR}" NAME)
set(MITK_MODULES_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Modules")
if(EXISTS "${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake")
set(MITK_MODULES "")
include("${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake")
foreach(mitk_module ${MITK_MODULES})
add_subdirectory("${MITK_MODULES_EXTENSION_DIR}/${mitk_module}" "Modules/${mitk_module}")
endforeach()
endif()
set(MITK_MODULE_NAME_PREFIX ${MITK_DEFAULT_MODULE_NAME_PREFIX})
endforeach()
set(MITK_ROOT_FOLDER "${MITK_ROOT_FOLDER_BACKUP}")
add_subdirectory(Wrapping)
set(MITK_DOXYGEN_OUTPUT_DIR "${PROJECT_BINARY_DIR}/Documentation/Doxygen" CACHE PATH
"Output directory for doxygen generated documentation.")
if(MITK_USE_BLUEBERRY)
include("${CMAKE_CURRENT_SOURCE_DIR}/Plugins/PluginList.cmake")
mitkFunctionWhitelistPlugins(MITK MITK_PLUGINS)
set(mitk_plugins_fullpath "")
foreach(mitk_plugin ${MITK_PLUGINS})
list(APPEND mitk_plugins_fullpath Plugins/${mitk_plugin})
endforeach()
set(MITK_PLUGIN_REGEX_LIST "")
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
set(MITK_PLUGINS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Plugins")
if(EXISTS "${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake")
set(MITK_PLUGINS "")
include("${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake")
foreach(mitk_plugin ${MITK_PLUGINS})
list(APPEND mitk_plugins_fullpath "${MITK_PLUGINS_EXTENSION_DIR}/${mitk_plugin}")
endforeach()
endif()
endforeach()
if(EXISTS ${MITK_PRIVATE_MODULES}/PluginList.cmake)
include(${MITK_PRIVATE_MODULES}/PluginList.cmake)
foreach(mitk_plugin ${MITK_PRIVATE_PLUGINS})
list(APPEND mitk_plugins_fullpath ${MITK_PRIVATE_MODULES}/${mitk_plugin})
endforeach()
endif()
if(MITK_BUILD_EXAMPLES)
include("${CMAKE_CURRENT_SOURCE_DIR}/Examples/Plugins/PluginList.cmake")
set(mitk_example_plugins_fullpath )
foreach(mitk_example_plugin ${MITK_EXAMPLE_PLUGINS})
list(APPEND mitk_example_plugins_fullpath Examples/Plugins/${mitk_example_plugin})
list(APPEND mitk_plugins_fullpath Examples/Plugins/${mitk_example_plugin})
endforeach()
endif()
# Specify which plug-ins belong to this project
macro(GetMyTargetLibraries all_target_libraries varname)
set(re_ctkplugin_mitk "^org_mitk_[a-zA-Z0-9_]+$")
set(re_ctkplugin_bb "^org_blueberry_[a-zA-Z0-9_]+$")
set(_tmp_list)
list(APPEND _tmp_list ${all_target_libraries})
ctkMacroListFilter(_tmp_list re_ctkplugin_mitk re_ctkplugin_bb MITK_PLUGIN_REGEX_LIST OUTPUT_VARIABLE ${varname})
endmacro()
# Get infos about application directories and build options
set(mitk_apps_fullpath "")
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications")
if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake")
set(MITK_APPS "")
include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake")
foreach(mitk_app ${MITK_APPS})
# extract option_name
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 0 directory_name)
list(GET target_info_list 1 option_name)
if(${option_name})
list(APPEND mitk_apps_fullpath "${MITK_APPLICATIONS_EXTENSION_DIR}/${directory_name}^^${option_name}")
endif()
endforeach()
endif()
endforeach()
if (mitk_plugins_fullpath)
ctkMacroSetupPlugins(${mitk_plugins_fullpath}
BUILD_OPTION_PREFIX MITK_BUILD_
APPS ${mitk_apps_fullpath}
BUILD_ALL ${MITK_BUILD_ALL_PLUGINS}
COMPACT_OPTIONS)
endif()
set(MITK_PLUGIN_USE_FILE "${MITK_BINARY_DIR}/MitkPluginUseFile.cmake")
if(${PROJECT_NAME}_PLUGIN_LIBRARIES)
ctkFunctionGeneratePluginUseFile(${MITK_PLUGIN_USE_FILE})
else()
file(REMOVE ${MITK_PLUGIN_USE_FILE})
set(MITK_PLUGIN_USE_FILE )
endif()
endif()
#-----------------------------------------------------------------------------
# Documentation
#-----------------------------------------------------------------------------
if(DOXYGEN_FOUND)
add_subdirectory(Documentation)
endif()
#-----------------------------------------------------------------------------
# Installation
#-----------------------------------------------------------------------------
# set MITK cpack variables
# These are the default variables, which can be overwritten ( see below )
include(mitkSetupCPack)
set(use_default_config ON)
set(ALL_MITK_APPS "")
set(activated_apps_no 0)
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications")
if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake")
set(MITK_APPS "")
include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake")
foreach(mitk_app ${MITK_APPS})
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 0 directory_name)
list(GET target_info_list 1 option_name)
list(GET target_info_list 2 executable_name)
list(APPEND ALL_MITK_APPS "${MITK_EXTENSION_DIR}/Applications/${directory_name}^^${option_name}^^${executable_name}")
if(${option_name} OR MITK_BUILD_ALL_APPS)
MATH(EXPR activated_apps_no "${activated_apps_no} + 1")
endif()
endforeach()
endif()
endforeach()
list(LENGTH ALL_MITK_APPS app_count)
if(app_count EQUAL 1 AND (activated_apps_no EQUAL 1 OR MITK_BUILD_ALL_APPS))
# Corner case if there is only one app in total
set(use_project_cpack ON)
elseif(activated_apps_no EQUAL 1 AND NOT MITK_BUILD_ALL_APPS)
# Only one app is enabled (no "build all" flag set)
set(use_project_cpack ON)
else()
# Less or more then one app is enabled
set(use_project_cpack OFF)
endif()
foreach(mitk_app ${ALL_MITK_APPS})
# extract target_dir and option_name
string(REPLACE "^^" "\\;" target_info ${mitk_app})
set(target_info_list ${target_info})
list(GET target_info_list 0 target_dir)
list(GET target_info_list 1 option_name)
list(GET target_info_list 2 executable_name)
# check if the application is enabled
if(${option_name} OR MITK_BUILD_ALL_APPS)
# check whether application specific configuration files will be used
if(use_project_cpack)
# use files if they exist
if(EXISTS "${target_dir}/CPackOptions.cmake")
include("${target_dir}/CPackOptions.cmake")
endif()
if(EXISTS "${target_dir}/CPackConfig.cmake.in")
set(CPACK_PROJECT_CONFIG_FILE "${target_dir}/CPackConfig.cmake")
configure_file(${target_dir}/CPackConfig.cmake.in
${CPACK_PROJECT_CONFIG_FILE} @ONLY)
set(use_default_config OFF)
endif()
endif()
# add link to the list
list(APPEND CPACK_CREATE_DESKTOP_LINKS "${executable_name}")
endif()
endforeach()
# if no application specific configuration file was used, use default
if(use_default_config)
configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in
${MITK_BINARY_DIR}/MITKCPackOptions.cmake @ONLY)
set(CPACK_PROJECT_CONFIG_FILE "${MITK_BINARY_DIR}/MITKCPackOptions.cmake")
endif()
# include CPack model once all variables are set
include(CPack)
# Additional installation rules
include(mitkInstallRules)
#-----------------------------------------------------------------------------
# Last configuration steps
#-----------------------------------------------------------------------------
# ---------------- Export targets -----------------
set(MITK_EXPORTS_FILE "${MITK_BINARY_DIR}/MitkExports.cmake")
file(REMOVE ${MITK_EXPORTS_FILE})
set(targets_to_export)
get_property(module_targets GLOBAL PROPERTY MITK_MODULE_TARGETS)
if(module_targets)
list(APPEND targets_to_export ${module_targets})
endif()
if(MITK_USE_BLUEBERRY)
if(MITK_PLUGIN_LIBRARIES)
list(APPEND targets_to_export ${MITK_PLUGIN_LIBRARIES})
endif()
endif()
export(TARGETS ${targets_to_export} APPEND
FILE ${MITK_EXPORTS_FILE})
set(MITK_EXPORTED_TARGET_PROPERTIES )
foreach(target_to_export ${targets_to_export})
get_target_property(autoload_targets ${target_to_export} MITK_AUTOLOAD_TARGETS)
if(autoload_targets)
set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_TARGETS \"${autoload_targets}\")")
endif()
get_target_property(autoload_dir ${target_to_export} MITK_AUTOLOAD_DIRECTORY)
if(autoload_dir)
set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_DIRECTORY \"${autoload_dir}\")")
endif()
get_target_property(deprecated_module ${target_to_export} MITK_MODULE_DEPRECATED_SINCE)
if(deprecated_module)
set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES}
set_target_properties(${target_to_export} PROPERTIES MITK_MODULE_DEPRECATED_SINCE \"${deprecated_module}\")")
endif()
endforeach()
# ---------------- External projects -----------------
get_property(MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS_CONFIG GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS)
set(MITK_CONFIG_EXTERNAL_PROJECTS )
#string(REPLACE "^^" ";" _mitk_external_projects ${MITK_EXTERNAL_PROJECTS})
foreach(ep ${MITK_EXTERNAL_PROJECTS})
get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS)
set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS}
set(MITK_USE_${ep} ${MITK_USE_${ep}})
set(MITK_${ep}_DIR \"${${ep}_DIR}\")
set(MITK_${ep}_COMPONENTS ${_components})
")
endforeach()
foreach(ep ${MITK_EXTERNAL_PROJECTS})
get_property(_package GLOBAL PROPERTY MITK_${ep}_PACKAGE)
get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS)
if(_components)
set(_components_arg COMPONENTS \${_components})
else()
set(_components_arg)
endif()
if(_package)
set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS}
if(MITK_USE_${ep})
set(${ep}_DIR \${MITK_${ep}_DIR})
if(MITK_${ep}_COMPONENTS)
mitkMacroFindDependency(${_package} COMPONENTS \${MITK_${ep}_COMPONENTS})
else()
mitkMacroFindDependency(${_package})
endif()
endif()")
endif()
endforeach()
# ---------------- Tools -----------------
configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in
${MITK_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY)
configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in
${MITK_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY)
configure_file(${MITK_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in
${MITK_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY)
# ---------------- Configure files -----------------
configure_file(mitkVersion.h.in ${MITK_BINARY_DIR}/mitkVersion.h)
configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h)
set(IPFUNC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipFunc)
set(UTILITIES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities)
configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h)
configure_file(MITKConfig.cmake.in ${MITK_BINARY_DIR}/MITKConfig.cmake @ONLY)
write_basic_config_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake
VERSION ${MITK_VERSION_STRING} COMPATIBILITY AnyNewerVersion)
#-----------------------------------------------------------------------------
# MITK Applications
#-----------------------------------------------------------------------------
# This must come after MITKConfig.h was generated, since applications
# might do a find_package(MITK REQUIRED).
add_subdirectory(Applications)
if(MSVC AND TARGET MitkWorkbench)
set_directory_properties(PROPERTIES VS_STARTUP_PROJECT MitkWorkbench)
endif()
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications")
if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/CMakeLists.txt")
add_subdirectory("${MITK_APPLICATIONS_EXTENSION_DIR}" "Applications")
endif()
endforeach()
#-----------------------------------------------------------------------------
# MITK Examples
#-----------------------------------------------------------------------------
if(MITK_BUILD_EXAMPLES)
# This must come after MITKConfig.h was generated, since applications
# might do a find_package(MITK REQUIRED).
add_subdirectory(Examples)
endif()
#-----------------------------------------------------------------------------
# Print configuration summary
#-----------------------------------------------------------------------------
message("\n\n")
feature_summary(
DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------"
WHAT ALL
)
diff --git a/Documentation/CMakeLists.txt b/Documentation/CMakeLists.txt
index 9a25867947..a25b37f09e 100644
--- a/Documentation/CMakeLists.txt
+++ b/Documentation/CMakeLists.txt
@@ -1,166 +1,166 @@
# Different doxygen versions produce significantly different behaviour in the MITK documentation
# especially in regards to the MITK Qt assistant help files and markdown files.
# The HTML documentation is supposed to be build with Doxygen 1.8.7 or newer, the
# Qt assistant QCH files are supposed to be generated with Doxygen 1.8.7 or newer.
# So we check for 1.8.7 here and QCH generation support is checked in
# BlueBerry/CMakeLists.txt
set(supported_doxygen_version "1.8.7")
if(DOXYGEN_VERSION VERSION_LESS ${supported_doxygen_version})
MESSAGE(WARNING "Unsupported doxygen version ${DOXYGEN_VERSION}. The MITK HTML documentation has been tested to work with doxygen ${supported_doxygen_version} or newer.")
endif()
option(USE_DOT "Use dot program for generating graphical class diagrams with doxygen, if available" ON)
option(MITK_DOXYGEN_BUILD_ALWAYS "Always build the MITK documentation when building the default target" OFF)
option(MITK_DOXYGEN_GENERATE_QCH_FILES "Use doxygen to generate Qt compressed help files for MITK docs" OFF)
mark_as_advanced(USE_DOT MITK_DOXYGEN_BUILD_ALWAYS MITK_DOXYGEN_GENERATE_QCH_FILES)
if (MITK_DOXYGEN_GENERATE_QCH_FILES AND DOXYGEN_VERSION VERSION_LESS "1.8.7")
message(WARNING "> Forcing MITK_DOXYGEN_GENERATE_QCH_FILES to OFF because Doxygen version 1.8.7 or newer not found.")
set(MITK_DOXYGEN_GENERATE_QCH_FILES OFF CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE)
endif()
set(HAVE_DOT "NO")
if(DOXYGEN_DOT_EXECUTABLE AND USE_DOT)
set(HAVE_DOT "YES")
endif()
set(MITK_DOXYGEN_TAGFILE_NAME ${MITK_DOXYGEN_OUTPUT_DIR}/MITK.tag CACHE INTERNAL "MITK Doxygen tag file")
# This is relative to the working directory of the doxygen command
set(MITK_DOXYGEN_STYLESHEET mitk_doxygen_extra.css)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/${MITK_DOXYGEN_STYLESHEET}
${CMAKE_CURRENT_BINARY_DIR}/${MITK_DOXYGEN_STYLESHEET} COPYONLY)
# Create QCH files for MITK and external projects
set(MITK_DOXYGEN_GENERATE_QHP "NO")
if(MITK_DOXYGEN_GENERATE_QCH_FILES)
find_program(QT_HELPGENERATOR_EXECUTABLE
NAMES qhelpgenerator qhelpgenerator-qt5 qhelpgenerator5
PATHS ${QT_BINARY_DIR}
DOC "The location of the the Qt help generator executable"
NO_DEFAULT_PATH
)
mark_as_advanced(QT_HELPGENERATOR_EXECUTABLE)
if(NOT QT_HELPGENERATOR_EXECUTABLE)
message(SEND_ERROR "The Qt help generator could not be found. Disabling qch generation")
else()
set(MITK_DOXYGEN_GENERATE_QHP "YES")
endif()
# The name of the generated MITK qch file, relative to the
# Doxygen HTML output folder
set(MITK_DOXYGEN_QCH_FILE "${MITK_BINARY_DIR}/MITK-${MITK_REVISION_ID}.qch")
# Generating ITK and VTK docs it not done yet
#option(MITK_DOXYGEN_GENERATE_VTK_QCH_FILE "Use doxygen to generate a Qt compressed help file for VTK docs" OFF)
#option(MITK_DOXYGEN_GENERATE_ITK_QCH_FILE "Use doxygen to generate a Qt compressed help file for ITK docs" OFF)
#mark_as_advanced(MITK_DOXYGEN_GENERATE_VTK_QCH_FILE MITK_DOXYGEN_GENERATE_ITK_QCH_FILE)
endif()
# Compile a doxygen input filter for processing CMake scripts
include(mitkFunctionCMakeDoxygenFilterCompile)
mitkFunctionCMakeDoxygenFilterCompile(NAMESPACE "CMake")
# Configure some doxygen options
if(NOT MITK_DOXYGEN_INTERNAL_DOCS)
set(MITK_DOXYGEN_INTERNAL_DOCS "NO")
set(MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS "YES")
set(MITK_DOXYGEN_EXCLUDE_PATTERNS "*_p.* *Private.h */internal/*")
else()
set(MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS "NO")
set(MITK_DOXYGEN_EXCLUDE_PATTERNS "")
endif()
if(NOT MITK_DOXYGEN_GENERATE_TODOLIST)
set(MITK_DOXYGEN_GENERATE_TODOLIST "NO")
endif()
if(NOT MITK_DOXYGEN_GENERATE_BUGLIST)
set(MITK_DOXYGEN_GENERATE_BUGLIST "NO")
endif()
if(NOT MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS)
set(MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS "NO")
endif()
if(NOT MITK_DOXYGEN_UML_LOOK)
set(MITK_DOXYGEN_UML_LOOK "NO")
endif()
if(NOT MITK_DOXYGEN_GENERATE_DEPRECATEDLIST)
set(MITK_DOXYGEN_GENERATE_DEPRECATEDLIST "YES")
endif()
if(NOT DEFINED MITK_DOXYGEN_DOT_NUM_THREADS)
set(MITK_DOXYGEN_DOT_NUM_THREADS 0)
endif()
if(NOT DEFINED US_PLATFORM)
if(UNIX)
if(APPLE)
set(US_PLATFORM "US_PLATFORM_APPLE=1")
else()
set(US_PLATFORM "US_PLATFORM_LINUX=1")
endif()
set(US_PLATFORM "${US_PLATFORM} \\\nUS_PLATFORM_POSIX=1")
else()
set(US_PLATFORM "US_PLATFORM_WINDOWS=1")
endif()
endif()
-# parse which plug-in documentation to activate
+#[[ parse which plug-in documentation to activate
set(USERS_GUIDE_INPUT "${MITK_SOURCE_DIR}/Documentation/Doxygen/UserManual/")
if(MITK_USE_BLUEBERRY)
if(MITK_BUILD_ALL_PLUGINS)
set(USERS_GUIDE_INPUT "${USERS_GUIDE_INPUT} \\
${MITK_SOURCE_DIR}/Plugins/")
else()
foreach(mitk_plugin ${${CMAKE_PROJECT_NAME}_PLUGIN_LIBRARIES})
# we want each line to end in " \" and each directory be on a separate line
set(USERS_GUIDE_INPUT "${USERS_GUIDE_INPUT} \\
${${mitk_plugin}_SOURCE_DIR}/")
endforeach()
endif()
if(MITK_BUILD_EXAMPLES)
set(USERS_GUIDE_INPUT "${USERS_GUIDE_INPUT} \\
${MITK_SOURCE_DIR}/Examples/Plugins/")
endif()
-endif()
+endif()]]
-# create output directories for the guides
+#[[ create output directories for the guides
file(MAKE_DIRECTORY ${MITK_DOXYGEN_OUTPUT_DIR}/Guides/Users_Guide/)
-file(MAKE_DIRECTORY ${MITK_DOXYGEN_OUTPUT_DIR}/Guides/Developers_Guide/)
+file(MAKE_DIRECTORY ${MITK_DOXYGEN_OUTPUT_DIR}/Guides/Developers_Guide/)]]
configure_file(doxygen.conf.in
${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf)
-configure_file(doxygen_users_guide.conf.in
+#[[configure_file(doxygen_users_guide.conf.in
${CMAKE_CURRENT_BINARY_DIR}/doxygen_users_guide.conf)
configure_file(doxygen_developers_guide.conf.in
- ${CMAKE_CURRENT_BINARY_DIR}/doxygen_developers_guide.conf)
+ ${CMAKE_CURRENT_BINARY_DIR}/doxygen_developers_guide.conf)]]
if(MITK_DOXYGEN_BUILD_ALWAYS)
set(_doc_in_all "ALL")
else()
set(_doc_in_all "")
endif()
add_custom_target(doc ${_doc_in_all}
${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen.conf
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
)
-add_custom_target(doc_usersguide
+#[[add_custom_target(doc_usersguide
${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen_users_guide.conf
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
)
add_custom_target(doc_developersguide
${DOXYGEN} ${CMAKE_CURRENT_BINARY_DIR}/doxygen_developers_guide.conf
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- )
+ )]]
-set_property(TARGET doc doc_usersguide doc_developersguide PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Documentation")
+set_property(TARGET doc #[[doc_usersguide doc_developersguide]] PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Documentation")
diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
index 28d65a2336..a85370db75 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
@@ -1,73 +1,71 @@
/**
\page PluginListPage MITK Plugin Manuals
The plugins and bundles provide much of the extended functionality of MITK. Each encapsulates a solution to a problem and associated features. This way one can easily assemble the necessary capabilites for a workflow without adding a lot of bloat, by combining plugins as needed.
\subpage PluginListGeneralPage
<ul>
<li> \ref org_mitk_views_basicimageprocessing </li>
<li> \ref org_mitk_views_datamanager </li>
<li> \ref org_mitk_editors_dicombrowser </li>
<li> \ref org_mitk_views_dicominspector </li>
<li> \ref org_mitk_views_imagecropper </li>
<li> \ref org_mitk_views_imagenavigator </li>
<li> \ref org_blueberry_views_logview </li>
<li> \ref org_mitk_views_matchpoint_algorithm_browser </li>
<li> \ref org_mitk_views_matchpoint_algorithm_control </li>
<li> \ref org_mitk_views_matchpoint_evaluator </li>
<li> \ref org_mitk_views_matchpoint_framereg </li>
<li> \ref org_mitk_views_matchpoint_manipulator </li>
<li> \ref org_mitk_views_matchpoint_mapper </li>
<li> \ref org_mitk_views_matchpoint_visualizer </li>
<li> \ref org_mitk_views_measurement </li>
<li> \ref org_mitk_views_imagestatistics </li>
<li> \ref org_mitk_views_moviemaker </li>
<li> \ref org_mitk_views_multilabelsegmentation </li>
<li> \ref org_mitk_views_pointsetinteraction </li>
<li> \ref org_mitk_views_python </li>
<li> \ref org_mitk_views_remeshing </li>
<li> \ref org_mitk_views_screenshotmaker </li>
<li> \ref org_mitk_views_segmentation </li>
<li> \ref org_mitk_views_deformableclippingplane </li>
<li> \ref org_mitk_views_viewnavigatorview </li>
<li> \ref org_mitk_views_volumevisualization </li>
<li> \ref org_mitk_views_properties </li>
</ul>
\subpage PluginListSpecificPage
<ul>
<li> \ref org_mitk_gui_qt_flowapplication </li>
<li> \ref org_mitk_gui_qt_aicpregistration </li>
<li> \ref org_mitk_gui_qt_cest </li>
<li> \ref org_mitk_gui_qt_classificationsegmentation </li>
<li> \ref org_mitk_views_cmdlinemodules </li>
<li> \ref org_mitk_views_pharmacokinetics_concentration_mri </li>
<li> \ref org_mitk_views_pharmacokinetics_mri </li>
<li> \ref org_mitk_views_pharmacokinetics_pet </li>
<li> \ref org_mitk_gui_qt_examples </li>
<li> \ref org_mitk_gui_qt_geometrytools </li>
<li> \ref org_mitk_gui_qt_igtexample </li>
<li> \ref org_mitk_gui_qt_igttracking </li>
<li> \ref org_mitk_views_igttrackingsemiautomaticmeasurement </li>
<li> \ref org_mitk_views_fit_demo </li>
<li> \ref org_mitk_views_fit_genericfitting </li>
<li> \ref org_mitk_views_fit_inspector </li>
<li> \ref org_mitkexamplesopencv </li>
<li> \ref org_mitk_gui_qt_overlaymanager </li>
<li> \ref org_mitk_gui_qt_mitkphenotyping </li>
<li> \ref org_mitk_gui_qt_preprocessing_resampling </li>
<li> \ref org_mitk_views_pharmacokinetics_curvedescriptor </li>
- <li> \ref org_mitk_views_photoacoustics_imageprocessing </li>
<li> \ref org_mitk_gui_qt_pharmacokinetics_simulation </li>
- <li> \ref org_mitk_gui_qt_photoacoustics_spectralunmixing </li>
<li> \ref org_surfacematerialeditor </li>
<li> \ref org_toftutorial </li>
<li> \ref org_blueberry_ui_qt_objectinspector </li>
<li> \ref org_mitk_gui_qt_ultrasound </li>
<li> \ref org_mitk_gui_qt_xnat </li>
</ul>
*/
diff --git a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
index 9f1a98ced2..a6e4f4d28f 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginSpecificManualsList.dox
@@ -1,36 +1,34 @@
/**
\page PluginListSpecificPage List of Application-specific Plugins
\li \subpage org_mitk_gui_qt_aicpregistration
\li \subpage org_mitk_gui_qt_cest
\li \subpage org_mitk_gui_qt_classificationsegmentation
\li \subpage org_mitk_gui_qt_flowapplication
\li \subpage org_mitk_views_cmdlinemodules
\li \subpage org_mitk_views_pharmacokinetics_concentration_mri
\li \subpage org_mitk_views_pharmacokinetics_mri
\li \subpage org_mitk_views_pharmacokinetics_pet
\li \subpage org_mitk_views_pharmacokinetics_simulation
\li \subpage org_mitk_gui_qt_examples
\li \subpage org_mitk_gui_qt_geometrytools
\li \subpage org_mitk_gui_qt_igtexample
\li \subpage org_mitk_gui_qt_igttracking
\li \subpage org_mitk_views_igttrackingsemiautomaticmeasurement
\li \subpage org_mitk_views_imagestatistics
\li \subpage org_mitk_views_fit_demo
\li \subpage org_mitk_views_fit_genericfitting
\li \subpage org_mitk_views_fit_inspector
\li \subpage org_mitkexamplesopencv
\li \subpage org_mitk_gui_qt_overlaymanager
\li \subpage org_mitk_gui_qt_mitkphenotyping
\li \subpage org_mitk_gui_qt_preprocessing_resampling
\li \subpage org_mitk_views_pharmacokinetics_curvedescriptor
- \li \subpage org_mitk_views_photoacoustics_imageprocessing
\li \subpage org_mitk_gui_qt_pharmacokinetics_simulation
- \li \subpage org_mitk_gui_qt_photoacoustics_spectralunmixing
\li \subpage org_surfacematerialeditor
\li \subpage org_blueberry_ui_qt_objectinspector
\li \subpage org_toftutorial
\li \subpage org_mitk_gui_qt_ultrasound
\li \subpage org_mitk_gui_qt_xnat
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox b/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox
index b88bc16275..ca06401761 100644
--- a/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox
@@ -1,18 +1,17 @@
/**
\page MITKModuleManualsList List of Module Manuals
\li \subpage AnnotationModulePage
\li \subpage ChartModule
\li \subpage IGTConcepts
\li \subpage NavigationGeneralModulePage
\li \subpage IGTTutorialOverview
\li \subpage MitkOpenCL_Overview
\li \subpage LegacyGLModule
- \li \subpage PAModulePage
\li \subpage mitkPython_Overview
\li \subpage RESTModule
\li \subpage GeneratingDeviceModulesPage
\li \subpage USModulePage
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox
index 9d0ec93913..26f23d216f 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox
@@ -1,214 +1,214 @@
/**
\page BuildInstructionsPage Build Instructions
\tableofcontents
\section BuildInstructions_Introduction Introduction
The CMake-based build system of MITK supports a "superbuild" process,
meaning that it will download, configure, and build all required third-party
libraries (except Qt) automatically. These instructions will show you how to use
the MITK superbuild.
\note This page explains explicitly how to build MITK itself. If you want to
create your own project based on MITK, the process described below is completely
automated. Please see \ref HowToNewProject.
For more advanced users, the last sections explains how to inject custom build
libraries into the superbuild process.
\section BuildInstructions_Prerequisites Prerequisites
You need:
-# <a href="https://git-scm.com/">Git</a> (there are also numerous third-party graphical
clients available). We recommend using Git, but see below for a way how to
get the current source code without using it.
-# <a href="https://cmake.org/">CMake</a> (version \minimumCMakeVersion or higher)
- -# <a href="https://www.qt.io/">Qt</a> 5.12 if you plan to develop Qt-based
+ -# <a href="https://www.qt.io/">Qt</a> \minimumQt5Version if you plan to develop Qt-based
applications
-# If you are using <b>macOS</b> you need an XCode installation and the
Command Line Tools as it provides the neccessary compilers and SDKs
\section BuildInstructions_Qt A note about Qt
As we do not provide Qt in the MITK superbuild you need to install Qt manually.
The Qt Company provides <a href="https://www.qt.io/download/">online installers
for all supported platforms</a>.
\section BuildInstructions_Get_Source Get a source tree
Since MITK is under active development we recommend to use Git to check out
the latest stable release from the homepage. If you decide to use the most
current nightly release, make sure to get a stable tree: Check the
<a href="https://cdash.mitk.org/index.php?project=MITK">MITK dashboard</a>
before checking out. If the build tree is not clean, you can specify an
older revision for the checkout or get a stable tar ball from
<a href="https://www.mitk.org">www.mitk.org</a>.
To clone MITK's current Git repository do:
\code
git clone https://phabricator.mitk.org/source/mitk.git MITK
\endcode
\section BuildInstructions_Build_With_CMake Build MITK with CMake
Create a new directory for the superbuild binary tree, change to it and call CMake:
In the shell (assuming your current directory is the same as the one where you
issued the git clone command):
\code
mkdir MITK-superbuild
cd MITK-superbuild
ccmake ../MITK
\endcode
If you use <b>Windows</b> or prefer to use the CMake GUI, start the CMake GUI and enter the
location of the source tree and binary tree, choose a suitable generator
and configure the project.
CMake will present you a couple of options, these are the most important ones:
- <tt><b>CMAKE_PREFIX_PATH</b></tt> The path to your Qt installation, e.g., <i>C:/Qt/5.12.9/msvc2017_64</i> or <i>/home/user/Qt/5.12.9/gcc_64</i>
- <tt><b>MITK_USE_BLUEBERRY</b></tt> Build the BlueBerry application framework
- <tt><b>MITK_USE_Boost_LIBRARIES</b></tt> If you need binary Boost libraries,
specify them here.
- <tt><b>MITK_USE_OpenCV</b></tt> Build MITK code which depends on OpenCV (this
will download and build OpenCV 2.4)
- <tt><b>MITK_USE_Python3</b></tt> Enables Python wrapping in MITK. This will also
configure ITK, VTK, and OpenCV (if enabled) to build Python wrappers.
- <tt><b>MITK_USE_Qt5</b></tt> Build MITK code which depends on Qt 5
If you are satisfied with the configuration of your MITK superbuild, generate
the project files with CMake by pressing "Generate".
<b>Linux</b> and <b>macOS</b> users usually just enter "make" (optionally
supplying the number threads to be used for a parallel build):
\code
make -j6
\endcode
<b>Windows</b> users using Visual Studio can open the generated
<tt>MITK-superbuild.sln</tt> solution file in the <tt>MITK-superbuild</tt>
directory and start the build by building the <tt>BUILD_ALL</tt> project.
\section BuildInstructions_Customize Customize your MITK superbuild
The MITK superbuild configures MITK as well as all external libraries. The
build directories of these libraries, and of MITK itself are located inside
the <tt>MITK-superbuild</tt> directory. For example, the directory layout may
look like:
\code
MITK-superbuild
|- ep "external projects"
|-bin
|-lib
|-include
|-src
|- MITK-build
\endcode
To change the configuration of the MITK build itself, choose the MITK-build directory
as the binary directory in the CMake GUI (not the MITK-superbuild directory).
After generating the project files, build the MITK project by either issuing "make"
in the MITK-build directory (Linux, macOS), or by opening MITK-build/MITK.sln (Windows).
You may also change the configuration of any project configured via the
superbuild process. Make sure to also build the changed project and also the
projects which depend on it.
\section BuildInstructions_Running Running Applications
On Linux, just execute the application you want to run. MITK executables are
located in <tt>MITK-superbuild/MITK-build/bin</tt>
On Windows, the <tt>PATH</tt> environment variable must contain the directories
containing the third-party libraries. This is automatically done from Visual Studio.
For running the applications directly use the generated batch files in the
<tt>MITK-superbuild/MITK-build/bin</tt>.
\section BuildInstructions_Documentation Documentation
If you have the <a href="https://www.doxygen.nl/">Doxygen</a> documentation tool
installed, you get a new project (Visual Studio) or "make" target named "doc".
You can build this to generate the HTML documentation of MITK in the
Documentation/Doxygen directory of your MITK-build binary tree or in the
<tt>MITK_DOXYGEN_OUTPUT_DIR</tt> CMake variable (if specified).
\section BuildInstructions_Extending Extend MITK on your own (using the application framework BlueBerry)
Please see \ref NewPluginPage
\section BuildInstructions_As_Toolkit Use MITK in your own project (as a toolkit)
To use MITK in your external project, add the CMake command
<code>find_package(MITK REQUIRED)</code> to your CMakeLists.txt and make use of
the CMake macros <code>mitk_create_module()</code> and
<code>mitk_create_executable()</code> provided by MITK.
Here is a very basic example CMakeLists.txt including MITK as a project:
\code
cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
project(MyProject)
find_package(MITK 2018.04.02 REQUIRED)
add_executable(MyApp main.cpp)
target_link_libraries(MyApp MitkCore)
\endcode
with the main.ccp being
\code
#include <iostream>
#include <mitkLogMacros.h>
int main()
{
MITK_INFO << "Hello world!";
return 0;
}
\endcode
\section BuildInstructions_Advanced_Customization Superbuild customization
You can inject pre-build third-party libraries into the MITK superbuild by
setting certain CMake variables before the first configure step. MITK will
then use these third-party libraries instead of downloading and building them
by itself. Note that you must take care of configuring those libraries with all options
MITK requires.
The variables listed below are provided for injecting third-party libraries.
Their occurrence in the CMake GUI or in ccmake may depend on specific
MITK_USE_* options set to ON. You may also use the variable names below without
the <tt>EXTERNAL_</tt> prefix, for example when providing their values on a
command line call to CMake.
- <tt><b>EXTERNAL_BOOST_ROOT</b></tt> Set this variable to your custom Boost
installation
- <tt><b>EXTERNAL_CTK_DIR</b></tt> Set this variable to your CTK binary tree
(the directory containing the CTKConfig.cmake file)
- <tt><b>EXTERNAL_CableSwig_DIR</b></tt> Set this variable to your CableSwig
binary tree for Python wrapping (the directory containing the
CableSwigConfig.cmake file)
- <tt><b>EXTERNAL_DCMTK_DIR</b></tt> Set this variable to your DCMTK binary
tree (the directory containing the DCMTKConfig.cmake file)
- <tt><b>EXTERNAL_GDCM_DIR</b></tt> Set this variable to your GDCM binary
tree (the directory containing the GDCMConfig.cmake file)
- <tt><b>EXTERNAL_ITK_DIR</b></tt> Set this variable to your ITK binary tree
(the directory containing the ITKConfig.cmake file)
- <tt><b>EXTERNAL_OpenCV_DIR</b></tt> Set this variable to your OpenCV binary
tree (the directory containing the OpenCVConfig.cmake file)
- <tt><b>EXTERNAL_VTK_DIR</b></tt> Set this variable to your VTK binary tree
(the directory containing the VTKConfig.cmake file)
To set CMake options before the first configure step is invoked, supply them
on the command line, i.e.
\code
ccmake -DITK_DIR:PATH=/opt/ITK-release ../MITK
\endcode
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox
index 5babea66ab..2b93804d69 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox
@@ -1,107 +1,107 @@
/**
\page thirdpartylibs Third-party libraries
The following third-party libraries can be used with MITK by default and can, in part, be automatically downloaded during superbuild.
\par ANN
https://www.cs.umd.edu/~mount/ANN/
\par Boost
https://www.boost.org/
\par C++ REST SDK
https://github.com/Microsoft/cpprestsdk/
\par CppUnit
https://sourceforge.net/projects/cppunit/
\par CTK
https://commontk.org/
\par DCMTK
https://dicom.offis.de/dcmtk
\par Eigen
http://eigen.tuxfamily.org/index.php?title=Main_Page
\par GDCM
https://gdcm.sourceforge.net/
\par HDF5
https://support.hdfgroup.org/HDF5/
\par ITK
https://itk.org/
\par MatchPoint
https://www.dkfz.de/en/sidt/projects/MatchPoint/info.html
\par OpenCL
https://www.khronos.org/opencl/
\par OpenCV
https://opencv.org/
\par OpenIGTLink
http://openigtlink.org/
\par OpenMesh
https://www.openmesh.org/
\par PCRE
https://www.pcre.org/
\par POCO
https://pocoproject.org/
\par Python
https://www.python.org/
\par Qt
https://www.qt.io/
\par Qwt
http://qwt.sourceforge.net/
\par SWIG
http://www.swig.org/
-\par tinyxml
+\par TinyXML-2
-http://www.grinninglizard.com/tinyxml/
+http://www.grinninglizard.com/tinyxml2/
\par VIGRA
https://ukoethe.github.io/vigra/
\par VTK
https://vtk.org/
\par zlib
https://zlib.net/
For copyright information on any of the above toolkits see the corresponding home page or the corresponding source folder.
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox
index ee981d8a3a..1891d949b6 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox
@@ -1,36 +1,35 @@
/**
\page MITKModuleManualsListPage MITK Module Manuals
Overview
The modules are shared libraries that provide functionality that can be used by developers.
\subpage MITKModuleManualsList List of Module Manuals
<ul>
<li> \ref AnnotationModulePage
<li> \ref ChartModule
<li> \ref IGTConcepts
<li> \ref NavigationGeneralModulePage
<li> \ref IGTTutorialOverview
<li> \ref MitkOpenCL_Overview
<li> \ref LegacyGLModule
- <li> \ref PAModulePage
<li> \ref mitkPython_Overview
<li> \ref RESTModule
<li> \ref GeneratingDeviceModulesPage
<li> \ref USModulePage
</ul>
\subpage MITKModuleManualsListPageAdditionalInformation Additional Information on Certain Modules
<ul>
<li> \ref PlanarPropertiesPage
</ul>
\subpage MITKMigrationGuides Migration Guides
<ul>
<li> \ref GeometryMigration
<li> \ref InteractionMigration
<li> \ref OverlayMigration
</ul>
*/
diff --git a/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt b/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt
index 24b2612a99..0f1dc85585 100644
--- a/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt
+++ b/Examples/FirstSteps/NewModule/autoload/IO/CMakeLists.txt
@@ -1,8 +1,8 @@
MITK_CREATE_MODULE( NewModuleIO
INCLUDE_DIRS
PRIVATE src/IO
DEPENDS PUBLIC MitkNewModule MitkSceneSerialization
PACKAGE_DEPENDS
- PRIVATE tinyxml
+ PRIVATE tinyxml2
AUTOLOAD_WITH MitkCore
)
diff --git a/Examples/FirstSteps/NewModule/cmdapps/CMakeLists.txt b/Examples/FirstSteps/NewModule/cmdapps/CMakeLists.txt
index 4b257e3d5c..1508687d56 100644
--- a/Examples/FirstSteps/NewModule/cmdapps/CMakeLists.txt
+++ b/Examples/FirstSteps/NewModule/cmdapps/CMakeLists.txt
@@ -1,11 +1,10 @@
option(BUILD_NewModuleMiniApps "Build commandline tools for the example module" OFF)
if(BUILD_NewModuleMiniApps)
mitkFunctionCreateCommandLineApp(
NAME ExampleToUpperCaseMiniApp
DEPENDS MitkNewModule
- PACKAGE_DEPENDS ITK
- )
+ )
endif()
diff --git a/Examples/Plugins/org.mitk.example.gui.regiongrowing/CMakeLists.txt b/Examples/Plugins/org.mitk.example.gui.regiongrowing/CMakeLists.txt
index 5b90620ad8..ee279d1db8 100644
--- a/Examples/Plugins/org.mitk.example.gui.regiongrowing/CMakeLists.txt
+++ b/Examples/Plugins/org.mitk.example.gui.regiongrowing/CMakeLists.txt
@@ -1,9 +1,8 @@
project(org_mitk_example_gui_regiongrowing)
mitk_create_plugin(
EXPORT_DIRECTIVE REGIONGROWING_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgetsExt
- PACKAGE_DEPENDS ITK|ITKRegionGrowing
NO_INSTALL
)
diff --git a/Examples/Tutorial/Step6/CMakeLists.txt b/Examples/Tutorial/Step6/CMakeLists.txt
index 14f5b14c0f..8fb1bbb466 100644
--- a/Examples/Tutorial/Step6/CMakeLists.txt
+++ b/Examples/Tutorial/Step6/CMakeLists.txt
@@ -1,5 +1,3 @@
mitk_create_executable(
DEPENDS MitkQtWidgetsExt
- PACKAGE_DEPENDS ITK|ITKCurvatureFlow+ITKRegionGrowing
)
-
diff --git a/Examples/Tutorial/Step7/CMakeLists.txt b/Examples/Tutorial/Step7/CMakeLists.txt
index 0bb009bb25..13c7b070a6 100644
--- a/Examples/Tutorial/Step7/CMakeLists.txt
+++ b/Examples/Tutorial/Step7/CMakeLists.txt
@@ -1,6 +1,5 @@
include_directories(${CMAKE_CURRENT_SOURCE_DIR}/../Step6)
mitk_create_executable(
DEPENDS MitkQtWidgetsExt
- PACKAGE_DEPENDS ITK|ITKCurvatureFlow+ITKRegionGrowing
- )
+)
diff --git a/Examples/Tutorial/Step8/CMakeLists.txt b/Examples/Tutorial/Step8/CMakeLists.txt
index c52a311f4b..a090d34d9e 100644
--- a/Examples/Tutorial/Step8/CMakeLists.txt
+++ b/Examples/Tutorial/Step8/CMakeLists.txt
@@ -1,9 +1,8 @@
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}/../Step6
${CMAKE_CURRENT_SOURCE_DIR}/../Step7
- )
+)
mitk_create_executable(
DEPENDS MitkQtWidgetsExt
- PACKAGE_DEPENDS ITK|ITKCurvatureFlow+ITKRegionGrowing
- )
+)
diff --git a/MITKConfig.cmake.in b/MITKConfig.cmake.in
index e638db3c1d..bedd4e6385 100644
--- a/MITKConfig.cmake.in
+++ b/MITKConfig.cmake.in
@@ -1,313 +1,313 @@
if(CMAKE_VERSION VERSION_LESS @MITK_CMAKE_MINIMUM_REQUIRED_VERSION@)
message(FATAL_ERROR "MITK requires at least CMake Version @MITK_CMAKE_MINIMUM_REQUIRED_VERSION@")
endif()
# The MITK version number
set(MITK_VERSION_MAJOR "@MITK_VERSION_MAJOR@")
set(MITK_VERSION_MINOR "@MITK_VERSION_MINOR@")
set(MITK_VERSION_PATCH "@MITK_VERSION_PATCH@")
set(MITK_VERSION_STRING "@MITK_VERSION_STRING@")
#-----------------------------------------------------------------------------
# C++ language standard
#-----------------------------------------------------------------------------
set(MITK_CXX_STANDARD @MITK_CXX_STANDARD@)
#-----------------------------------------------------------------------------
# Include required CMake scripts
#-----------------------------------------------------------------------------
# Update the CMake module path
set(MITK_CMAKE_MODULE_PATH "@MITK_SOURCE_DIR@/CMake")
list(APPEND CMAKE_MODULE_PATH ${MITK_CMAKE_MODULE_PATH})
# Standard CMake macros
include(CMakeParseArguments)
include(FeatureSummary)
include(FindPackageHandleStandardArgs)
include(GenerateExportHeader)
# Include MITK macros
include(MacroParseArguments)
include(mitkFunctionAddCustomModuleTest)
include(mitkFunctionCheckMitkCompatibility)
include(mitkFunctionCheckModuleDependencies)
include(mitkFunctionConfigureVisualStudioUserProjectFile)
include(mitkFunctionCreateBlueBerryApplication)
include(mitkFunctionCreateCommandLineApp)
include(mitkFunctionCreateModule)
include(mitkFunctionCreatePlugin)
include(mitkFunctionCreateProvisioningFile)
include(mitkFunctionCreateWindowsBatchScript)
include(mitkFunctionGetLibrarySearchPaths)
include(mitkFunctionInstallAutoLoadModules)
include(mitkFunctionInstallCTKPlugin)
include(mitkFunctionInstallProvisioningFiles)
include(mitkFunctionInstallThirdPartyCTKPlugins)
include(mitkFunctionOrganizeSources)
include(mitkFunctionUseModules)
include(mitkMacroCreateExecutable)
include(mitkMacroCreateModuleTests)
include(mitkMacroFindDependency)
include(mitkMacroGenerateToolsLibrary)
include(mitkMacroGetPMDPlatformString)
include(mitkMacroInstall)
include(mitkMacroInstallHelperApp)
include(mitkMacroInstallTargets)
include(mitkMacroMultiplexPicType)
#-----------------------------------------------------------------------------
# MITK flags and directories
#-----------------------------------------------------------------------------
# MITK compiler flags
set(MITK_C_FLAGS "@MITK_C_FLAGS@")
set(MTTK_C_FLAGS_DEBUG "@MITK_C_FLAGS_DEBUG@")
set(MITK_C_FLAGS_RELEASE "@MITK_C_FLAGS_RELEASE@")
set(MITK_CXX_FLAGS "@MITK_CXX_FLAGS@")
set(MTTK_CXX_FLAGS_DEBUG "@MITK_CXX_FLAGS_DEBUG@")
set(MITK_CXX_FLAGS_RELEASE "@MITK_CXX_FLAGS_RELEASE@")
# MITK linker flags
set(MITK_EXE_LINKER_FLAGS "@MITK_EXE_LINKER_FLAGS@")
set(MITK_SHARED_LINKER_FLAGS "@MITK_SHARED_LINKER_FLAGS@")
set(MITK_MODULE_LINKER_FLAGS "@MITK_MODULE_LINKER_FLAGS@")
# MITK specific directories
set(MITK_SOURCE_DIR "@MITK_SOURCE_DIR@")
set(MITK_BINARY_DIR "@MITK_BINARY_DIR@")
set(MITK_CMAKE_DIR "@MITK_CMAKE_DIR@")
# MITK output directories
set(MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY "@MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY@")
set(MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY "@MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY@")
set(MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY "@MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY@")
#-----------------------------------------------------------------------------
# Miscellaneous variables
#-----------------------------------------------------------------------------
# Internal version numbers, used for approximate compatibility checks
# of a MITK development version (non-release).
set(MITK_VERSION_PLUGIN_SYSTEM 2) # dropped legacy BlueBerry plug-in CMake support
set(MITK_DATA_DIR "@MITK_DATA_DIR@")
set(UTILITIES_DIR "@UTILITIES_DIR@")
set(REGISTER_QFUNCTIONALITY_CPP_IN "@REGISTER_QFUNCTIONALITY_CPP_IN@")
set(MITK_DOXYGEN_TAGFILE_NAME "@MITK_DOXYGEN_TAGFILE_NAME@")
set(MITK_LEGACY_EXPORT_MACRO_NAME 1)
set(DCMTK_CMAKE_DEBUG_POSTFIX @DCMTK_CMAKE_DEBUG_POSTFIX@)
# Get the canonical name of the directory to avoid potential case mismatch,
# e.g. in the drive letter on Windows.
get_filename_component(CMAKE_CURRENT_LIST_DIR_REALPATH ${CMAKE_CURRENT_LIST_DIR} REALPATH)
if(CMAKE_CURRENT_LIST_DIR_REALPATH STREQUAL MITK_BINARY_DIR)
set(MITK_EXTERNAL_PROJECT_PREFIX @MITK_EXTERNAL_PROJECT_PREFIX@)
endif()
set(MITK_MODULES_PACKAGE_DEPENDS_DIR "@MITK_MODULES_PACKAGE_DEPENDS_DIR@")
if(MODULES_PACKAGE_DEPENDS_DIRS)
list(APPEND MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR})
list(REMOVE_DUPLICATES MODULES_PACKAGE_DEPENDS_DIRS)
else()
set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR})
endif()
#-----------------------------------------------------------------------------
# External dependencies
#-----------------------------------------------------------------------------
list(APPEND CMAKE_PREFIX_PATH "@MITK_EXTERNAL_PROJECT_PREFIX@")
# -----------------------------------------
# Qt variables and dependencies
set(MITK_USE_Qt5 @MITK_USE_Qt5@)
if(MITK_USE_Qt5)
set(MITK_QT5_MINIMUM_VERSION @MITK_QT5_MINIMUM_VERSION@)
set(MITK_QT5_COMPONENTS @MITK_QT5_COMPONENTS@)
mitkMacroFindDependency(Qt5 ${MITK_QT5_MINIMUM_VERSION} COMPONENTS ${MITK_QT5_COMPONENTS})
endif()
# -----------------------------------------
# Special Python variables
set(MITK_USE_Python3 @MITK_USE_Python3@)
if(MITK_USE_Python3)
set(PYTHON_EXECUTABLE "@PYTHON_EXECUTABLE@" CACHE FILEPATH "")
set(PYTHON_INCLUDE_DIR "@PYTHON_INCLUDE_DIR@" CACHE PATH "")
set(PYTHON_LIBRARY "@PYTHON_LIBRARY@" CACHE FILEPATH "")
set(PYTHON_INCLUDE_DIR2 "@PYTHON_INCLUDE_DIR2@" CACHE PATH "")
mitkMacroFindDependency(Python3 COMPONENTS Interpreter Development NumPy)
endif()
# -----------------------------------------
# Special Boost variables
set(MITK_USE_Boost_LIBRARIES @MITK_USE_Boost_LIBRARIES@)
set(MITK_USE_SYSTEM_Boost @MITK_USE_SYSTEM_Boost@)
set(BOOST_ROOT "@BOOST_ROOT@" CACHE PATH "")
set(BOOST_LIBRARYDIR "@BOOST_LIBRARYDIR@" CACHE PATH "")
-set(Boost_ADDITIONAL_VERSIONS 1.68 1.68.0)
+set(Boost_ADDITIONAL_VERSIONS 1.74 1.74.0)
# We need this later for a DCMTK workaround
set(_dcmtk_dir_orig "@DCMTK_DIR@")
# -----------------------------------------
# External dependencies from the superbuild
# or injected from somewhere else via
# <project>_DIR variables.
@MITK_CONFIG_EXTERNAL_PROJECTS@
# Ensure the MITK module path comes first
set(CMAKE_MODULE_PATH ${MITK_CMAKE_MODULE_PATH} ${CMAKE_MODULE_PATH})
# -----------------------------------------
# Special handling for DCMTK
if(MITK_USE_DCMTK)
# Due to the preferred CONFIG mode in find_package calls above,
# the DCMTKConfig.cmake file is read, which does not provide useful
# package information. We explictly need MODULE mode to find DCMTK.
if(${_dcmtk_dir_orig} MATCHES "${MITK_EXTERNAL_PROJECT_PREFIX}.*")
# Help our FindDCMTK.cmake script find our super-build DCMTK
set(DCMTK_DIR ${MITK_EXTERNAL_PROJECT_PREFIX})
else()
# Use the original value
set(DCMTK_DIR ${_dcmtk_dir_orig})
endif()
find_package(DCMTK REQUIRED MODULE)
endif()
# -----------------------------------------
# Special handling for DCMQI
if(MITK_USE_DCMQI)
# Due to the preferred CONFIG mode in find_package calls above,
# the DCMQIConfig.cmake file is read, which does not provide useful
# package information. We explictly need MODULE mode to find DCMQI.
# Help our FindDCMQI.cmake script find our super-build DCMQI
set(DCMQI_DIR ${MITK_EXTERNAL_PROJECT_PREFIX})
find_package(DCMQI REQUIRED)
endif()
# -----------------------------------------
# Special handling for Boost
if(MITK_USE_Boost)
link_directories(${Boost_LIBRARY_DIRS})
endif()
# -----------------------------------------
# Special handling for OpenIGTLink
if(MITK_USE_OpenIGTLink)
link_directories(${OpenIGTLink_LIBRARY_DIRS})
endif()
# -----------------------------------------
# Internal project dependencies
set(CppMicroServices_DIR "@CppMicroServices_DIR@")
mitkMacroFindDependency(CppMicroServices)
set(MITK_USE_BLUEBERRY @MITK_USE_BLUEBERRY@)
if(MITK_USE_BLUEBERRY)
set(MITK_PLUGIN_USE_FILE "@MITK_PLUGIN_USE_FILE@")
if(MITK_PLUGIN_USE_FILE)
if(EXISTS "${MITK_PLUGIN_USE_FILE}")
include("${MITK_PLUGIN_USE_FILE}")
endif()
endif()
set(MITK_PLUGIN_PROVISIONING_FILE "@MITK_EXTAPP_PROVISIONING_FILE@")
set(MITK_PROVISIONING_FILES
"${BLUEBERRY_PLUGIN_PROVISIONING_FILE}"
"${MITK_PLUGIN_PROVISIONING_FILE}")
endif()
set(BLUEBERRY_USE_QT_HELP @BLUEBERRY_USE_QT_HELP@)
if(BLUEBERRY_USE_QT_HELP AND DOXYGEN_VERSION VERSION_LESS "1.8.7")
message("Setting BLUEBERRY_USE_QT_HELP to OFF because Doxygen version 1.8.7 or newer not found.")
set(BLUEBERRY_USE_QT_HELP OFF)
endif()
set(BLUEBERRY_QTPLUGIN_PATH "@BLUEBERRY_QTPLUGIN_PATH@")
set(QT_HELPGENERATOR_EXECUTABLE "@QT_HELPGENERATOR_EXECUTABLE@")
set(QT_COLLECTIONGENERATOR_EXECUTABLE "@QT_COLLECTIONGENERATOR_EXECUTABLE@")
set(QT_ASSISTANT_EXECUTABLE "@QT_ASSISTANT_EXECUTABLE@")
set(QT_XMLPATTERNS_EXECUTABLE "@QT_XMLPATTERNS_EXECUTABLE@")
#-----------------------------------------------------------------------------
# MITK sub-project variables
#-----------------------------------------------------------------------------
# External SDK directories
set(MITK_PMD_SDK_DIR @MITK_PMD_SDK_DIR@)
# MITK ToF use variables
set(MITK_TOF_PMDCAMCUBE_AVAILABLE @MITK_USE_TOF_PMDCAMCUBE@)
if(MITK_TOF_PMDCAMCUBE_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK")
option(MITK_USE_TOF_PMDCAMCUBE "Enable support for PMD Cam Cube" @MITK_USE_TOF_PMDCAMCUBE@)
mark_as_advanced(MITK_USE_TOF_PMDCAMCUBE)
endif()
set(MITK_TOF_PMDCAMBOARD_AVAILABLE @MITK_USE_TOF_PMDCAMBOARD@)
if(MITK_TOF_PMDCAMBOARD_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK")
option(MITK_USE_TOF_PMDCAMBOARD "Enable support for PMD Cam Board" @MITK_USE_TOF_PMDCAMBOARD@)
mark_as_advanced(MITK_USE_TOF_PMDCAMBOARD)
endif()
set(MITK_TOF_PMDO3_AVAILABLE @MITK_USE_TOF_PMDO3@)
if(MITK_TOF_PMDO3_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK")
option(MITK_USE_TOF_PMDO3 "Enable support for PMD =3" @MITK_USE_TOF_PMDO3@)
mark_as_advanced(MITK_USE_TOF_PMDO3)
endif()
set(MITK_TOF_KINECT_AVAILABLE @MITK_USE_TOF_KINECT@)
if(MITK_TOF_KINECT_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK")
option(MITK_USE_TOF_KINECT "Enable support for Kinect" @MITK_USE_TOF_KINECT@)
mark_as_advanced(MITK_USE_TOF_KINECT)
endif()
set(MITK_TOF_MESASR4000_AVAILABLE @MITK_USE_TOF_MESASR4000@)
if(MITK_TOF_MESASR4000_AVAILABLE AND NOT ${PROJECT_NAME} STREQUAL "MITK")
option(MITK_USE_TOF_MESASR4000 "Enable support for MESA SR4000" @MITK_USE_TOF_MESASR4000@)
mark_as_advanced(MITK_USE_TOF_MESASR4000)
endif()
if(MITK_USE_IGT)
#include("${MITK_DIR}/mitkIGTConfig.cmake")
endif()
#-----------------------------------------------------------------------------
# Import MITK targets and set custom properties
#-----------------------------------------------------------------------------
if(NOT MITK_EXPORTS_FILE_INCLUDED)
if(EXISTS "@MITK_EXPORTS_FILE@")
set(MITK_EXPORTS_FILE_INCLUDED 1)
include("@MITK_EXPORTS_FILE@")
endif()
endif()
# Set properties on exported targets
@MITK_EXPORTED_TARGET_PROPERTIES@
#-----------------------------------------------------------------------------
# Install rules
#-----------------------------------------------------------------------------
# Install rules for ToF libraries loaded at runtime
if(EXISTS "@MITK_BINARY_DIR@/mitkToFHardwareInstallRules.cmake")
include("@MITK_BINARY_DIR@/mitkToFHardwareInstallRules.cmake")
endif()
diff --git a/Modules/AlgorithmsExt/CMakeLists.txt b/Modules/AlgorithmsExt/CMakeLists.txt
index 4e593dfe19..9afd8aad97 100644
--- a/Modules/AlgorithmsExt/CMakeLists.txt
+++ b/Modules/AlgorithmsExt/CMakeLists.txt
@@ -1,16 +1,12 @@
mitk_create_module(
DEPENDS MitkDataTypesExt MitkLegacyGL
PACKAGE_DEPENDS
- PUBLIC ITK|ITKThresholding
- PRIVATE ANN ITK|ITKIOImageBase VTK|ImagingGeneral
+ PUBLIC OpenMP
+ PRIVATE ANN VTK|ImagingGeneral
)
if(TARGET ${MODULE_TARGET})
- if(MITK_USE_OpenMP)
- target_link_libraries(${MODULE_TARGET} PUBLIC OpenMP::OpenMP_CXX)
- endif()
-
if(BUILD_TESTING)
add_subdirectory(test)
endif()
endif()
diff --git a/Modules/BasicImageProcessing/CMakeLists.txt b/Modules/BasicImageProcessing/CMakeLists.txt
index b4e12f4b38..f529ea8639 100644
--- a/Modules/BasicImageProcessing/CMakeLists.txt
+++ b/Modules/BasicImageProcessing/CMakeLists.txt
@@ -1,8 +1,6 @@
-MITK_CREATE_MODULE(
+mitk_create_module(
DEPENDS MitkCore MitkMatchPointRegistration
- PACKAGE_DEPENDS
- PUBLIC
- PRIVATE ITK|ITKIOImageBase+ITKIOGDCM
+ TARGET_DEPENDS PRIVATE IsotropicWavelets
)
add_subdirectory(MiniApps)
diff --git a/Modules/Biophotonics/CMakeLists.txt b/Modules/Biophotonics/CMakeLists.txt
deleted file mode 100644
index f45b05b564..0000000000
--- a/Modules/Biophotonics/CMakeLists.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-MITK_CREATE_MODULE(mitkBiophotonics
-)
-if( MITK_USE_Python3 )
- ADD_SUBDIRECTORY(python)
-endif()
diff --git a/Modules/Biophotonics/python/iMC/mc/__init__.py b/Modules/Biophotonics/python/iMC/mc/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/mc/batches.py b/Modules/Biophotonics/python/iMC/mc/batches.py
deleted file mode 100644
index 2706262dc6..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/batches.py
+++ /dev/null
@@ -1,375 +0,0 @@
-'''
-Created on Oct 15, 2015
-
-@author: wirkert
-'''
-
-import numpy as np
-from pandas import DataFrame
-import pandas as pd
-
-
-class AbstractBatch(object):
- """summarizes a batch of simulated mc spectra"""
-
- def __init__(self):
- self._nr_layers = 0 # internally keeps track of number of layers
- my_index = pd.MultiIndex(levels=[[], []],
- labels=[[], []])
- self.df = DataFrame(columns=my_index)
-
- def create_parameters(self, nr_samples):
- """create the parameters for the batch, the simulation has
- to create the resulting reflectances"""
- pass
-
- def nr_elements(self):
- return self.df.shape[0]
-
-
-class GenericBatch(AbstractBatch):
- """generic n-layer batch with each layer having the same oxygenation """
-
- def __init__(self):
- super(GenericBatch, self).__init__()
-
- def append_one_layer(self, saO2, nr_samples):
- """helper function to create parameters for one layer"""
-
- # scales data to lie between maxi and mini instead of 0 and 1
- scale = lambda x, mini, maxi: x * (maxi - mini) + mini
- # shortcut to random generator
- gen = np.random.random_sample
- gen_n = np.random.normal
-
- # create layer elements
- self.df["layer" + str(self._nr_layers), "vhb"] = \
- scale(gen(nr_samples), 0, 1.)
- self.df["layer" + str(self._nr_layers), "sao2"] = \
- saO2
- self.df["layer" + str(self._nr_layers), "a_mie"] = \
- np.clip(gen_n(loc=18.9, scale=10.2, size=nr_samples),
- 0.1, np.inf) * 100 # to 1/m
- self.df["layer" + str(self._nr_layers), "b_mie"] = \
- np.clip(gen_n(loc=1.286, scale=0.521, size=nr_samples), 0, np.inf)
- self.df["layer" + str(self._nr_layers), "d"] = \
- scale(gen(nr_samples), 0, 1.)
- self.df["layer" + str(self._nr_layers), "n"] = \
- scale(gen(nr_samples), 1.33, 1.54)
- self.df["layer" + str(self._nr_layers), "g"] = \
- scale(gen(nr_samples), 0.8, 0.95)
- self._nr_layers += 1
-
- def create_parameters(self, nr_samples):
- """Create generic three layer batch with a total diameter of 2mm.
- saO2 is the same in all layers, but all other parameters vary randomly
- within each layer"""
- saO2 = np.random.random_sample(size=nr_samples)
-
- # create three layers with random samples
- self.append_one_layer(saO2, nr_samples)
- self.append_one_layer(saO2, nr_samples)
- self.append_one_layer(saO2, nr_samples)
-
- # "normalize" d to 2mm
- # first extract all layers from df
- self.df
-
- layers = [l for l in self.df.columns.levels[0] if "layer" in l]
- # summarize all ds
- sum_d = 0
- for l in layers:
- sum_d += self.df[l, "d"]
- for l in layers:
- self.df[l, "d"] = self.df[l, "d"] / sum_d * 2000. * 10 ** -6
- self.df[l, "d"] = np.clip(self.df[l, "d"], 25 * 10 ** -6, np.inf)
-
- return self.df
-
-
-class GenericBatch(AbstractBatch):
- """generic n-layer batch with each layer having the same oxygenation """
-
- def __init__(self):
- super(GenericBatch, self).__init__()
-
- def append_one_layer(self, saO2, nr_samples):
- """helper function to create parameters for one layer"""
-
- # scales data to lie between maxi and mini instead of 0 and 1
- scale = lambda x, mini, maxi: x * (maxi - mini) + mini
- # shortcut to random generator
- gen = np.random.random_sample
- gen_n = np.random.normal
-
- # create layer elements
- self.df["layer" + str(self._nr_layers), "vhb"] = \
- scale(gen(nr_samples), 0, 1.)
- self.df["layer" + str(self._nr_layers), "sao2"] = \
- saO2
- self.df["layer" + str(self._nr_layers), "a_mie"] = \
- np.clip(gen_n(loc=18.9, scale=10.2, size=nr_samples),
- 0.1, np.inf) * 100 # to 1/m
- self.df["layer" + str(self._nr_layers), "b_mie"] = \
- np.clip(gen_n(loc=1.286, scale=0.521, size=nr_samples), 0, np.inf)
- self.df["layer" + str(self._nr_layers), "d"] = \
- scale(gen(nr_samples), 0, 1.)
- self.df["layer" + str(self._nr_layers), "n"] = \
- scale(gen(nr_samples), 1.33, 1.54)
- self.df["layer" + str(self._nr_layers), "g"] = \
- scale(gen(nr_samples), 0.8, 0.95)
- self._nr_layers += 1
-
- def create_parameters(self, nr_samples):
- """Create generic three layer batch with a total diameter of 2mm.
- saO2 is the same in all layers, but all other parameters vary randomly
- within each layer"""
- saO2 = np.random.random_sample(size=nr_samples)
-
- # create three layers with random samples
- self.append_one_layer(saO2, nr_samples)
- self.append_one_layer(saO2, nr_samples)
- self.append_one_layer(saO2, nr_samples)
-
- # "normalize" d to 2mm
- # first extract all layers from df
- self.df
-
- layers = [l for l in self.df.columns.levels[0] if "layer" in l]
- # summarize all ds
- sum_d = 0
- for l in layers:
- sum_d += self.df[l, "d"]
- for l in layers:
- self.df[l, "d"] = self.df[l, "d"] / sum_d * 2000. * 10 ** -6
- self.df[l, "d"] = np.clip(self.df[l, "d"], 25 * 10 ** -6, np.inf)
-
- return self.df
-
-
-class LessGenericBatch(AbstractBatch):
- """less generic three layer batch. This only varies blood volume fraction
- w.r.t. the ColonMuscleBatch. Let's see if DA works in this case."""
-
- def __init__(self):
- super(LessGenericBatch, self).__init__()
-
- def append_one_layer(self, saO2, n, d_ranges, nr_samples):
- """helper function to create parameters for one layer"""
-
- # scales data to lie between maxi and mini instead of 0 and 1
- scale = lambda x, mini, maxi: x * (maxi - mini) + mini
- # shortcut to random generator
- gen = np.random.random_sample
-
- # create as generic batch
- super(LessGenericBatch, self).append_one_layer(saO2, nr_samples)
- self._nr_layers -= 1 # we're not finished
-
- # but some changes in specific layer elements
- # more specific layer thicknesses
- self.df["layer" + str(self._nr_layers), "d"] = \
- scale(gen(nr_samples), d_ranges[0], d_ranges[1])
- # more specific n
- self.df["layer" + str(self._nr_layers), "n"] = \
- n
-
- self._nr_layers += 1
-
- def create_parameters(self, nr_samples):
- """Create generic three layer batch with a total diameter of 2mm.
- saO2 is the same in all layers, but all other parameters vary randomly
- within each layer"""
- saO2 = np.random.random_sample(size=nr_samples)
- n = np.ones_like(saO2)
- # create three layers with random samples
- # muscle
- self.append_one_layer(saO2, n * 1.36, (600.*10 ** -6, 1010.*10 ** -6),
- nr_samples)
- # submucosa
- self.append_one_layer(saO2, n * 1.36, (415.*10 ** -6, 847.*10 ** -6),
- nr_samples)
- # mucosa
- self.append_one_layer(saO2, n * 1.38, (395.*10 ** -6, 603.*10 ** -6),
- nr_samples)
-
- return self.df
-
-
-class ColonMuscleBatch(GenericBatch):
- """three layer batch simulating colonic tissue"""
-
- def __init__(self):
- super(ColonMuscleBatch, self).__init__()
-
- def append_one_layer(self, saO2, n, d_ranges, nr_samples):
- """helper function to create parameters for one layer"""
-
- # scales data to lie between maxi and mini instead of 0 and 1
- scale = lambda x, mini, maxi: x * (maxi - mini) + mini
- # shortcut to random generator
- gen = np.random.random_sample
-
- # create as generic batch
- super(ColonMuscleBatch, self).append_one_layer(saO2, nr_samples)
- self._nr_layers -= 1 # we're not finished
-
- # but some changes in specific layer elements
- # less blood
- self.df["layer" + str(self._nr_layers), "vhb"] = \
- scale(gen(nr_samples), 0, 0.1)
- # more specific layer thicknesses
- self.df["layer" + str(self._nr_layers), "d"] = \
- scale(gen(nr_samples), d_ranges[0], d_ranges[1])
- # more specific n
- self.df["layer" + str(self._nr_layers), "n"] = \
- n
-
- self._nr_layers += 1
-
- def create_parameters(self, nr_samples):
- """Create generic three layer batch with a total diameter of 2mm.
- saO2 is the same in all layers, but all other parameters vary randomly
- within each layer"""
- saO2 = np.random.random_sample(size=nr_samples)
- n = np.ones_like(saO2)
- # create three layers with random samples
- # muscle
- self.append_one_layer(saO2, n * 1.36, (600.*10 ** -6, 1010.*10 ** -6),
- nr_samples)
- # submucosa
- self.append_one_layer(saO2, n * 1.36, (415.*10 ** -6, 847.*10 ** -6),
- nr_samples)
- # mucosa
- self.append_one_layer(saO2, n * 1.38, (395.*10 ** -6, 603.*10 ** -6),
- nr_samples)
-
- return self.df
-
-
-class GenericMeanScatteringBatch(GenericBatch):
- """three layer batch simulating colonic tissue"""
-
- def __init__(self):
- super(GenericMeanScatteringBatch, self).__init__()
-
- def append_one_layer(self, saO2, nr_samples):
- """helper function to create parameters for one layer"""
-
- # create as generic batch
- super(GenericMeanScatteringBatch, self).append_one_layer(saO2,
- nr_samples)
- self._nr_layers -= 1 # we're not finished
-
- # restrict exponential scattering to mean value for soft tissue.
- self.df["layer" + str(self._nr_layers), "b_mie"] = 1.286
-
- self._nr_layers += 1
-
-
-class ColonMuscleMeanScatteringBatch(ColonMuscleBatch):
- """three layer batch simulating colonic tissue"""
-
- def __init__(self):
- super(ColonMuscleMeanScatteringBatch, self).__init__()
-
- def append_one_layer(self, saO2, n, d_ranges, nr_samples):
- """helper function to create parameters for one layer"""
-
- # create as generic batch
- super(ColonMuscleMeanScatteringBatch, self).append_one_layer(saO2,
- n,
- d_ranges,
- nr_samples)
- self._nr_layers -= 1 # we're not finished
-
- # restrict exponential scattering to mean value for soft tissue.
- self.df["layer" + str(self._nr_layers), "b_mie"] = 1.286
-
- self._nr_layers += 1
-
-
-class VisualizationBatch(AbstractBatch):
- """batch used for visualization of different spectra. Feel free to adapt
- for your visualization purposes."""
-
- def __init__(self):
- super(VisualizationBatch, self).__init__()
-
- def append_one_layer(self, vhb, sao2, a_mie, b_mie, d, n, g, nr_samples):
- """helper function to create parameters for one layer"""
-
- # create layer elements
- self.df["layer" + str(self._nr_layers), "vhb"] = vhb
- self.df["layer" + str(self._nr_layers), "sao2"] = sao2
- self.df["layer" + str(self._nr_layers), "a_mie"] = a_mie
- self.df["layer" + str(self._nr_layers), "b_mie"] = b_mie
- self.df["layer" + str(self._nr_layers), "d"] = d
- self.df["layer" + str(self._nr_layers), "n"] = n
- self.df["layer" + str(self._nr_layers), "g"] = g
- self._nr_layers += 1
-
- def create_parameters(self, nr_samples):
- # bvf = np.linspace(0.0, .1, nr_samples)
- # saO2 = np.linspace(0., 1., nr_samples)
- # d = np.linspace(175, 735, nr_samples) * 10 ** -6
- # a_mie = np.linspace(5., 30., nr_samples) * 100
- # a_ray = np.linspace(0., 60., nr_samples) * 100
- # n = np.linspace(1.33, 1.54, nr_samples)
- # g = np.linspace(0, 0.95, nr_samples)
- # create three layers with random samples
- self.append_one_layer([0.1, 0.02], [0.7, 0.1], 18.9*100., 1.286,
- 500 * 10 ** -6, 1.38, 0.9,
- nr_samples)
- self.append_one_layer(0.04, 0.7, 18.9*100., 1.286, 500 * 10 ** -6,
- 1.36, 0.9,
- nr_samples)
- self.append_one_layer(0.04, 0.7, 18.9*100., 1.286, 500 * 10 ** -6,
- 1.36, 0.9,
- nr_samples)
-
- return self.df
-
-
-class IntralipidPhantomBatch(AbstractBatch):
- """batch used for visualization of different spectra. Feel free to adapt
- for your visualization purposes."""
-
- def __init__(self):
- super(IntralipidPhantomBatch, self).__init__()
-
- def append_one_layer(self, nr_samples):
- """helper function to create parameters for one layer"""
-
- # scales data to lie between maxi and mini instead of 0 and 1
- scale = lambda x, mini, maxi: x * (maxi - mini) + mini
- # shortcut to random generator
- gen = np.random.random_sample
-
- # create layer elements
- self.df["layer" + str(self._nr_layers), "vhb"] = \
- scale(gen(nr_samples), 0.001, 0.1)
- self.df["layer" + str(self._nr_layers), "sao2"] = \
- scale(gen(nr_samples), 0., 1.)
- self.df["layer" + str(self._nr_layers), "a_mie"] = \
- scale(gen(nr_samples), 5., 40.) * 100 # to 1/m
- self.df["layer" + str(self._nr_layers), "b_mie"] = \
- scale(gen(nr_samples), 2.3, 2.4)
- self.df["layer" + str(self._nr_layers), "d"] = \
- 2000.*10**-6
- self.df["layer" + str(self._nr_layers), "n"] = \
- scale(gen(nr_samples), 1.33, 1.54)
- self.df["layer" + str(self._nr_layers), "g"] = \
- scale(gen(nr_samples), 0.8, 0.95)
- self._nr_layers += 1
-
- def create_parameters(self, nr_samples):
- """Create intralipid batch with a total diameter of 2mm.
- all other parameters vary randomly
- within each layer to simulate the interlipid scattering/absorption
- properties."""
-
- # create three layers with random samples
- self.append_one_layer(nr_samples)
-
- return self.df
diff --git a/Modules/Biophotonics/python/iMC/mc/create_spectrum.py b/Modules/Biophotonics/python/iMC/mc/create_spectrum.py
deleted file mode 100644
index 8d42ea197c..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/create_spectrum.py
+++ /dev/null
@@ -1,41 +0,0 @@
-
-import logging
-import time
-import os
-
-from mc.sim import get_diffuse_reflectance
-
-
-def create_spectrum(tissue_model, sim_wrapper, wavelengths):
- """
- Create a whole spectrum from one instance (dataframe_row) using our
- tissue model at wavelength wavelength.
-
- Args:
- tissue_model: the model which should be used to generate the
- spectrum
- sim_wrapper: the simulation which should be used to generate the
- reflectances
- wavelengths: the wavelengths which shall be simulated
-
- Returns: the simulated reflectances
- """
- start = time.time()
- # map the _wavelengths array to reflectance list
-
- def wavelength_to_reflectance(wavelength):
- # helper function to determine the reflectance for a given
- # wavelength using the current model and simulation
- tissue_model.set_wavelength(wavelength)
- tissue_model.create_mci_file()
- sim_wrapper.run_simulation()
- simulation_path = os.path.split(sim_wrapper.mcml_executable)[0]
- return get_diffuse_reflectance(os.path.join(simulation_path,
- tissue_model.
- get_mco_filename()))
- reflectances = map(wavelength_to_reflectance, wavelengths)
- end = time.time()
- # success!
- logging.info("successfully ran simulation in " +
- "{:.2f}".format(end - start) + " seconds")
- return reflectances
diff --git a/Modules/Biophotonics/python/iMC/mc/data/beta_carotin.txt b/Modules/Biophotonics/python/iMC/mc/data/beta_carotin.txt
deleted file mode 100644
index 902019d56c..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/data/beta_carotin.txt
+++ /dev/null
@@ -1,1924 +0,0 @@
-lambda beta carotin
-##Wavelength (nm) Molar Extinction (cm-1/M)
-219.74 860669
-219.99 866939
-220.24 873996
-220.49 887103
-220.74 901200
-220.99 914068
-221.24 931102
-221.49 952261
-221.74 984397
-221.99 1006831
-222.24 1032652
-222.49 1061135
-222.74 1081015
-222.99 1093144
-223.24 1101278
-223.49 1095590
-223.74 1087870
-223.99 1078610
-224.24 1055667
-224.49 1019649
-224.74 984279
-224.99 942523
-225.24 897948
-225.49 847468
-225.74 802920
-225.99 750521
-226.24 704257
-226.49 657528
-226.74 612102
-226.99 568332
-227.24 522203
-227.49 483550
-227.74 445839
-227.99 410272
-228.24 376479
-228.49 346892
-228.74 317864
-228.99 291931
-229.24 267330
-229.49 244432
-229.74 224462
-229.99 206460
-230.24 189372
-230.49 174797
-230.74 162312
-230.99 149431
-231.24 139576
-231.49 129411
-231.74 119268
-231.99 111778
-232.24 104297
-232.49 97028
-232.74 91749
-232.99 85840
-233.24 82466
-233.49 78359
-233.74 74179
-233.99 71819
-234.24 68531
-234.49 65721
-234.74 62361
-234.99 60073
-235.24 57992
-235.49 56889
-235.74 54353
-235.99 52961
-236.24 51795
-236.49 51443
-236.74 49052
-236.99 49363
-237.24 49200
-237.49 48552
-237.74 47755
-237.99 47755
-238.24 47872
-238.49 46494
-238.74 45877
-238.99 45503
-239.24 46845
-239.49 45570
-239.74 46489
-239.99 45822
-240.24 45151
-240.49 45629
-240.74 45232
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-241.49 45723
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-242.74 44710
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-243.24 44814
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-245.24 44796
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-276.99 97663
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-277.74 98523
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-278.24 100099
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-279.74 102865
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-281.49 105247
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-281.99 105954
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-282.49 108333
-282.74 109679
-282.99 110400
-283.24 111179
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-283.99 110323
-284.24 108968
-284.49 108432
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-284.99 104653
-285.24 102905
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-286.24 92771
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-286.74 88344
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-287.24 83975
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-287.74 80728
-287.99 79206
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-289.24 77125
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-291.24 76454
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-291.74 74440
-291.99 75175
-292.24 73260
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-292.99 71576
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-293.49 71535
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-293.99 70319
-294.24 70306
-294.49 71035
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-294.99 70896
-295.24 70797
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-295.74 69067
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-296.49 64874
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-297.24 59316
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-298.24 48412
-298.49 44381
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-298.99 39296
-299.24 36734
-299.49 34342
-299.74 32923
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-300.24 30667
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-300.99 28383
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-302.24 23591
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-303.24 21889
-303.49 22100
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-304.24 20664
-304.49 20551
-304.74 20934
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-305.24 20736
-305.49 19983
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-305.99 20245
-306.24 18448
-306.49 18254
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-307.24 16777
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diff --git a/Modules/Biophotonics/python/iMC/mc/data/bilirubin.txt b/Modules/Biophotonics/python/iMC/mc/data/bilirubin.txt
deleted file mode 100644
index 3ca6e8e1c0..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/data/bilirubin.txt
+++ /dev/null
@@ -1,1844 +0,0 @@
-# taken from http://omlc.org/spectra/PhotochemCAD/data/119-abs.txt
-##Wavelength (nm) Molar Extinction (cm-1/M)
-239.75 17208
-240 16074
-240.25 18576
-240.5 16910
-240.75 17810
-241 17784
-241.25 17734
-241.5 18617
-241.75 17737
-242 17532
-242.25 17582
-242.5 17609
-242.75 17141
-243 17102
-243.25 16666
-243.5 16594
-243.75 16111
-244 16576
-244.25 15964
-244.5 15470
-244.75 15805
-245 15304
-245.25 15243
-245.5 15230
-245.75 14725
-246 14481
-246.25 14588
-246.5 14454
-246.75 14002
-247 14152
-247.25 13951
-247.5 13735
-247.75 13755
-248 13531
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diff --git a/Modules/Biophotonics/python/iMC/mc/data/colon_default.mci b/Modules/Biophotonics/python/iMC/mc/data/colon_default.mci
deleted file mode 100644
index 9017b775cb..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/data/colon_default.mci
+++ /dev/null
@@ -1,14 +0,0 @@
-1.0 # file version
-1 # number of runs
-
-temp.mco A # output filename, ASCII/Binary
-1000000 # No. of photons
-0.002 2 # dz, dr
-500 1 1 # No. of dz, dr & da.
-
-2 # No. of layers
-# n mua mus g d # One line for each layer
-1.0 # n for medium above.
-1.380 1.78741 20.00000 0.000 0.050
-1.380 1.78741 20.00000 0.000 0.050
-1.0 # n for medium below.
diff --git a/Modules/Biophotonics/python/iMC/mc/data/correct.mci b/Modules/Biophotonics/python/iMC/mc/data/correct.mci
deleted file mode 100644
index 3548fe2f84..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/data/correct.mci
+++ /dev/null
@@ -1,15 +0,0 @@
-1.0 # file version
-1 # number of runs
-
-temp.mco A # output filename, ASCII/Binary
-1000000 # No. of photons
-0.002 2 # dz, dr
-500 1 1 # No. of dz, dr & da.
-
-3 # No. of layers
-# n mua mus g d # One line for each layer
-1.0 # n for medium above.
-1.000 0.02100 0.03200 4.300 540.000
-1.000 0.01000 0.01000 1.000 100.000
-100.100 1.01100 1.02100 103.100 10410.000
-1.0 # n for medium below.
diff --git a/Modules/Biophotonics/python/iMC/mc/data/haemoglobin.txt b/Modules/Biophotonics/python/iMC/mc/data/haemoglobin.txt
deleted file mode 100644
index b5e87f7035..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/data/haemoglobin.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-lambda Hb02 Hb
-nm cm-1/M cm-1/M
-250 106112 112736
-252 105552 112736
-254 107660 112736
-256 109788 113824
-258 112944 115040
-260 116376 116296
-262 120188 117564
-264 124412 118876
-266 128696 120208
-268 133064 121544
-270 136068 122880
-272 137232 123096
-274 138408 121952
-276 137424 120808
-278 135820 119840
-280 131936 118872
-282 127720 117628
-284 122280 114820
-286 116508 112008
-288 108484 107140
-290 104752 98364
-292 98936 91636
-294 88136 85820
-296 79316 77100
-298 70884 69444
-300 65972 64440
-302 63208 61300
-304 61952 58828
-306 62352 56908
-308 62856 57620
-310 63352 59156
-312 65972 62248
-314 69016 65344
-316 72404 68312
-318 75536 71208
-320 78752 74508
-322 82256 78284
-324 85972 82060
-326 89796 85592
-328 93768 88516
-330 97512 90856
-332 100964 93192
-334 103504 95532
-336 104968 99792
-338 106452 104476
-340 107884 108472
-342 109060 110996
-344 110092 113524
-346 109032 116052
-348 107984 118752
-350 106576 122092
-352 105040 125436
-354 103696 128776
-356 101568 132120
-358 97828 133632
-360 94744 134940
-362 92248 136044
-364 89836 136972
-366 88484 137900
-368 87512 138856
-370 88176 139968
-372 91592 141084
-374 95140 142196
-376 98936 143312
-378 103432 144424
-380 109564 145232
-382 116968 145232
-384 125420 148668
-386 135132 153908
-388 148100 159544
-390 167748 167780
-392 189740 180004
-394 212060 191540
-396 231612 202124
-398 248404 212712
-400 266232 223296
-402 284224 236188
-404 308716 253368
-406 354208 270548
-408 422320 287356
-410 466840 303956
-412 500200 321344
-414 524280 342596
-416 521880 363848
-418 515520 385680
-420 480360 407560
-422 431880 429880
-424 376236 461200
-426 326032 481840
-428 283112 500840
-430 246072 528600
-432 214120 552160
-434 165332 552160
-436 132820 547040
-438 119140 501560
-440 102580 413280
-442 92780 363240
-444 81444 282724
-446 76324 237224
-448 67044 173320
-450 62816 103292
-452 58864 62640
-454 53552 36170
-456 49496 30698.8
-458 47496 25886.4
-460 44480 23388.8
-462 41320 20891.2
-464 39807.2 19260.8
-466 37073.2 18142.4
-468 34870.8 17025.6
-470 33209.2 16156.4
-472 31620 15310
-474 30113.6 15048.4
-476 28850.8 14792.8
-478 27718 14657.2
-480 26629.2 14550
-482 25701.6 14881.2
-484 25180.4 15212.4
-486 24669.6 15543.6
-488 24174.8 15898
-490 23684.4 16684
-492 23086.8 17469.6
-494 22457.6 18255.6
-496 21850.4 19041.2
-498 21260 19891.2
-500 20932.8 20862
-502 20596.4 21832.8
-504 20418 22803.6
-506 19946 23774.4
-508 19996 24745.2
-510 20035.2 25773.6
-512 20150.4 26936.8
-514 20429.2 28100
-516 21001.6 29263.2
-518 22509.6 30426.4
-520 24202.4 31589.6
-522 26450.4 32851.2
-524 29269.2 34397.6
-526 32496.4 35944
-528 35990 37490
-530 39956.8 39036.4
-532 43876 40584
-534 46924 42088
-536 49752 43592
-538 51712 45092
-540 53236 46592
-542 53292 48148
-544 52096 49708
-546 49868 51268
-548 46660 52496
-550 43016 53412
-552 39675.2 54080
-554 36815.2 54520
-556 34476.8 54540
-558 33456 54164
-560 32613.2 53788
-562 32620 52276
-564 33915.6 50572
-566 36495.2 48828
-568 40172 46948
-570 44496 45072
-572 49172 43340
-574 53308 41716
-576 55540 40092
-578 54728 38467.6
-580 50104 37020
-582 43304 35676.4
-584 34639.6 34332.8
-586 26600.4 32851.6
-588 19763.2 31075.2
-590 14400.8 28324.4
-592 10468.4 25470
-594 7678.8 22574.8
-596 5683.6 19800
-598 4504.4 17058.4
-600 3200 14677.2
-602 2664 13622.4
-604 2128 12567.6
-606 1789.2 11513.2
-608 1647.6 10477.6
-610 1506 9443.6
-612 1364.4 8591.2
-614 1222.8 7762
-616 1110 7344.8
-618 1026 6927.2
-620 942 6509.6
-622 858 6193.2
-624 774 5906.8
-626 707.6 5620
-628 658.8 5366.8
-630 610 5148.8
-632 561.2 4930.8
-634 512.4 4730.8
-636 478.8 4602.4
-638 460.4 4473.6
-640 442 4345.2
-642 423.6 4216.8
-644 405.2 4088.4
-646 390.4 3965.08
-648 379.2 3857.6
-650 368 3750.12
-652 356.8 3642.64
-654 345.6 3535.16
-656 335.2 3427.68
-658 325.6 3320.2
-660 319.6 3226.56
-662 314 3140.28
-664 308.4 3053.96
-666 302.8 2967.68
-668 298 2881.4
-670 294 2795.12
-672 290 2708.84
-674 285.6 2627.64
-676 282 2554.4
-678 279.2 2481.16
-680 277.6 2407.92
-682 276 2334.68
-684 274.4 2261.48
-686 272.8 2188.24
-688 274.4 2115
-690 276 2051.96
-692 277.6 2000.48
-694 279.2 1949.04
-696 282 1897.56
-698 286 1846.08
-700 290 1794.28
-702 294 1741
-704 298 1687.76
-706 302.8 1634.48
-708 308.4 1583.52
-710 314 1540.48
-712 319.6 1497.4
-714 325.2 1454.36
-716 332 1411.32
-718 340 1368.28
-720 348 1325.88
-722 356 1285.16
-724 364 1244.44
-726 372.4 1203.68
-728 381.2 1152.8
-730 390 1102.2
-732 398.8 1102.2
-734 407.6 1102.2
-736 418.8 1101.76
-738 432.4 1100.48
-740 446 1115.88
-742 459.6 1161.64
-744 473.2 1207.4
-746 487.6 1266.04
-748 502.8 1333.24
-750 518 1405.24
-752 533.2 1515.32
-754 548.4 1541.76
-756 562 1560.48
-758 574 1560.48
-760 586 1548.52
-762 598 1508.44
-764 610 1459.56
-766 622.8 1410.52
-768 636.4 1361.32
-770 650 1311.88
-772 663.6 1262.44
-774 677.2 1213
-776 689.2 1163.56
-778 699.6 1114.8
-780 710 1075.44
-782 720.4 1036.08
-784 730.8 996.72
-786 740 957.36
-788 748 921.8
-790 756 890.8
-792 764 859.8
-794 772 828.8
-796 786.4 802.96
-798 807.2 782.36
-800 816 761.72
-802 828 743.84
-804 836 737.08
-806 844 730.28
-808 856 723.52
-810 864 717.08
-812 872 711.84
-814 880 706.6
-816 887.2 701.32
-818 901.6 696.08
-820 916 693.76
-822 930.4 693.6
-824 944.8 693.48
-826 956.4 693.32
-828 965.2 693.2
-830 974 693.04
-832 982.8 692.92
-834 991.6 692.76
-836 1001.2 692.64
-838 1011.6 692.48
-840 1022 692.36
-842 1032.4 692.2
-844 1042.8 691.96
-846 1050 691.76
-848 1054 691.52
-850 1058 691.32
-852 1062 691.08
-854 1066 690.88
-856 1072.8 690.64
-858 1082.4 692.44
-860 1092 694.32
-862 1101.6 696.2
-864 1111.2 698.04
-866 1118.4 699.92
-868 1123.2 701.8
-870 1128 705.84
-872 1132.8 709.96
-874 1137.6 714.08
-876 1142.8 718.2
-878 1148.4 722.32
-880 1154 726.44
-882 1159.6 729.84
-884 1165.2 733.2
-886 1170 736.6
-888 1174 739.96
-890 1178 743.6
-892 1182 747.24
-894 1186 750.88
-896 1190 754.52
-898 1194 758.16
-900 1198 761.84
-902 1202 765.04
-904 1206 767.44
-906 1209.2 769.8
-908 1211.6 772.16
-910 1214 774.56
-912 1216.4 776.92
-914 1218.8 778.4
-916 1220.8 778.04
-918 1222.4 777.72
-920 1224 777.36
-922 1225.6 777.04
-924 1227.2 776.64
-926 1226.8 772.36
-928 1224.4 768.08
-930 1222 763.84
-932 1219.6 752.28
-934 1217.2 737.56
-936 1215.6 722.88
-938 1214.8 708.16
-940 1214 693.44
-942 1213.2 678.72
-944 1212.4 660.52
-946 1210.4 641.08
-948 1207.2 621.64
-950 1204 602.24
-952 1200.8 583.4
-954 1197.6 568.92
-956 1194 554.48
-958 1190 540.04
-960 1186 525.56
-962 1182 511.12
-964 1178 495.36
-966 1173.2 473.32
-968 1167.6 451.32
-970 1162 429.32
-972 1156.4 415.28
-974 1150.8 402.28
-976 1144 389.288
-978 1136 374.944
-980 1128 359.656
-982 1120 344.372
-984 1112 329.084
-986 1102.4 313.796
-988 1091.2 298.508
-990 1080 283.22
-992 1068.8 267.932
-994 1057.6 252.648
-996 1046.4 237.36
-998 1035.2 222.072
-1000 1024 206.784
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/mc/dfmanipulations.py b/Modules/Biophotonics/python/iMC/mc/dfmanipulations.py
deleted file mode 100644
index 6bb2c76258..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/dfmanipulations.py
+++ /dev/null
@@ -1,45 +0,0 @@
-'''
-Created on Oct 19, 2015
-
-@author: wirkert
-'''
-
-from scipy.interpolate import interp1d
-import pandas as pd
-
-
-def fold_by_sliding_average(df, window_size):
- """take a batch and apply a sliding average with given window size to
- the reflectances.
- window_size is elements to the left and to the right.
- There will be some boundary effect on the edges."""
- # next line does the folding.
- df.reflectances = pd.rolling_mean(df.reflectances.T, window_size,
- center=True).T
- # let's get rid of NaN columns which are created at the boundaries
- df.dropna(axis="columns", inplace=True)
- return df
-
-
-def switch_reflectances(df, new_wavelengths, new_reflectances):
- df.drop(df["reflectances"].columns, axis=1, level=1, inplace=True)
- for i, nw in enumerate(new_wavelengths):
- df["reflectances", nw] = new_reflectances[:, i]
- return df
-
-
-def interpolate_wavelengths(df, new_wavelengths):
- """ interpolate image data to fit new_wavelengths. Current implementation
- performs simple linear interpolation. Neither existing nor new _wavelengths
- need to be sorted. """
- # build an interpolator using the inormation provided by the dataframes
- # reflectance column
- interpolator = interp1d(df.reflectances.columns.astype(float),
- df.reflectances.as_matrix(), assume_sorted=False,
- bounds_error=False)
- # use this to create new reflectances
- new_reflectances = interpolator(new_wavelengths)
- # build a new dataframe out of this information and set the original df
- # to the new information. This seems hacky, can't it be done easier?
- switch_reflectances(df, new_wavelengths, new_reflectances)
- return df
diff --git a/Modules/Biophotonics/python/iMC/mc/factories.py b/Modules/Biophotonics/python/iMC/mc/factories.py
deleted file mode 100644
index dd6c317f9c..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/factories.py
+++ /dev/null
@@ -1,115 +0,0 @@
-'''
-Created on Oct 15, 2015
-
-@author: wirkert
-'''
-
-from mc.tissuemodels import AbstractTissue, GenericTissue, PhantomTissue
-from mc.batches import AbstractBatch
-from mc.batches import GenericBatch, LessGenericBatch, GenericMeanScatteringBatch
-from mc.batches import ColonMuscleBatch, ColonMuscleMeanScatteringBatch
-from mc.batches import VisualizationBatch, IntralipidPhantomBatch
-
-
-class AbstractMcFactory(object):
- '''
- Monte Carlo Factory.
- Will create fitting models and batches, dependent on your task
- '''
-
- def create_tissue_model(self):
- return AbstractTissue()
-
- def create_batch_to_simulate(self):
- return AbstractBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
-
-
-class GenericMcFactory(AbstractMcFactory):
-
- def create_tissue_model(self):
- return GenericTissue()
-
- def create_batch_to_simulate(self):
- return GenericBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
-
-
-class LessGenericMcFactory(GenericMcFactory):
-
- def create_batch_to_simulate(self):
- return LessGenericBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
-
-
-class ColonMuscleMcFactory(GenericMcFactory):
-
- def create_batch_to_simulate(self):
- return ColonMuscleBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
-
-
-class GenericMeanScatteringFactory(GenericMcFactory):
-
- def create_batch_to_simulate(self):
- return GenericMeanScatteringBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
-
-
-class ColonMuscleMeanScatteringFactory(GenericMcFactory):
-
- def create_batch_to_simulate(self):
- return ColonMuscleMeanScatteringBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
-
-
-class VisualizationMcFactory(AbstractMcFactory):
-
- def create_tissue_model(self):
- return GenericTissue()
-
- def create_batch_to_simulate(self):
- return VisualizationBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
-
-
-class PhantomFactory(AbstractMcFactory):
-
- def create_tissue_model(self):
- return PhantomTissue()
-
- def create_batch_to_simulate(self):
- return IntralipidPhantomBatch()
-
- def __init__(self):
- '''
- Constructor
- '''
diff --git a/Modules/Biophotonics/python/iMC/mc/plot.py b/Modules/Biophotonics/python/iMC/mc/plot.py
deleted file mode 100644
index 2706a15c2b..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/plot.py
+++ /dev/null
@@ -1,43 +0,0 @@
-'''
-Created on Oct 16, 2015
-
-@author: wirkert
-'''
-
-
-import numpy as np
-import matplotlib.pyplot as plt
-
-
-class PlotFunctor(object):
- """helping functor necessary because we need to save color for plotting"""
-
- def __init__(self, axes, wavelengths, nr_plot_elements):
- self.axes = axes
- self.sortedIndices = sorted(range(len(wavelengths)),
- key=lambda k: wavelengths[k])
- self.sortedWavelenghts = wavelengths[self.sortedIndices]
- self.nr_plot_elements = nr_plot_elements
- self.i = 0
-
-
- def __call__(self, r):
- pass
- # set color so it slowly moves from blue to red
- plt_color = (1. / float(self.nr_plot_elements) * self.i,
- 0.,
- 1. - (1. / float(self.nr_plot_elements) * self.i))
- self.axes.plot(self.sortedWavelenghts, r[self.sortedIndices], "-o",
- color=plt_color)
- self.i += 1
- return self.i
-
-def plot(batch, axes=None):
- if axes is None:
- axes = plt.gca()
-
- f = PlotFunctor(axes, batch._wavelengths, batch.reflectances.shape[0])
-
- np.apply_along_axis(f,
- axis=1,
- arr=batch.reflectances)
diff --git a/Modules/Biophotonics/python/iMC/mc/sim.py b/Modules/Biophotonics/python/iMC/mc/sim.py
deleted file mode 100644
index f629a25d99..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/sim.py
+++ /dev/null
@@ -1,211 +0,0 @@
-'''
-Created on Sep 8, 2015
-
-This file contains methods which wrap the mcml simulation so it can be
-conveniently called from python. One example for a mcml simulation would be
-gpumcml:
-https://code.google.com/p/gpumcml/
-
-@author: wirkert
-'''
-
-import os
-import contextlib
-import logging
-
-import subprocess32
-
-""" helper method to change to the correct path and back again """
-@contextlib.contextmanager
-def cd(newPath):
- savedPath = os.getcwd()
- os.chdir(newPath)
- yield
- os.chdir(savedPath)
-
-
-class MciWrapper(object):
- '''
- this class provides a wrapper to the mcml monte carlo file.
- Its purpose is to create a .mci file which the mcml simulation can use to
- create the simulation
- '''
-
- def set_mci_filename(self, mci_filename):
- self.mci_filename = mci_filename
-
- def set_mco_filename(self, mco_filename):
- """path of the mco file.
- This can be either a path relative to the mcml executable
- or an absolute path.
- BUG: it seems that it can only be relative file name
- """
- self.mco_filename = mco_filename
-
- def set_nr_photons(self, nr_photons):
- self.nr_photons = nr_photons
-
- def add_layer(self, n=None, ua=None, us=None, g=None, d=None):
- """adds a layer below the currently existing ones.
-
- Arguments:
- n: Refraction index of medium
- ua: absorption coefficient [1/m]
- us: scattering coefficient [1/m]
- g: anisotropy factor
- d: thickness of layer [m]
- """
- if n is None:
- n = 1.
- if ua is None:
- ua = 0.
- if us is None:
- us = 0.
- if g is None:
- g = 1.
- if d is None:
- d = 500.*10 ** -6
- self.layers.append([n, ua, us, g, d])
-
- def set_layer(self, layer_nr, n, ua, us, g, d):
- """set a layer with a specific layer_nr (stariting with layer_nr 0).
- Note that the layer must already exist, otherwise an error will occure
- """
- self.layers[layer_nr] = [n, ua, us, g, d]
-
- def set_file_version(self, file_version):
- self.file_version = file_version
-
- def set_nr_runs(self, nr_runs):
- self.nr_runs = nr_runs
-
- def set_dz_dr(self, dz, dr):
- self.dz = dz
- self.dr = dr
-
- def set_nr_dz_dr_da(self, nr_dz, nr_dr, nr_da):
- self.nr_dz = nr_dz
- self.nr_dr = nr_dr
- self.nr_da = nr_da
-
- def set_n_medium_above(self, n_above):
- self.n_above = n_above
-
- def set_n_medium_below(self, n_below):
- self.n_below = n_below
-
- def create_mci_file(self):
- """this method creates the mci file at the location self.mci_filename"""
- open(self.mci_filename, 'a').close()
- f = open(self.mci_filename, 'w')
- # write general information
- f.write(str(self.file_version) + " # file version\n")
- f.write(str(self.nr_runs) + " # number of runs\n\n")
- # write the data for run
- f.write(self.mco_filename + " A # output filename, ASCII/Binary\n")
- f.write(str(self.nr_photons) + " # No. of photons\n")
- f.write(repr(self.dz) + " " + repr(self.dr) + " # dz, dr\n")
- f.write(repr(self.nr_dz) + " " +
- repr(self.nr_dr) + " " +
- repr(self.nr_da) + " # No. of dz, dr & da.\n\n")
- # write layer information
- f.write(str(len(self.layers)) + " # No. of layers\n")
- f.write("# n mua mus g d # One line for each layer\n")
- f.write(repr(self.n_above) + " # n for medium above.\n")
- for layer in self.layers:
-
- # factors (/100.; *100.) to convert to mcml expected units:
- f.write("%.3f" % layer[0] + " " + # n
- "%.5f" % (layer[1] / 100.) + " " + # ua
- "%.5f" % (layer[2] / 100.) + " " + # us
- "%.3f" % layer[3] + " " + # g
- "%.3f" % (layer[4] * 100.) + "\n") # d
- f.write(repr(self.n_below) + " # n for medium below.\n")
- f.close()
- if not os.path.isfile(self.mci_filename):
- raise IOError("input file for monte carlo simulation not " +
- "succesfully created")
-
- def __init__(self):
- # set standard parameters
- self.file_version = 1.0
- self.nr_photons = 10**6
- self.nr_runs = 1
- self.dz = 0.002
- self.dr = 2
- self.nr_dz = 500
- self.nr_dr = 1
- self.nr_da = 1
- self.n_above = 1.0
- self.n_below = 1.0
- # initialize to 0 layers
- self.layers = []
-
-
-class SimWrapper(object):
-
- def set_mci_filename(self, mci_filename):
- """the full path to the input file. E.g. ./data/my.mci
- """
- self.mci_filename = mci_filename
-
- def set_mcml_executable(self, mcml_executable):
- """ the full path of the excutable. E.g. ./mcml/mcml.exe"""
- self.mcml_executable = mcml_executable
-
- def run_simulation(self):
- """this method runs a monte carlo simulation"""
- mcml_path, mcml_file = os.path.split(self.mcml_executable)
- abs_mci_filename = os.path.abspath(self.mci_filename)
- # note: the -A option makes gpumcml much faster, but is not available
- # in original mcml. Maybe a switch should be introduced here
- args = ("./" + mcml_file, "-A", abs_mci_filename)
- # switch to folder where mcml resides in and execute it.
- with cd(mcml_path):
- try:
- popen = subprocess32.Popen(args, stdout=subprocess32.PIPE)
- popen.wait(timeout=100)
- except:
- logging.error("couldn't run simulation")
- # popen.kill()
-
- def __init__(self):
- pass
-
-
-def get_diffuse_reflectance(mco_filename):
- """
- extract reflectance from mco file.
- Attention: mco_filename specifies full path.
-
- Returns: the reflectance
- """
- with open(mco_filename) as myFile:
- for line in myFile:
- if "Diffuse reflectance" in line:
- return float(line.split(' ', 1)[0])
-
-
-def get_specular_reflectance(mco_filename):
- """
- extract reflectance from mco file.
- Attention: mco_filename specifies full path.
-
- Returns: the reflectance
- """
- with open(mco_filename) as myFile:
- for line in myFile:
- if "Specular reflectance" in line:
- return float(line.split(' ', 1)[0])
-
-
-def get_total_reflectance(mco_filename):
- """
- extract reflectance from mco file.
- Attention: mco_filename specifies full path.
-
- Returns: the reflectance
- """
- return get_diffuse_reflectance(mco_filename) + \
- get_specular_reflectance(mco_filename)
-
diff --git a/Modules/Biophotonics/python/iMC/mc/test/__init__.py b/Modules/Biophotonics/python/iMC/mc/test/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/mc/test/test_dfmanipulations.py b/Modules/Biophotonics/python/iMC/mc/test/test_dfmanipulations.py
deleted file mode 100644
index 7e62886813..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/test/test_dfmanipulations.py
+++ /dev/null
@@ -1,78 +0,0 @@
-'''
-Created on Oct 19, 2015
-
-@author: wirkert
-'''
-import unittest
-
-import numpy as np
-from pandas.util.testing import assert_frame_equal
-
-from mc.batches import ColonMuscleBatch
-import mc.dfmanipulations as dfmani
-
-class Test(unittest.TestCase):
-
- def setUp(self):
- # create a colon batch with 2 samples
- self.test_batch = ColonMuscleBatch()
- self.test_batch.create_parameters(2)
-
- # artificially add 10 fake "reflectances" to this batch
- # at 10 fake "wavelengths"
- WAVELENGHTS = np.linspace(450, 720, 10)
- reflectance1 = np.arange(0, 30, 3)
- reflectance2 = np.arange(30, 60, 3)
- for w in WAVELENGHTS:
- self.test_batch.df["reflectances", w] = np.NAN
- for r1, r2, w in zip(reflectance1, reflectance2, WAVELENGHTS):
- self.test_batch.df["reflectances", w][0] = r1
- self.test_batch.df["reflectances", w][1] = r2
-
- # shortcut to dataframe that we are interested in:
- self.df = self.test_batch.df
-
- def test_sliding_average(self):
- # by test design folding should not alter elements (only at boundaries,
- # which are excluded by array slicing:
- expected_elements = self.df.reflectances.iloc[:, 1:-1].copy()
- dfmani.fold_by_sliding_average(self.df, 3)
-
- assert_frame_equal(self.df.reflectances, expected_elements)
-
- def test_interpolation(self):
- new_wavelengths = [465, 615, 555]
-
- dfmani.interpolate_wavelengths(self.df, new_wavelengths)
-
- expected = np.array([[1.5, 16.5, 10.5], [31.5, 46.5, 40.5]])
- np.testing.assert_almost_equal(self.df.reflectances.as_matrix(),
- expected,
- err_msg="test if interpolation " +
- "works fine on batches")
-
- def test_select_n(self):
- """ this is less a test and more a showing of how to select n elements
- from a dataframe."""
- # draw one sample. Look into documentation for sample to see all the
- # options. Sample is quite powerfull.
- self.df = self.df.sample(1)
- self.assertEqual(self.df.shape[0], 1,
- "one sample selected")
-
- def test_sortout_bands(self):
- """ this is less a test and more a showing of how to sortout specific
- bands from a dataframe """
- # drop the 510 and 720 nm band
- band_names_to_sortout = [510, 720]
- self.df.drop(band_names_to_sortout, axis=1, level=1, inplace=True)
-
- df_r = self.df["reflectances"]
- self.assertTrue(not (510 in df_r.columns))
- self.assertTrue(not 720 in df_r.columns)
- self.assertTrue(690 in df_r.columns)
-
-
-if __name__ == "__main__":
- # import sys;sys.argv = ['', 'Test.testName']
- unittest.main()
diff --git a/Modules/Biophotonics/python/iMC/mc/test/test_sim.py b/Modules/Biophotonics/python/iMC/mc/test/test_sim.py
deleted file mode 100644
index 313341c081..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/test/test_sim.py
+++ /dev/null
@@ -1,125 +0,0 @@
-'''
-Created on Sep 8, 2015
-
-@author: wirkert
-'''
-import unittest
-import filecmp
-import os
-
-from mc.sim import MciWrapper, SimWrapper, \
- get_total_reflectance, get_diffuse_reflectance
-
-
-path_to_gpumcml = "/home/wirkert/workspace/monteCarlo/gpumcml/" + \
- "fast-gpumcml/gpumcml.sm_20"
-skip_gpu_tests = not os.path.exists(path_to_gpumcml)
-
-
-class Test(unittest.TestCase):
-
- def setUp(self):
- self.mci_filename = "temp.mci"
- self.mco_filename = "temp.mco"
- # create a mci_wrapper which shall create a mci file
- self.mci_wrapper = MciWrapper()
- self.mci_wrapper.set_mci_filename(self.mci_filename)
- self.mci_wrapper.set_mco_filename(self.mco_filename)
- self.mci_wrapper.set_nr_photons(10 ** 6)
- self.mci_wrapper.add_layer(1.0, 2.1, 3.2, 4.3, 5.4)
- self.mci_wrapper.add_layer(6.5, 7.8, 8.9, 9.10, 10.11)
- self.mci_wrapper.add_layer(100.1001, 101.10001, 102.100001,
- 103.1000001, 104.10000001)
- self.mci_wrapper.set_layer(1, 1, 1, 1, 1, 1)
- # expected mci file
- self.correct_mci_filename = "./mc/data/correct.mci"
- # path to the externaly installed mcml simulation. This is machine
- # dependent. Thus tests depending on the execution of mcml will only
- # be performed if this file exists.
- # Should the file be located somewhere else on your computer,
- # change this path to your actual location.
-
- def tearDown(self):
- os.remove(self.mci_filename)
- mcml_path, mcml_file = os.path.split(path_to_gpumcml)
- created_mco_file = mcml_path + "/" + self.mco_filename
- if os.path.isfile(created_mco_file):
- os.remove(created_mco_file)
-
- def test_mci_wrapper(self):
- self.mci_wrapper.create_mci_file()
- self.assertTrue(os.path.isfile(self.mci_filename),
- "mci file was created")
- self.assertTrue(filecmp.cmp(self.mci_filename,
- self.correct_mci_filename, shallow=False),
- "the written mci file is the same as the stored " +
- "reference file")
-
- @unittest.skipIf(skip_gpu_tests, "skip if gpumcml not installed")
- def test_sim_wrapper(self):
- mcml_path, mcml_file = os.path.split(path_to_gpumcml)
- if os.path.isfile(path_to_gpumcml):
- self.mci_wrapper.create_mci_file()
- sim_wrapper = SimWrapper()
- sim_wrapper.set_mci_filename(self.mci_filename)
- sim_wrapper.set_mcml_executable(path_to_gpumcml)
- sim_wrapper.run_simulation()
- self.assertTrue(os.path.isfile(os.path.join(mcml_path,
- self.mco_filename)),
- "mco file was created")
-
- @unittest.skipIf(skip_gpu_tests, "skip if gpumcml not installed")
- def test_mci_wrapper_book_example(self):
- """see if our result matches the one from
- Biomedical Optics
- Principles and Imaging
- page 55 (Table 3.1)"""
- # create a book_p55_mci which shall create a mci file
- book_p55_mci = MciWrapper()
- book_p55_mci.set_mci_filename(self.mci_filename)
- book_p55_mci.set_mco_filename(self.mco_filename)
- book_p55_mci.set_nr_photons(10**6)
- book_p55_mci.add_layer(1, 1000, 9000, 0.75, 0.0002)
-
- mcml_path, mcml_file = os.path.split(path_to_gpumcml)
- if os.path.isfile(path_to_gpumcml):
- book_p55_mci.create_mci_file()
- sim_wrapper = SimWrapper()
- sim_wrapper.set_mci_filename(self.mci_filename)
- sim_wrapper.set_mcml_executable(path_to_gpumcml)
- sim_wrapper.run_simulation()
- self.assertTrue(os.path.isfile(mcml_path + "/" + self.mco_filename),
- "mco file was created")
- refl = get_diffuse_reflectance(os.path.join(mcml_path,
- self.mco_filename))
- self.assertAlmostEqual(refl, 0.09734, 3,
- "correct reflectance determined " +
- "according to book table 3.1")
-
- @unittest.skipIf(skip_gpu_tests, "skip if gpumcml not installed")
- def test_mci_wrapper_book_example_2(self):
- """see if our result matches the one from
- Biomedical Optics
- Principles and Imaging
- page 56 (Table 3.2)"""
- # create a book_p56_mci which shall create a mci file
- book_p56_mci = MciWrapper()
- book_p56_mci.set_mci_filename(self.mci_filename)
- book_p56_mci.set_mco_filename(self.mco_filename)
- book_p56_mci.set_nr_photons(10**6)
- book_p56_mci.add_layer(1.5, 1000, 9000, 0., 1)
-
- mcml_path, mcml_file = os.path.split(path_to_gpumcml)
- if os.path.isfile(path_to_gpumcml):
- book_p56_mci.create_mci_file()
- sim_wrapper = SimWrapper()
- sim_wrapper.set_mci_filename(self.mci_filename)
- sim_wrapper.set_mcml_executable(path_to_gpumcml)
- sim_wrapper.run_simulation()
- self.assertTrue(os.path.isfile(mcml_path + "/" + self.mco_filename),
- "mco file was created")
- refl = get_total_reflectance(os.path.join(mcml_path,
- self.mco_filename))
- self.assertAlmostEqual(refl, 0.26, delta=0.01,
- msg="correct reflectance determined " +
- "according to book table 3.2")
diff --git a/Modules/Biophotonics/python/iMC/mc/test/test_tissuemodels.py b/Modules/Biophotonics/python/iMC/mc/test/test_tissuemodels.py
deleted file mode 100644
index bd708c2fe7..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/test/test_tissuemodels.py
+++ /dev/null
@@ -1,50 +0,0 @@
-'''
-Created on Sep 9, 2015
-
-@author: wirkert
-'''
-
-import unittest
-import filecmp
-import os
-
-from mc.tissuemodels import GenericTissue
-
-this_dir, this_filename = os.path.split(__file__)
-DATA_PATH = os.path.join(this_dir, "..", "data")
-
-
-class TestTissueModels(unittest.TestCase):
-
- def setUp(self):
- self.mci_filename = "temp.mci"
- self.mco_filename = "temp.mco"
- # in this file we stored the expected result created from the
- # "old" implementation of our algorithm:
- self.correct_mci_filename = os.path.join(DATA_PATH, "colon_default.mci")
-
- def tearDown(self):
- os.remove(self.mci_filename)
-
- def test_tissue_model(self):
- # create nice colon model
- tissue = GenericTissue(nr_layers=2)
- tissue.set_mci_filename(self.mci_filename)
- tissue.set_mco_filename(self.mco_filename)
- tissue.wavelength = 500. * 10 ** -9
- # just use the default parameters for this test
- # now create the simulation file
- tissue.create_mci_file()
- # and assert its correct
- self.assertTrue(os.path.isfile(self.mci_filename),
- "mci file was created")
- self.assertTrue(filecmp.cmp(self.mci_filename,
- self.correct_mci_filename,
- shallow=False),
- "the written mci file is the same as the stored " +
- "reference file")
-
-
-if __name__ == "__main__":
- # import sys;sys.argv = ['', 'Test.testName']
- unittest.main()
diff --git a/Modules/Biophotonics/python/iMC/mc/test/test_ua.py b/Modules/Biophotonics/python/iMC/mc/test/test_ua.py
deleted file mode 100644
index d29f2f5f4c..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/test/test_ua.py
+++ /dev/null
@@ -1,40 +0,0 @@
-'''
-Created on Sep 8, 2015
-
-@author: wirkert
-'''
-
-import unittest
-
-from mc.usuag import Ua
-
-class test_ua(unittest.TestCase):
-
- def setUp(self):
- self.ua_l2 = Ua()
- self.ua532 = self.ua_l2(532.*10 ** -9) / 100.
- self.ua800 = self.ua_l2(800.*10 ** -9) / 100.
-
- def test_uA532(self):
- self.assertTrue(3. < self.ua532 < 4., "test if calculated ua_l2 takes " +
- "reasonable values " +
- "(according to \"Determination of optical" +
- " properties of normal and adenomatous human colon " +
- "tissues in vitro using integrating sphere " +
- "techniques\")")
-
- def test_uA800(self):
- self.assertTrue(0.05 < self.ua800 < 0.15, "test if calculated ua_l2 " +
- "takes reasonable values " +
- "(according to \"Differences in" +
- " optical properties between healthy and " +
- "pathological human colon tissues using a Ti:sapphire" +
- " laser: an in vitro study using the Monte Carlo " +
- "inversion technique\")")
-
- def test_saO2_makes_difference(self):
- self.ua_l2.saO2 = 1.0
- self.assertNotAlmostEqual(self.ua532,
- self.ua_l2(532.*10 ** -9) / 100.,
- msg="changing oxygenation changes result")
-
diff --git a/Modules/Biophotonics/python/iMC/mc/test/test_usg.py b/Modules/Biophotonics/python/iMC/mc/test/test_usg.py
deleted file mode 100644
index 2af36b493c..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/test/test_usg.py
+++ /dev/null
@@ -1,26 +0,0 @@
-'''
-Created on Oct 23, 2015
-
-@author: wirkert
-'''
-import unittest
-
-from mc.usuag import UsgJacques
-
-
-class TestUs(unittest.TestCase):
-
- def setUp(self):
- self.usg = UsgJacques()
-
- def test_no_rayleigh_high_wavelengths(self):
- self.usg.a_ray = 2.*100
- self.usg.a_mie = 20.*100
- w = 500. * 10 ** -9
- print self.usg(w)[0] / 100.
- # todo write test
-
-
-if __name__ == "__main__":
- # import sys;sys.argv = ['', 'Test.testName']
- unittest.main()
diff --git a/Modules/Biophotonics/python/iMC/mc/tissuemodels.py b/Modules/Biophotonics/python/iMC/mc/tissuemodels.py
deleted file mode 100644
index f6a31821c1..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/tissuemodels.py
+++ /dev/null
@@ -1,149 +0,0 @@
-'''
-Created on Sep 9, 2015
-
-@author: wirkert
-'''
-
-import numpy as np
-
-from mc.sim import MciWrapper
-from mc.usuag import Ua, UsgJacques, UsgIntralipid
-
-
-class AbstractTissue(object):
- '''
- Initializes a abstract tissue model"
- '''
-
- def set_nr_photons(self, nr_photons):
- self._mci_wrapper.set_nr_photons(nr_photons)
-
- def set_mci_filename(self, mci_filename):
- self._mci_wrapper.set_mci_filename(mci_filename)
-
- def set_mco_filename(self, mco_filename):
- self._mci_wrapper.set_mco_filename(mco_filename)
-
- def get_mco_filename(self):
- return self._mci_wrapper.mco_filename
-
- def set_wavelength(self, wavelength):
- self.wavelength = wavelength
-
- def create_mci_file(self):
- # set layers
- for i, ua in enumerate(self.uas):
- self._mci_wrapper.set_layer(i, # layer nr
- self.ns[i], # refraction index
- self.uas[i](self.wavelength), # ua
- self.usgs[i](self.wavelength)[0], # us
- self.usgs[i](self.wavelength)[1], # g
- self.ds[i]) # d
- # now that the layers have been updated: create file
- self._mci_wrapper.create_mci_file()
-
- def __str__(self):
- """ Overwrite this method!
- print the current model"""
- model_string = ""
- return model_string
-
- def __init__(self, ns, uas, usgs, ds):
- self._mci_wrapper = MciWrapper()
-
- self.wavelength = 500.*10**9 # standard wavelength, should be set.
- self.uas = uas
- self.usgs = usgs
- self.ds = ds
- self.ns = ns
- # initially create layers. these will be overwritten as soon
- # as create_mci_file is called.
- for i in enumerate(uas):
- self._mci_wrapper.add_layer()
-
-
-class GenericTissue(AbstractTissue):
- '''
- Initializes a 3-layer generic tissue model
- '''
-
- def set_dataframe_row(self, df_row):
- """take one example (one row) of a created batch and set the tissue to
- resemble the structure specified by this row
-
- Args:
- df_row: one row of a dataframe created by a batch."""
- layers = [l for l in df_row.index.levels[0] if "layer" in l]
- for i, l in enumerate(layers):
- self.set_layer(i,
- df_row[l, "vhb"],
- df_row[l, "sao2"],
- df_row[l, "a_mie"],
- df_row[l, "b_mie"],
- df_row[l, "d"],
- df_row[l, "n"],
- df_row[l, "g"])
-
- def set_layer(self, layer_nr=0,
- bvf=None, saO2=None, a_mie=None, b_mie=None, d=None,
- n=None, g=None):
- """Helper function to set one layer."""
- if bvf is None:
- bvf = 0.02
- if saO2 is None:
- saO2 = 0.7
- if a_mie is None:
- a_mie = 10. * 100
- if d is None:
- d = 500. * 10 ** -6
- if b_mie is None:
- b_mie = 1.286
- if n is None:
- n = 1.38
- if g is None:
- g = 0.
- # build obejct for absorption coefficient determination
- self.uas[layer_nr].bvf = bvf
- self.uas[layer_nr].saO2 = saO2
- # and one for scattering coefficient
- self.usgs[layer_nr].a_mie = a_mie
- self.usgs[layer_nr].a_ray = 0.
- self.usgs[layer_nr].b_mie = b_mie
- self.usgs[layer_nr].g = g
- self.ds[layer_nr] = d
- self.ns[layer_nr] = n
-
- def __str__(self):
- """print the current model"""
- model_string = ""
- for i, ua in enumerate(self.uas):
- layer_string = "layer " + str(i) + \
- " - vhb: " + "%.1f" % (self.uas[i].bvf * 100.) + \
- "%; sao2: " + "%.1f" % (self.uas[i].saO2 * 100.) + \
- "%; a_mie: " + "%.2f" % (self.usgs[i].a_mie / 100.) + \
- "cm^-1; a_ray: " + "%.2f" % (self.usgs[i].a_ray / 100.) + \
- "cm^-1; b_mie: " + "%.3f" % self.usgs[i].b_mie + \
- "; d: " + "%.0f" % (self.ds[i] * 10 ** 6) + "um" + \
- "; n: " + "%.2f" % (self.ns[i]) + \
- "; g: " + "%.2f" % self.usgs[i].g + "\n"
- model_string += layer_string
- return model_string
-
- def __init__(self, nr_layers=3):
- uas = []
- usgs = []
- for i in range(nr_layers):
- uas.append(Ua())
- usgs.append(UsgJacques())
- ds = np.ones(nr_layers, dtype=float) * 500.*10 ** -6
- ns = np.ones(nr_layers, dtype=float) * 1.38
- super(GenericTissue, self).__init__(ns, uas, usgs, ds)
-
-
-class PhantomTissue(GenericTissue):
-
- def __init__(self, nr_layers=1):
- super(PhantomTissue, self).__init__(nr_layers=1)
- self.usgs = [UsgIntralipid()]
-
-
diff --git a/Modules/Biophotonics/python/iMC/mc/usuag.py b/Modules/Biophotonics/python/iMC/mc/usuag.py
deleted file mode 100644
index d60d8173f6..0000000000
--- a/Modules/Biophotonics/python/iMC/mc/usuag.py
+++ /dev/null
@@ -1,217 +0,0 @@
-'''
-Created on Sep 8, 2015
-
-@author: wirkert
-'''
-
-import math
-import os
-
-import numpy as np
-from scipy.interpolate import interp1d
-
-
-this_dir, this_filename = os.path.split(__file__)
-DATA_PATH = os.path.join(this_dir, "data")
-
-def get_haemoglobin_extinction_coefficients(reference_filename=None):
- """
- helper method to get reference data for eHbO2 and eHb from Scott Prahls
- reference file:
- http://omlc.org/spectra/hemoglobin/summary.html
- """
- if reference_filename is None:
- reference_filename = os.path.join(DATA_PATH, "haemoglobin.txt")
- # table with wavelength at 1st row,
- # HbO2 molar extinction coefficient [cm**-1/(moles/l)] at 2nd row,
- # Hb molar extinction coefficient [cm**-1/(moles/l)] at 3rd row
- haemoLUT = np.loadtxt(reference_filename, skiprows=2)
- # we calculate everything in [m] instead of [nm] and [1/cm]
- haemoLUT[:, 0] = haemoLUT[:, 0] * 10 ** -9
- haemoLUT[:, 1:] = haemoLUT[:, 1:] * 10 ** 2
- # get the data into an interpolation map for oxy and deoxy haemoglobin
- eHbO2 = interp1d(haemoLUT[:, 0], haemoLUT[:, 1])
- eHb = interp1d(haemoLUT[:, 0], haemoLUT[:, 2])
- return eHbO2, eHb
-
-
-def get_beta_carotin_extinction_coefficients(reference_filename=None):
- """
- Reference data taken from
- http://omlc.org/spectra/PhotochemCAD/data/041-abs.txt
- """
- if reference_filename is None:
- reference_filename = os.path.join(DATA_PATH, "beta_carotin.txt")
- # table with wavelength at 1st row,
- # beta carotin molar extinction coefficient [cm**-1/(M)]
- betaLUT = np.loadtxt(reference_filename, skiprows=2)
- # we calculate everything in [m] instead of [nm] and [1/cm]
- betaLUT[:, 0] = betaLUT[:, 0] * 10 ** -9
- betaLUT[:, 1:] = betaLUT[:, 1:] * 10 ** 2
- # get the data into an interpolation map
- eBc = interp1d(betaLUT[:, 0], betaLUT[:, 1], bounds_error=False,
- fill_value=0.)
- return eBc
-
-
-def get_bilirubin_extinction_coefficients(reference_filename=None):
- """
- Reference data taken from
- http://omlc.org/spectra/PhotochemCAD/data/041-abs.txt
- """
- if reference_filename is None:
- reference_filename = os.path.join(DATA_PATH, "bilirubin.txt")
- # table with wavelength at 1st row,
- # beta carotin molar extinction coefficient [cm**-1/(M)]
- biliLUT = np.loadtxt(reference_filename, skiprows=2)
- # we calculate everything in [m] instead of [nm] and [1/cm]
- biliLUT[:, 0] = biliLUT[:, 0] * 10 ** -9
- biliLUT[:, 1:] = biliLUT[:, 1:] * 10 ** 2
- # get the data into an interpolation map
- eBili = interp1d(biliLUT[:, 0], biliLUT[:, 1], bounds_error=False,
- fill_value=0.)
- return eBili
-
-
-class Ua(object):
-
- def __init__(self):
- self.bvf = 0.02 # %
- self.cHb = 120. # g*Hb/l
- self.saO2 = 0. # %
- self.eHbO2, self.eHb = \
- get_haemoglobin_extinction_coefficients()
-
- self.cBetaCarotinUgProDl = 0. # 2000.
- # g / l
- self.cBili = 0. # 1.23 * 10 ** -2
- self.eBc = get_beta_carotin_extinction_coefficients()
- self.eBili = get_bilirubin_extinction_coefficients()
-
-
- def __call__(self, wavelength):
- """ determine ua [1/m] as combination of
- Haemoglobin extinction coefficients.
- For more on this equation, please refer to
- http://omlc.org/spectra/hemoglobin/
- """
- ua_haemoglobin = math.log(10) * self.cHb * \
- (self.saO2 * self.eHbO2(wavelength) +
- (1 - self.saO2) * self.eHb(wavelength)) \
- / 64500. * self.bvf
- ua_bilirubin = math.log(10) * self.cBili / 574.65 * \
- self.eBili(wavelength)
- # second line is to convert from ug/dl to g/ mole
- ua_beta_carotin = math.log(10) * self.cBetaCarotinUgProDl / \
- 536.8726 * 10 ** -5 * \
- self.eBc(wavelength)
-
- return ua_haemoglobin + ua_bilirubin + ua_beta_carotin
-
-
-class UaMuscle():
- """helper class for setting ua in muscle layer.
- for ua_sm in the muscle layer we don't use mie theory but the
- approximation presented in
- Rowe et al.
- "Modelling and validation of spectral reflectance for the colon"
- calculated to retrieve an absorption of 11.2 cm-1 at 515nm
- """
- def __init__(self):
- self.ua = Ua()
-
- def __call__(self, wavelength):
- A = 1.7923385088285804
- self.ua.bvf = 0.1 * A
- self.ua.saO2 = 0.7
- self.ua.cHb = 120.
- return self.ua(wavelength)
-
-
-class UsgJacques(object):
-
- def __init__(self):
- """
- To be set externally:
-
- a':
- """
- self.a_ray = 0. * 100.
- self.a_mie = 20. * 100.
- self.b_mie = 1.286
- self.g = 0.
-
- def __call__(self, wavelength):
- """
- Calculate the scattering parameters relevant for monte carlo simulation.
-
- Uses equation (2) from: Optical properties of biological tissues:
- a Review
-
- Args
- ____
- wavelength:
- wavelength of the incident light [m]
-
- Returns:
- ____
- (us, g)
- scattering coefficient us [1/m] and anisotropy factor g
- """
- norm_wavelength = (wavelength / (500 * 10 ** -9))
-
- us_ray = self.a_ray * norm_wavelength ** (-4)
- us_mie = self.a_mie * norm_wavelength ** (-self.b_mie)
-
- us_prime = (us_ray + us_mie) # * 100. to convert to m^-1
- # actually we calculated the reduced scattering coefficent, so
- # assume g is 0
- us = us_prime / (1 - self.g)
-
- return us, self.g
-
-
-class UsGMuscle(object):
- """helper object for setting us in muscle layer.
- for us in the muscle layer we don't use mie theory but the
- approximation presented in
- Rowe et al.
- "Modelling and validation of spectral reflectance for the colon"
- """
-
- def __init__(self):
- pass
-
-
- def __call__(self, wavelength):
- us = 168.52 * (wavelength * 10 ** 9) ** -0.332 / (1. - 0.96) * 100.
- g = 0.96
- return us, g
-
-
-class UsgIntralipid(object):
- """helper object for setting us and g in intralipid
- We use the formulas from
- http://omlc.org/spectra/intralipid/ to calculate
- """
-
- def __init__(self):
- self.a_ray = 0. * 100.
- self.a_mie = 20. * 100.
- self.b_mie = 2.33
- self.g = 0.85
-
- def __call__(self, wavelength):
-
- norm_wavelength = (wavelength / (500 * 10 ** -9))
-
- us_ray = self.a_ray * norm_wavelength ** (-4)
- us_mie = self.a_mie * norm_wavelength ** (-self.b_mie)
-
- us_prime = (us_ray + us_mie) # * 100. to convert to m^-1
-
- g = 2.25 * (wavelength * 10**9)**-0.155
-
- us = us_prime / (1 - g)
-
- return us, g
diff --git a/Modules/Biophotonics/python/iMC/msi/__init__.py b/Modules/Biophotonics/python/iMC/msi/__init__.py
deleted file mode 100644
index 0e9a801a5f..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 14 15:54:35 2015
-
-@author: wirkert
-"""
-
diff --git a/Modules/Biophotonics/python/iMC/msi/data/Transmission_15-49-35-978_filter700nm.txt b/Modules/Biophotonics/python/iMC/msi/data/Transmission_15-49-35-978_filter700nm.txt
deleted file mode 100755
index 5f619b446a..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/data/Transmission_15-49-35-978_filter700nm.txt
+++ /dev/null
@@ -1,2064 +0,0 @@
-Data from Transmission_15-49-35-978.txt Node
-
-Date: Mon Jun 01 15:49:35 CEST 2015
-User: thomaskirchnerbackup
-Spectrometer: HR+C3363
-Autoset integration time: false
-Trigger mode: 0
-Integration Time (sec): 1.600000E-2
-Scans to average: 1
-Electric dark correction enabled: true
-Nonlinearity correction enabled: false
-Boxcar width: 0
-XAxis mode: Wavelengths
-Stop averaging: false
-Number of Pixels in Spectrum: 2048
->>>>>Begin Spectral Data<<<<<
-187.255 70.50
-187.731 70.51
-188.206 70.51
-188.682 -0
-189.158 303.75
-189.634 135.85
-190.109 109.35
-190.585 9.89
-191.061 5400
-191.536 -476.47
-192.012 17100
-192.488 -54
-192.963 46.61
-193.439 -211.22
-193.914 114.18
-194.389 225
-194.865 137.65
-195.34 270
-195.816 -8100
-196.291 407.81
-196.766 -276.92
-197.242 51.43
-197.717 591.43
-198.192 -140.63
-198.667 135
-199.142 161.8
-199.618 -990
-200.093 139.75
-200.568 2.79
-201.043 -794.12
-201.518 101.61
-201.993 -50.4
-202.468 -3.35
-202.943 90
-203.418 -252.34
-203.893 -42.35
-204.368 112.5
-204.842 100.41
-205.317 331.58
-205.792 -203.77
-206.267 -900
-206.741 43.55
-207.216 -488.57
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-1047.313 -6.99
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-1055.359 -22.08
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-1080.282 42.49
-1080.703 -85.34
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-1102.171 33.54
-1102.591 13.71
-1103.011 -67.29
-1103.431 3.72
-1103.852 68.13
diff --git a/Modules/Biophotonics/python/iMC/msi/data/testMsi.nrrd b/Modules/Biophotonics/python/iMC/msi/data/testMsi.nrrd
deleted file mode 100644
index 82708c6160..0000000000
Binary files a/Modules/Biophotonics/python/iMC/msi/data/testMsi.nrrd and /dev/null differ
diff --git a/Modules/Biophotonics/python/iMC/msi/imgmani.py b/Modules/Biophotonics/python/iMC/msi/imgmani.py
deleted file mode 100644
index ceb06a581b..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/imgmani.py
+++ /dev/null
@@ -1,66 +0,0 @@
-'''
-Created on Aug 28, 2015
-
-@author: wirkert
-'''
-
-import numpy as np
-
-
-def collapse_image(img):
- """ helper method which transorms the n x m x nrWavelengths image to a
- (n*m) x nrWavelength image.
-
- note that this function doesn't take an object of class Msi but
- msi.get_image() """
- return img.reshape(-1, img.shape[-1])
-
-
-def remove_masked_elements(img):
- """ helper method which removes masked pixels.
- Note that by applying this method, the img loses it's shape."""
- collapsed_image = collapse_image(img)
- # if one reflectance is masked msis are defined to have all refl.
- # masked. Thus we can just have a look at the first column
- one_column = collapsed_image[:, 0]
- if (isinstance(one_column, np.ma.masked_array)):
- masked_elems = np.where(one_column.mask)
- collapsed_image = np.delete(collapsed_image, masked_elems, 0)
- return collapsed_image
-
-
-def select_n_reflectances(img, n):
- """ randomly select n reflectances from image.
- The output is of shape n x nr_wavelengths """
- collapsed_image = collapse_image(img)
- perms = np.random.permutation(collapsed_image.shape[0])
- first_n_perms = perms[0:n]
- return collapsed_image[first_n_perms, :]
-
-
-def get_bands(img, bands):
- """get the bands bands (np.array) from the multispectral image.
- Example: image is 2048x2048x8. get_bands(img, [0,3] will return
- img[:,:,[0,3]]. The advantage of this function is that the image does not
- need to be 2d + wavelength."""
- original_shape = img.shape
- collapsed_image = collapse_image(img)
- img_bands = collapsed_image[ :, bands]
- new_nr_bands = 1
- if hasattr(bands, "__len__"):
- new_nr_bands = len(bands)
- new_shape = original_shape[:-1] + (new_nr_bands,)
- return np.reshape(img_bands, new_shape)
-
-
-def sortout_bands(img, bands):
- """delete bands bands (np.array) from the multispectral image.
- Example: image is 2048x2048x8. sortout_bands(img, [0,3] will return
- img[:,:,[1,2,4,5,6,7]]. The advantage of this function is that the image does not
- need to be 2d + wavelength.
-
- TODO SW: Test"""
- all_bands = np.arange(img.shape[-1])
- bands_to_get = np.setdiff1d(all_bands, bands)
- return get_bands(img, bands_to_get)
-
diff --git a/Modules/Biophotonics/python/iMC/msi/io/__init__.py b/Modules/Biophotonics/python/iMC/msi/io/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/msi/io/msireader.py b/Modules/Biophotonics/python/iMC/msi/io/msireader.py
deleted file mode 100644
index 6bb7413ad8..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/msireader.py
+++ /dev/null
@@ -1,22 +0,0 @@
-'''
-Created on Aug 25, 2015
-
-@author: wirkert
-'''
-
-import pickle
-
-class MsiReader(object):
- '''
- The MsiReader reads the Msi from the serialized python object.
- This is the prefered way of reading an Msi.
- '''
-
- def __init__(self):
- pass
-
- def read(self, filename_to_read):
- msi_file = open(filename_to_read, 'r')
- msi = pickle.load(msi_file)
- msi_file.close()
- return msi
diff --git a/Modules/Biophotonics/python/iMC/msi/io/msiwriter.py b/Modules/Biophotonics/python/iMC/msi/io/msiwriter.py
deleted file mode 100644
index 815c465a54..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/msiwriter.py
+++ /dev/null
@@ -1,25 +0,0 @@
-'''
-Created on Aug 25, 2015
-
-@author: wirkert
-'''
-
-import pickle
-
-from writer import Writer
-
-class MsiWriter(Writer):
- '''
- The MsiReader writing the Msi as a serialized python object.
- '''
-
- def __init__(self, msiToWrite):
- """
- initialize the write with a specific multi spectral image (class Msi)
- """
- self.msiToWrite = msiToWrite
-
- def write (self, uri):
- f = open(uri, 'w')
- pickle.dump(self.msiToWrite, f)
- f.close()
diff --git a/Modules/Biophotonics/python/iMC/msi/io/nrrdreader.py b/Modules/Biophotonics/python/iMC/msi/io/nrrdreader.py
deleted file mode 100644
index 637ac7ab43..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/nrrdreader.py
+++ /dev/null
@@ -1,48 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Mon Aug 10 16:29:20 2015
-
-@author: wirkert
-"""
-
-import logging
-import numpy as np
-
-import SimpleITK as sitk
-
-from msi.io.reader import Reader
-from msi.msi import Msi
-
-
-class NrrdReader(Reader):
-
- def __init__(self):
- pass
-
- def read(self, fileToRead):
- """ read the nrrd image.
- TODO: properties are not correctly extracted from nrrd."""
-
- image = None
-
- try:
- reader = sitk.ImageFileReader()
- reader.SetFileName(fileToRead)
-
- image = reader.Execute()
- image = sitk.GetArrayFromImage(image)
-
- except RuntimeError as re:
- # image could not be read
- logging.warning("image " + fileToRead +
- " could not be loaded: " +
- str(re))
- # rethrow exception after logging
- raise
-
- # if image is too low dimensional singleton dimensions
- # are added when saving. Done because sitk can only handle dimensions
- # 2,3,4. This removes these singleton dimensions again.
- squeezed_image = np.squeeze(image)
- msi = Msi(squeezed_image)
- return msi
diff --git a/Modules/Biophotonics/python/iMC/msi/io/nrrdwriter.py b/Modules/Biophotonics/python/iMC/msi/io/nrrdwriter.py
deleted file mode 100644
index a07694a0e0..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/nrrdwriter.py
+++ /dev/null
@@ -1,39 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 09:48:18 2015
-
-@author: wirkert
-"""
-
-import logging
-import numpy as np
-
-import SimpleITK as sitk
-
-from msi.io.writer import Writer
-
-
-class NrrdWriter(Writer):
-
- def __init__(self, msiToWrite):
- """
- initialize the write with a specific multi spectral image (class Msi)
- """
- self.msiToWrite = msiToWrite
-
- def write(self, uri):
- """
- write the msi image to the specified uri
- """
- img_to_write = self.msiToWrite.get_image()
-
- # sitk can only write images of dimension 2,3,4. This hack is
- # to fake 1d images as being 2d. 1d images e.g. occure after taking
- # the mean of an image.
- if len(img_to_write.shape) == 1:
- img_to_write = np.reshape(img_to_write, (1, 1, img_to_write.shape[0]))
-
- img = sitk.GetImageFromArray(img_to_write, isVector=True)
- sitk.WriteImage(img, uri)
- logging.info("written file " + uri + " to disk")
- return None
diff --git a/Modules/Biophotonics/python/iMC/msi/io/pngreader.py b/Modules/Biophotonics/python/iMC/msi/io/pngreader.py
deleted file mode 100644
index 48ee12e81e..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/pngreader.py
+++ /dev/null
@@ -1,58 +0,0 @@
-'''
-Created on Sep 28, 2015
-
-@author: wirkert
-'''
-
-
-import os
-import itertools
-
-# PIL always rescales the image, thus PIL and skimage (which uses PIL) cannot
-# be used
-import png
-import numpy as np
-
-from msi.io.reader import Reader
-from msi.msi import Msi
-
-
-class PngReader(Reader):
- """
- Assumes bitdepth 16bit.
- TODO SW: document and test"""
-
- def __init__(self):
- pass
-
-
- def read(self, fileToRead):
- """ read the msi from pngs.
- The fileToRead is a string prefix, all files starting with this
- prefix will be summarized to one msi"""
-
- path, file_prefix = os.path.split(fileToRead)
- files = os.listdir(path)
- files_to_read = [os.path.join(path, f) for f in files
- if f.startswith(file_prefix)]
- files_to_read.sort()
- image_array = [toImage(f)
- for f in files_to_read]
- image = reduce(lambda x, y: np.dstack((x, y)), image_array)
-
- msi = Msi(image)
- return msi
-
-
-def toImage(f):
- reader = png.Reader(f)
- column_count, row_count, pngdata, params = reader.asDirect()
- plane_count = params['planes']
- image_2d = np.vstack(itertools.imap(np.uint16, pngdata))
- # this is needed for rgb images. probably better would be a mean in case
- # we convert "real" rgb data. This is just for rgb images which
- # contain the same values for r,g and b for every pixel.
- image_3d = np.reshape(image_2d,
- (row_count, column_count, plane_count))
- return image_3d[:, :, 0]
-
diff --git a/Modules/Biophotonics/python/iMC/msi/io/reader.py b/Modules/Biophotonics/python/iMC/msi/io/reader.py
deleted file mode 100644
index 99d6b678c3..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/reader.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 7 13:39:16 2015
-
-@author: wirkert
-"""
-
-
-class Reader:
- """
- Abstract reader base class
- """
-
- def __init__(self):
- pass
-
- def read(self, fileToRead):
- return None
-
diff --git a/Modules/Biophotonics/python/iMC/msi/io/spectrometerreader.py b/Modules/Biophotonics/python/iMC/msi/io/spectrometerreader.py
deleted file mode 100644
index b182201d7a..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/spectrometerreader.py
+++ /dev/null
@@ -1,43 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 7 12:04:18 2015
-
-@author: wirkert
-"""
-
-import numpy as np
-from msi.io.reader import Reader
-from msi.msi import Msi
-
-
-class SpectrometerReader(Reader):
-
- def __init__(self):
- pass
-
- def read(self, file_to_read):
- # our spectrometer like to follow german standards in files, we need
- # to switch to english ones
- transformed=""
- replacements = {',': '.', '\r\n': ''}
- with open(file_to_read) as infile:
- for line in infile:
- for src, target in replacements.iteritems():
- line = line.replace(src, target)
- transformed = "\n".join([transformed, line])
-
- for num, line in enumerate(transformed.splitlines(), 1):
- if ">>>>>Begin" in line:
- break
-
- for num_end, line in enumerate(transformed.splitlines(), 1):
- if ">>>>>End" in line:
- num_end -= 1
- break
- string_only_spectrum = "\n".join(transformed.splitlines()[num:num_end])
- data_vector = np.fromstring(string_only_spectrum,
- sep="\t").reshape(-1, 2)
- msi = Msi(data_vector[:, 1],
- {'wavelengths': data_vector[:, 0] * 10 ** -9})
- return msi
-
diff --git a/Modules/Biophotonics/python/iMC/msi/io/tiffreader.py b/Modules/Biophotonics/python/iMC/msi/io/tiffreader.py
deleted file mode 100644
index fdc7bae5fb..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/tiffreader.py
+++ /dev/null
@@ -1,100 +0,0 @@
-'''
-Created on Sep 28, 2015
-
-@author: wirkert
-'''
-
-
-import os
-
-import Image
-import scipy
-import numpy as np
-
-from msi.io.reader import Reader
-from msi.msi import Msi
-
-
-def sort_by_filter(s1, s2):
- '''
- Sorting function which takes two strings and sorts them lexigraphically by
- the last character before the file extension.
-
- say:
-
- blabla_w2_F0.tiff < blabla_w0_F1.tiff
-
- This is done to sort by the filter index, which is always written as the
- last thing by the tiff writer.
- '''
- s1_prefix = os.path.splitext(s1)[0]
- s2_prefix = os.path.splitext(s2)[0]
-
- result = 0
- if s1_prefix < s2_prefix:
- result = 1
- elif s1_prefix > s2_prefix:
- result = -1
-
- return result
-
-
-class TiffReader(Reader):
- """
- AAATTTEEENTION: Some big bug hiding somewhere here, ordering of files
- is corrupted, no time now to fix. TODO SW
-
- Assumes bitdepth 16bit on a 12bit camera.
- TODO SW: document and test"""
-
- # static member to globally set resizing for all images read by the reader
- # 1.0 for no resizing
- RESIZE_FACTOR = 1.0
-
- def __init__(self, shift_bits=4):
- self.shift_bits = shift_bits
-
- def read(self, file_to_read, resize_factor=None,
- sorting_function=sort_by_filter):
- """ read the msi from tiffs.
- The fileToRead is a string prefix, all files starting with this
- prefix will be summarized to one msi. they will be sorted as specified
- in the sorting_function
-
- Args:
- sorting_function: the function which defines the sorting of the
- strings that match the prefix. Pass none if normal
- lexicographical sorting is wished
- file_to_read: the prefix of the tiff file which shall be read
- """
-
- if resize_factor is None:
- resize_factor = TiffReader.RESIZE_FACTOR
-
- path, file_prefix = os.path.split(file_to_read)
- files = os.listdir(path)
- files_to_read = [os.path.join(path, f) for f in files
- if file_prefix[2:] in f]
- files_to_read.sort(cmp=sorting_function)
- image_array = [self.to_image(f, resize_factor=resize_factor)
- for f in files_to_read]
- image = reduce(lambda x, y: np.dstack((x, y)), image_array)
-
- msi = Msi(image)
- return msi
-
- def to_image(self, f, resize_factor):
- im = Image.open(f)
- im_array = np.array(im)
-
- im_array >>= self.shift_bits
-
- if do_resize(resize_factor):
- im_array = scipy.misc.imresize(im_array, resize_factor,
- interp="bilinear", mode="F")
-
- return im_array.astype('float')
-
-
-def do_resize(resize_factor):
- return not np.isclose(resize_factor, 1.0) and (resize_factor is not None)
diff --git a/Modules/Biophotonics/python/iMC/msi/io/tiffringreader.py b/Modules/Biophotonics/python/iMC/msi/io/tiffringreader.py
deleted file mode 100644
index b0bf6177b9..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/tiffringreader.py
+++ /dev/null
@@ -1,100 +0,0 @@
-'''
-Created on Nov 2, 2015
-
-@author: wirkert
-'''
-
-import os
-import logging
-
-import Image
-import scipy
-import numpy as np
-
-from msi.io.reader import Reader
-from msi.msi import Msi
-
-
-class TiffRingReader(Reader):
- '''
- TODO SW: document and test
- '''
-
- # static member to globally set resizing for all images read by the reader
- # 1.0 for no resizing
- RESIZE_FACTOR = 1.0
-
- def __init__(self, shift_bits=4):
- self.shift_bits = shift_bits
-
- def read(self, fileToRead, n, resize_factor=None,
- segmentation=None):
- """ read the msi from tiffs.
- The fileToRead is the first file to read,
- then n files will be read to one msi from a
- sorted file list
-
- segmentation: tiff filename of the segmentation. If none, it will be
- tried to get a segmentation from npy files with filenames like the
- tiff files + _seg.tiff. If this fails, no segmentation will be
- assumed
- """
-
- if resize_factor is None:
- resize_factor = TiffRingReader.RESIZE_FACTOR
-
- path, file_name = os.path.split(fileToRead)
- files = os.listdir(path)
- files_in_folder = [os.path.join(path, f) for f in files if
- os.path.isfile(os.path.join(path, f)) and
- f.endswith('.tiff')]
-
- files_in_folder.sort()
- position = files_in_folder.index(fileToRead)
- # take n images from found position
- image_array = [self.to_image(f, resize_factor)
- for f in files_in_folder[position:position + n]]
- image = reduce(lambda x, y: np.dstack((x, y)), image_array)
-
- # in case of 1 dimensional image: add a fake last dimension, since
- # we always assume the last dimension to be the wavelength domain.
- # TODO SW: Test this and implement for other readers
- if n is 1:
- image = np.expand_dims(image, -1)
-
- msi = Msi(image)
-
- # we pass an explicic image as segmentation
- if segmentation is not None:
- segmentation = self.to_image(segmentation, resize_factor)
- else: # otherwise: search for numpy segmentations
- try:
- segmentation_array = [to_segmentation(f)
- for f in
- files_in_folder[position:position + n]]
- if do_resize(resize_factor):
- segmentation = reduce(lambda x, y: x & y, segmentation_array)
- segmentation = scipy.misc.imresize(segmentation, resize_factor,
- interp="bilinear")
- except:
- logging.info("didn't find segmentation for all images")
- return msi, segmentation
-
- def to_image(self, f, resize_factor):
- im = Image.open(f)
- im_array = np.array(im)
- im_array >>= self.shift_bits
-
- if do_resize(resize_factor):
- im_array= scipy.misc.imresize(im_array, resize_factor,
- interp="bilinear", mode="F")
- return im_array.astype('float')
-
-
-def to_segmentation(f):
- seg = np.load(f + ".seg.npy")
- return seg
-
-
-def do_resize(resize_factor):
- return not np.isclose(resize_factor, 1.0) and (resize_factor is not None)
diff --git a/Modules/Biophotonics/python/iMC/msi/io/tiffwriter.py b/Modules/Biophotonics/python/iMC/msi/io/tiffwriter.py
deleted file mode 100644
index 36506aa850..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/tiffwriter.py
+++ /dev/null
@@ -1,72 +0,0 @@
-
-
-import logging
-
-import numpy as np
-from libtiff import TIFF
-
-from msi.io.writer import Writer
-
-
-class TiffWriter(Writer):
- """
- The tiff write will store nr_wavelength tiff files for one msi
- """
-
- def __init__(self, msi_to_write, convert_to_nm=True, scale_to_16_bit=False):
- """
- initialize the write with a specific multi spectral image (class Msi)
- """
- self.msi_to_write = msi_to_write
- self.convert_to_nm = convert_to_nm
- self.scale_to_16_bit = scale_to_16_bit
-
- def write(self, uri_prefix):
- """
- write the msi image to the specified uri_prefix
-
- Args:
- uri_prefix: the prefix off the uri. E.g. C:\example the image
- write will automatically extend this prefix path to include the
- wavelengths information and add a suffix. Your final
- file may look similar to: C:\example_w_470nm_F0.tiff
- convert_to_nm: if the wavelengths are saved in m they are hard to
- write as string. Thus they can be automatically expanded to nm.
- """
- img_to_write = self.msi_to_write.get_image()
-
- max_image_value = np.max(img_to_write)
-
- if self.scale_to_16_bit:
- img_to_write *= 2**16 / max_image_value
-
- nr_wavelengths = self.msi_to_write.get_wavelengths().size
- for wavelength_index in np.arange(nr_wavelengths):
- full_uri = self._build_full_uri(uri_prefix, wavelength_index)
- self._write_single_image(full_uri,
- img_to_write[:, :, wavelength_index])
-
- logging.info("written file " + full_uri + " to disk")
- return None
-
- @staticmethod
- def _write_single_image(full_uri, image_array):
- """
- internally used method to write single tiff image
- """
- tiff = TIFF.open(full_uri, mode='w')
- tiff.write_image(image_array.astype('uint16'), write_rgb=False)
- tiff.close()
-
- def _build_full_uri(self, uri_prefix, wavelength_index):
- """
- Helper method to build full path of one image
- Returns: full uri containing the desired properties.
- """
- wavelength = self.msi_to_write.get_wavelengths()[wavelength_index]
- if self.convert_to_nm:
- wavelength *= 10**9
- full_uri = uri_prefix + "_w_" + str(wavelength) +\
- "_F" + str(wavelength_index) + ".tiff"
-
- return full_uri
diff --git a/Modules/Biophotonics/python/iMC/msi/io/writer.py b/Modules/Biophotonics/python/iMC/msi/io/writer.py
deleted file mode 100644
index 9342ff00fe..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/io/writer.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 09:47:31 2015
-
-@author: wirkert
-"""
-
-
-class Writer():
- """
- Abstract writer base class
- """
-
- def __init__(self):
- pass
-
- def write(self, fileToWrite):
- return None
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/msi/msi.py b/Modules/Biophotonics/python/iMC/msi/msi.py
deleted file mode 100644
index 5638d44ad7..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/msi.py
+++ /dev/null
@@ -1,128 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 6 18:21:36 2015
-
-@author: wirkert
-"""
-
-import numpy as np
-
-
-class Msi():
- """ a multi spectral image stack consisting of:
-
- image: a rows x columns x nrWavelengths dimensional array
- properties: additional, application dependent properties
- """
-
- def __init__(self, image=None, properties=None):
- if image is None:
- image = np.array([])
- if properties is None:
- properties = {}
- self._image = image
- self._properties = properties
- self._assure_basic_properties()
-
- self._test_image()
-
- def get_image(self):
- return self._image
-
- def set_image(self, image, wavelengths=None):
- """
- Put a new image into this msi
- Args:
- image: the rows x columns x nrWavelengths dimensional array
- np.array.
- wavelengths: a np.array of size nrWavelengths. If the number of
- wavelengths hasn't change this is not needed.
- """
- self._image = image
- if wavelengths is not None:
- self.set_wavelengths(wavelengths)
- self._assure_basic_properties()
- self._test_image()
-
- def get_wavelengths(self):
- """ shortcut to get the wavelengths property
- The wavelengths are given in [m] units and need not be sorted. """
- if 'wavelengths' not in self.get_properties():
- return None
- return self._properties['wavelengths']
-
- def set_wavelengths(self, wavelengths):
- """ shortcut to set the wavelengths property """
- w_prop = {"wavelengths":wavelengths}
- self.add_property(w_prop)
- self._test_image()
-
- def get_properties(self):
- return self._properties
-
- def add_property(self, newProperty):
- """ add a new property(ies) to the existing properties """
- self._properties.update(newProperty)
- self._test_image()
-
- def set_mask(self, mask):
- """" applies a masked to the Msi. After this call, the image is of
- type MaskedArray. If the image was already masked, the existing
- masked will be "or ed" with the new mask. mask is a boolean array of
- the same shape as self.get_image()
-
- Args:
- mask: a mask of the same size as the image. 1s stand for pixels
- masked out, 0s for pixels not masked."""
- if not isinstance(self.get_image(), np.ma.MaskedArray):
- self.set_image(np.ma.masked_array(self.get_image(), mask,
- fill_value=999999))
- else:
- self.get_image()[mask] = np.ma.masked
-
- def __eq__(self, other):
- """
- overrite the == operator
- Two Msi s are the same if they contain the same image and properties.
- Note: properties not implemented yet!
- """
- if isinstance(other, Msi):
- samesame = np.array_equal(other.get_image(), self.get_image())
- return samesame
- return NotImplemented
-
- def __ne__(self, other):
- """ != operator implemented by inverting to =="""
- result = self.__eq__(other)
- if result is NotImplemented:
- return result
- return not result
-
- def _assure_basic_properties(self):
- """
- helper method to automatically add the basic properties:
- wavelength
- to the msi if not added explicicly. basic wavelengths will just be
- integers from 0 to 1
- """
- if self._image.size > 0 and (
- ("wavelengths" not in self._properties.keys() or
- self._properties["wavelengths"].size == 0)):
- self._properties["wavelengths"] = np.arange(self._image.shape[-1])
- if self._image.size == 0 and "wavelengths" not in self._properties.keys():
- self._properties["wavelengths"] = np.array([])
-
- def _test_image(self):
- """
- helper method which tests for the integrity of the msi.
- E.g. the number of wavelengths must match the number of bands.
- """
- # either both image and wavelength property are empty
- if self._image.size == 0 and len(self._properties["wavelengths"]) != 0:
- raise RuntimeError("dimension of image and wavelength mismatch: " +
- "image size is zero, but wavelengths are set")
- # or both are same
- elif self._image.shape[-1] != len(self._properties["wavelengths"]):
- raise RuntimeError("dimension of image and wavelength mismatch: " +
- "image size and wavelenths do not match")
-
diff --git a/Modules/Biophotonics/python/iMC/msi/msimanipulations.py b/Modules/Biophotonics/python/iMC/msi/msimanipulations.py
deleted file mode 100644
index 9169fa35c1..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/msimanipulations.py
+++ /dev/null
@@ -1,142 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 13:42:00 2015
-
-@author: wirkert
-"""
-
-import logging
-import copy
-import numpy as np
-
-from scipy.interpolate import interp1d
-
-from imgmani import collapse_image
-import imgmani
-from msi import Msi
-
-
-'''
-The msi manipulations module includes usefull convenience operations on msis.
-
-E.g. calculate_mean_spectrum to calculate the average spectrum on all the image
-data or interpolate_wavelengths to change to a different wavelenght set by
-simple interpolation.
-
-All methods take a msi and change it in place. They also return the same msi
-object for convenience (can e.g. be used to chain msi manipulations).
-'''
-
-
-def apply_segmentation(msi, segmentation):
- """ applies a segmentation to an msi.
-
- If the msi has imaging data of n x m x nr_wavelengths the segmentation
- has to be a numpy array of n x m size. pixelvalues with values different
- than zero will be included in the segmentation.
- By applying the segmentation, not segmented elements will be np.ma.masked.
-
- Alternatively, one can input a msi with the mentioned n x m numpy array
- in from of a msi as segmentation (for convenience to be able to use the
- same reader for msis and segmentations)
- """
- if (isinstance(segmentation, Msi)):
- # expects just an image, but if a Msi is passed it's also ok
- segmentation = segmentation.get_image()
- segmentation = np.squeeze(segmentation)
- mask = (0 == segmentation)
- # mask needs to be expanded to cover all wavlengths
- wholeMask = np.zeros_like(msi.get_image(), dtype="bool")
- # doesn't seem elegant
- for i in range(wholeMask.shape[-1]):
- wholeMask[:, :, i] = mask
-
- msi.set_mask(wholeMask)
- return msi
-
-
-def calculate_mean_spectrum(msi):
- """ reduce this image to only its mean spectrum.
- If the msi.get_image() is a masked array these values will be ignored when
- calculating the mean spectrum """
- # reshape to collapse all but last dimension (which contains reflectances)
- collapsedImage = collapse_image(msi.get_image())
- msi.set_image(np.mean(collapsedImage, axis=0))
- # returns the same msi.
- return msi
-
-
-def interpolate_wavelengths(msi, newWavelengths):
- """ interpolate image data to fit newWavelengths. Current implementation
- performs simple linear interpolation. Neither existing nor new wavelengths
- need to be sorted. """
- interpolator = interp1d(msi.get_wavelengths(), msi.get_image(), assume_sorted=False)
- msi.set_image(interpolator(newWavelengths), wavelengths=newWavelengths)
- return msi
-
-
-def normalize_integration_times(msi):
- """ divides by integration times """
- if ('integration times' not in msi.get_properties()):
- logging.warn("warning: trying to normalize integration times for "
- "image without the integration time property")
- return msi
-
- original_shape = msi.get_image().shape
- collapsed_image = collapse_image(msi.get_image())
- collapsed_image = collapsed_image / msi.get_properties()['integration times']
- msi.set_image(collapsed_image.reshape(original_shape))
-
- msi.add_property({'integration times':
- np.ones_like(msi.get_properties()['integration times'])})
- return msi
-
-
-def dark_correction(msi, dark):
- """" subtract dark current from multi spectral image.
-
- The dark msi should either be of the same shape
- as msi or 1xnr_wavelengths (see tests)."""
- msi.set_image(msi.get_image() - dark.get_image())
- return msi
-
-
-def flatfield_correction(msi, flatfield):
- """ divide by flatfield to remove dependencies on light source form and
- imaging system.
-
- The flatfield msi should either be of the same shape
- as msi or 1xnr_wavelengths (see tests)."""
- # we copy the flatfield to ensure it is unchanged by the normalization
- flatfield_copy = copy.copy(flatfield)
- normalize_integration_times(flatfield_copy)
- normalize_integration_times(msi)
-
- msi.set_image(msi.get_image() / flatfield_copy.get_image())
- return msi
-
-
-def image_correction(msi, flatfield, dark):
- """ do the usual image correction:
- msi = ((msi - dark) / integration_time) / ((flatfield - dark) / integration_time)
- this function changes only the msi, flatfield and dark image
- are left unchanged.
- """
- # we need a copy of flatfield since otherwise the dark correction
- # changes the flatfield
- dark_correction(msi, dark)
- flatfield_copy = copy.copy(flatfield)
- dark_correction(flatfield_copy, dark)
- flatfield_correction(msi, flatfield_copy)
- return msi
-
-
-def get_bands(msi, bands):
- """
- TODO SW: document and test
- """
- msi.set_image(imgmani.get_bands(msi.get_image(), bands))
- if msi.get_wavelengths() is not None:
- msi.set_wavelengths(msi.get_wavelengths()[bands])
- return msi
-
diff --git a/Modules/Biophotonics/python/iMC/msi/normalize.py b/Modules/Biophotonics/python/iMC/msi/normalize.py
deleted file mode 100644
index 880bbffed4..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/normalize.py
+++ /dev/null
@@ -1,53 +0,0 @@
-
-import numpy as np
-from sklearn.preprocessing import Normalizer
-
-
-from imgmani import collapse_image
-
-
-class Normalize():
-
- def __init__(self):
- pass
-
- def normalize(self, msi):
- pass
-
-
-class NormalizeIQ(Normalize):
- """Normalize by image quotient"""
- def __init__(self, iqBand=None):
- if iqBand is None:
- iqBand = 0
- self.iqBand = iqBand
-
- def normalize(self, msi):
- # todo: guard if iqBand is outside of image dimension
- original_shape = msi.get_image().shape
- collapsed_image = collapse_image(msi.get_image())
- iqDimension = collapsed_image[ :, self.iqBand]
- normalized_image = collapsed_image / iqDimension[:, None]
- msi.set_image(np.reshape(normalized_image, original_shape))
-
-
-class NormalizeMean(Normalize):
- """Normalize by image mean"""
- def __init__(self):
- pass
-
- def normalize(self, msi, norm="l1"):
- original_shape = msi.get_image().shape
- collapsed_image = collapse_image(msi.get_image())
- # temporarily save mask, since scipy normalizer removes mask
- is_masked_array = isinstance(msi.get_image(), np.ma.MaskedArray)
- if is_masked_array:
- mask = msi.get_image().mask
- normalizer = Normalizer(norm=norm)
- normalized_image = normalizer.transform(collapsed_image)
- if is_masked_array:
- normalized_image = np.ma.MaskedArray(normalized_image, mask=mask)
- msi.set_image(np.reshape(normalized_image, original_shape))
-
-
-standard_normalizer = NormalizeMean()
diff --git a/Modules/Biophotonics/python/iMC/msi/plot.py b/Modules/Biophotonics/python/iMC/msi/plot.py
deleted file mode 100644
index 0ae653b2ce..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/plot.py
+++ /dev/null
@@ -1,85 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 11:13:31 2015
-
-@author: wirkert
-"""
-
-import copy
-import logging
-
-import numpy as np
-import matplotlib.pyplot as plt
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-
-import imgmani
-import msimanipulations as msimani
-
-def plot(msi, axes=None, color=None):
- """
- create a plot for the Msi with x axes being the wavelengths and
- y-axes being the corresponding image values (e.g. reflectances, absorptions)
- Takes image masks into account:
- doesn't plot a spectrum containing masked elements
- """
- if axes is None:
- axes = plt.gca()
-
- sortedIndices = sorted(range(len(msi.get_wavelengths())),
- key=lambda k: msi.get_wavelengths()[k])
- sortedWavelenghts = msi.get_wavelengths()[sortedIndices]
- # reshape to collapse all but last dimension (which contains reflectances)
- collapsedImage = imgmani.collapse_image(msi.get_image())
- # todo: simply use np.ma.compress_rows
-
- # print "filtered ", filteredImage.shape
- i = 0
- for i in range(collapsedImage.shape[0]):
- if (collapsedImage[i, 0] is not np.ma.masked):
- axes.plot(sortedWavelenghts,
- collapsedImage[i, :][sortedIndices], "-o", color=color)
-
-
-def plot_images(msi):
- """plot the images as a 2d image array, one image for
- each wavelength."""
- nr_wavelengths = msi.get_image().shape[-1]
- f, axarr = plt.subplots(1, nr_wavelengths)
- for i, a in enumerate(axarr):
- one_band_image = imgmani.get_bands(msi.get_image(), i)
- im = a.imshow(np.squeeze(one_band_image))
- a.set_title("band nr " + str(i), fontsize=5)
- divider_dsp = make_axes_locatable(a)
- cax_dsp = divider_dsp.append_axes("right", size="10%", pad=0.1)
- cbar = plt.colorbar(im, cax=cax_dsp)
- cbar.ax.tick_params(labelsize=5)
- a.xaxis.set_visible(False)
- a.yaxis.set_visible(False)
-
-
-def plotMeanError(msi, axes=None):
- """
- create a plot for the Msi with x axes being the wavelengths and
- y-axes being the corresponding mean image values
- (e.g. reflectances, absorptions). Plots also standard deviation bands
- Takes image masks into account:
- doesn't plot a spectrum containing masked elements
- """
- if axes is None:
- axes = plt.gca()
- # sort the wavelengths
- sortedIndices = sorted(range(len(msi.get_wavelengths())),
- key=lambda k: msi.get_wavelengths()[k])
- sortedWavelenghts = msi.get_wavelengths()[sortedIndices]
- # copy the msi, since it will be altered (mean will be built)
- msi_copy = copy.deepcopy(msi)
- image = msi_copy.get_image()
- image = imgmani.collapse_image(image)
- std_curve = np.ma.std(image, axis=0)
- msimani.calculate_mean_spectrum(msi_copy)
- # calculate std
- logging.info("percentual std: " +
- str(std_curve / msi_copy.get_image() * 100.))
- # plot as errorbar
- axes.errorbar(sortedWavelenghts, msi_copy.get_image()[sortedIndices],
- yerr=std_curve, fmt='-o')
diff --git a/Modules/Biophotonics/python/iMC/msi/test/__init__.py b/Modules/Biophotonics/python/iMC/msi/test/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/msi/test/helpers.py b/Modules/Biophotonics/python/iMC/msi/test/helpers.py
deleted file mode 100644
index 4565f7e63a..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/helpers.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 09:53:52 2015
-
-@author: wirkert
-"""
-
-import numpy as np
-from msi.msi import Msi
-
-
-def getFakeMsi():
-
- # build a fake multispectral image with 5 dimensions.
- image = np.concatenate((np.ones((5, 5, 1)),
- np.ones((5, 5, 1)) * 2,
- np.ones((5, 5, 1)) * 3,
- np.ones((5, 5, 1)) * 4,
- np.ones((5, 5, 1)) * 5),
- axis=-1)
- msi = Msi(image)
-
- msi.set_wavelengths(np.array([5, 4, 3, 2, 1]))
-
- return msi
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_imgmani.py b/Modules/Biophotonics/python/iMC/msi/test/test_imgmani.py
deleted file mode 100644
index c6960958ca..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_imgmani.py
+++ /dev/null
@@ -1,96 +0,0 @@
-'''
-Created on Aug 28, 2015
-
-@author: wirkert
-'''
-import unittest
-import numpy as np
-
-import msi.msimanipulations as msimani
-import msi.imgmani as imgmani
-import msi.test.helpers as helpers
-from msi.imgmani import remove_masked_elements, select_n_reflectances
-
-
-class TestImgMani(unittest.TestCase):
-
- def setUp(self):
- self.msi = helpers.getFakeMsi()
- # set one pixel to special values
- self.specialValue = np.arange(self.msi.get_image().shape[-1]) * 2
- self.msi.get_image()[2, 2, :] = self.specialValue
- # create a segmentation which sets all elements to invalid but the
- # one pixel with the special value
- self.segmentation = np.zeros(self.msi.get_image().shape[0:-1])
- self.segmentation[2, 2] = 1
- # apply this segmentation to the msi
- msimani.apply_segmentation(self.msi, self.segmentation)
- self.image = self.msi.get_image()
-
- def tearDown(self):
- self.msi = None
- self.specialValue = None
- self.segmentation = None
- self.image = None
-
- def test_collapse_image(self):
- image = self.image
- newShapedImage = imgmani.collapse_image(image)
-
- self.assertEqual(newShapedImage.shape,
- (image.shape[0] * image.shape[1], image.shape[2]),
- "collapsed image has correct shape")
- np.testing.assert_equal(newShapedImage[2 * 5 + 2, :],
- self.msi.get_image()[2, 2, :],
- "values have been correctly transformed")
-
- def test_collapse_image_retains_data(self):
- newShapedImage = imgmani.collapse_image(self.image)
- self.msi.get_image()[2, 2, 0] = 5000.
-
- self.assertEqual(newShapedImage[2 * 5 + 2, 0], 5000.,
- "collapse_image does not copy data")
-
- def test_remove_masked_elements(self):
- value = self.msi.get_image()[2, 2, :]
- image_without_masked = remove_masked_elements(self.image)
- np.testing.assert_array_equal(image_without_masked[0, :], value,
- "mask correctly removed")
- self.assertEqual(image_without_masked.shape,
- (1, self.image.shape[-1]),
- "shape of image without mask correct")
-
- def test_select_n_reflectances_selects(self):
- n = 10
- new_image = select_n_reflectances(self.image, n)
- self.assertEqual(new_image.shape, (n, self.image.shape[-1]),
- "correct shape after selection")
-
- def test_select_n_reflectances_permutes(self):
- image_shape = self.image.shape
- new_first_layer = np.random.random_sample(image_shape[0:-1])
- self.image[:, :, 0] = new_first_layer
- shuffled_image = select_n_reflectances(self.image,
- image_shape[0] * image_shape[1])
- # restore_shape
- shuffled_image = np.reshape(shuffled_image, image_shape)
- self.assertFalse(np.allclose(shuffled_image[:, :, 0],
- new_first_layer),
- "image has been shuffled")
-
- def test_get_bands_from_int(self):
- new_image_bands = imgmani.get_bands(self.image, 2)
- self.assertEqual(new_image_bands.shape, (5, 5, 1),
- "new image has correct shape")
- self.assertEqual(new_image_bands[2, 2, :], self.specialValue[2],
- "new image has correct values")
-
- def test_get_bands_from_array(self):
- new_image_bands = imgmani.get_bands(self.image, np.array([0, 1, 2]))
- self.assertEqual(new_image_bands.shape, (5, 5, 3),
- "new image has correct shape")
- np.testing.assert_allclose(new_image_bands[2, 2, :],
- self.specialValue[:3],
- err_msg="new image has correct values")
-
-
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_msi.py b/Modules/Biophotonics/python/iMC/msi/test/test_msi.py
deleted file mode 100644
index 128a0691df..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_msi.py
+++ /dev/null
@@ -1,50 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Mar 27 19:12:40 2015
-
-@author: wirkert
-"""
-
-import unittest
-import numpy as np
-
-from msi.msi import Msi
-from msi.test import helpers
-
-
-class TestMsi(unittest.TestCase):
-
- def setUp(self):
- self.msi = helpers.getFakeMsi()
-
- def tearDown(self):
- pass
-
- def test_create(self):
- self.assertTrue(True, "Created msi during setup")
-
- def test_add_property(self):
- self.msi.add_property({'test':np.array([1, 2, 3])})
- self.assertTrue(np.array_equal(self.msi.get_properties()['test'],
- np.array([1, 2, 3])), "property successfully added to msi")
-
- def test_properties_not_shared(self):
- msi1 = Msi()
- msi2 = Msi()
- msi1.add_property({"integration time": np.array([1, 2, 3])})
-
- self.assertTrue('integration time' not in msi2.get_properties())
-
- def test_add_dummy_wavelengths_automatically(self):
- msi_no_wavelengths_set = Msi()
- msi_no_wavelengths_set.set_image(self.msi.get_image())
-
- nr_wavelengths = msi_no_wavelengths_set.get_image().shape[-1]
-
- np.testing.assert_equal(msi_no_wavelengths_set.get_wavelengths(),
- np.arange(nr_wavelengths),
- "correct dummy wavelength values set")
-
-
-
-
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_msimanipulations.py b/Modules/Biophotonics/python/iMC/msi/test/test_msimanipulations.py
deleted file mode 100644
index 9b895a6cf4..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_msimanipulations.py
+++ /dev/null
@@ -1,203 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 13:52:23 2015
-
-@author: wirkert
-"""
-
-
-import unittest
-import copy
-import numpy as np
-
-from msi.test import helpers
-import msi.msimanipulations as mani
-
-
-class TestMsiManipulations(unittest.TestCase):
-
- def setUp(self):
- self.msi = helpers.getFakeMsi()
- self.specialmsi = helpers.getFakeMsi()
-
- # set one pixel to special values
- self.specialValue = np.arange(self.specialmsi.get_image().shape[-1]) * 2
- self.specialmsi.get_image()[2, 2, :] = self.specialValue
-
- # create a segmentation which sets all elements to invalid but the
- # one pixel with the special value
- self.segmentation = np.zeros(self.specialmsi.get_image().shape[0:-1])
- self.segmentation[2, 2] = 1
-
- def tearDown(self):
- pass
-
- def test_apply_segmentation(self):
-
- mani.apply_segmentation(self.specialmsi, self.segmentation)
-
- validImageEntries = self.specialmsi.get_image() \
- [~self.specialmsi.get_image().mask]
-
- np.testing.assert_equal(validImageEntries, self.specialValue,
- "image has been correctly segmented")
-
- def test_calculate_mean_spectrum(self):
-
- mani.calculate_mean_spectrum(self.specialmsi)
-
- np.testing.assert_equal(np.array([0.96, 2., 3.04, 4.08, 5.12]),
- self.specialmsi.get_image(),
- "mean spectrum is correctly calculated on image with " +
- "no mask applied")
-
- def test_calculate_mean_spectrum_masked_image(self):
-
- mani.apply_segmentation(self.specialmsi, self.segmentation)
- mani.calculate_mean_spectrum(self.specialmsi)
-
- np.testing.assert_equal(self.specialValue, self.specialmsi.get_image(),
- "mean spectrum is correctly calculated on image with " +
- "mask applied")
-
- def test_interpolate(self):
- # create not sorted new wavelengths
- newWavelengths = np.array([4.0, 2.5, 3.5, 1.5])
- mani.interpolate_wavelengths(self.msi, newWavelengths)
-
- np.testing.assert_equal(newWavelengths, self.msi.get_wavelengths(),
- "wavelengths correctly updated")
- # check if first image pixel was correctly calculated
- # (hopefully true for all then)
- np.testing.assert_equal(np.array([2.0, 3.5, 2.5, 4.5]),
- self.msi.get_image()[0, 0, :],
- "image elements correctly interpolated")
-
- def test_normalize_integration_times(self):
- old_shape = self.msi.get_image().shape
- integration_times = np.array([1., 2., 3., 4., 5.])
- self.msi.add_property({'integration times': integration_times})
- mani.normalize_integration_times(self.msi)
-
- np.testing.assert_equal(self.msi.get_image()[1, 3, :],
- np.ones_like(integration_times),
- "normalized integration times")
- np.testing.assert_equal(self.msi.get_properties()['integration times'],
- np.ones_like(integration_times),
- "integration time property set to ones")
- self.assertEqual(self.msi.get_image().shape, old_shape,
- "shape did not change from normalizing")
-
- def test_normalize_integration_times_none_given(self):
- msi_copy = copy.deepcopy(self.msi)
- mani.normalize_integration_times(msi_copy)
- np.testing.assert_equal(msi_copy.get_image(), self.msi.get_image(),
- "nothing change by normalizing without" + \
- "integration times given")
-
- def test_dark_correction(self):
- desired_image_data = copy.copy(self.msi.get_image())
- desired_image_data -= 1
-
- dark = copy.copy(self.msi)
- dark.set_image(np.ones_like(dark.get_image()))
-
- mani.dark_correction(self.msi, dark)
-
- np.testing.assert_equal(self.msi.get_image(),
- desired_image_data,
- "dark image correctly accounted for")
- np.testing.assert_equal(dark.get_image(),
- np.ones_like(dark.get_image()),
- "dark image unchanged by dark correction")
-
- def test_dark_correction_with_single_value(self):
- desired_image_data = copy.copy(self.specialmsi.get_image())
- desired_image_data -= 1
-
- dark = copy.copy(self.specialmsi)
- dark.set_image(np.ones_like(dark.get_image()))
- mani.calculate_mean_spectrum(dark)
-
- mani.dark_correction(self.specialmsi, dark)
-
- np.testing.assert_equal(self.specialmsi.get_image(),
- desired_image_data,
- "dark image correctly accounted for from singular dark value")
- np.testing.assert_equal(dark.get_image(),
- np.ones_like(dark.get_image()),
- "dark image unchanged by dark correction")
-
- def test_flatfield_correction(self):
- desired_image_data = np.ones_like(self.specialmsi.get_image())
- desired_image_data[2, 2, 0] = np.nan
-
- mani.flatfield_correction(self.specialmsi, self.specialmsi)
-
- np.testing.assert_equal(self.specialmsi.get_image(),
- desired_image_data,
- "correct image by itself should lead to only 1s ")
-
- def test_flatfield_correction_differing_integration_times(self):
- MSI_INTEGRATION_TIME = 3.0
- FLATFIELD_INTEGRATION_TIME = 2.0
- desired_image_data = np.ones_like(self.specialmsi.get_image()) * \
- FLATFIELD_INTEGRATION_TIME / MSI_INTEGRATION_TIME
- desired_image_data[2, 2, 0] = np.nan
- self.specialmsi.add_property({"integration times":
- np.ones_like(
- self.specialmsi.get_image()[0, 0, :])
- * MSI_INTEGRATION_TIME})
- flatfield = copy.deepcopy(self.specialmsi)
- flatfield.add_property({"integration times":
- np.ones_like(
- flatfield.get_image()[0, 0, :])
- * FLATFIELD_INTEGRATION_TIME})
- # for testing if flatfield does not changed by correction we copy it
- flatfield_copy = copy.deepcopy(flatfield)
-
- mani.flatfield_correction(self.specialmsi, flatfield_copy)
-
- np.testing.assert_almost_equal(self.specialmsi.get_image(),
- desired_image_data, 15,
- "corrected image is a division of integration times")
- np.testing.assert_equal(flatfield.get_image(),
- flatfield_copy.get_image(),
- "flatfield doesn't change by correction")
-
- def test_flatfield_correction_with_single_value(self):
- desired_image_data = np.ones_like(self.msi.get_image())
- flatfield = copy.copy(self.msi)
- mani.calculate_mean_spectrum(flatfield)
- unchanged_flatfield = copy.deepcopy(flatfield)
-
- mani.flatfield_correction(self.msi, flatfield)
-
- np.testing.assert_equal(self.msi.get_image(),
- desired_image_data,
- "flatfield correctly accounted for from singular reference value")
- np.testing.assert_equal(flatfield, unchanged_flatfield,
- "flatfield not changed by algorithm")
-
- def test_image_correction(self):
- dark = copy.copy(self.msi)
- dark.set_image(np.ones_like(dark.get_image()) * 0.5)
- flatfield = copy.copy(self.msi)
- flatfield_copy = copy.deepcopy(flatfield)
- dark_copy = copy.deepcopy(dark)
-
- mani.image_correction(self.msi, flatfield, dark)
-
- np.testing.assert_equal(flatfield.get_image(),
- flatfield_copy.get_image(),
- "image correction didn't change flatfield")
- np.testing.assert_equal(dark.get_image(), dark_copy.get_image(),
- "image correction didn't change dark image")
- np.testing.assert_almost_equal(self.msi.get_image(),
- np.ones_like(self.msi.get_image()),
- 15, "image correctly corrected :-)")
-
-
-
-
-
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_msireaderwriter.py b/Modules/Biophotonics/python/iMC/msi/test/test_msireaderwriter.py
deleted file mode 100644
index a3bed221b0..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_msireaderwriter.py
+++ /dev/null
@@ -1,40 +0,0 @@
-'''
-Created on Aug 25, 2015
-
-@author: wirkert
-'''
-import unittest
-import os
-import numpy as np
-
-import msi.test.helpers as helpers
-from msi.io.msiwriter import MsiWriter
-from msi.io.msireader import MsiReader
-
-
-class Test(unittest.TestCase):
-
- def setUp(self):
- self.msi = helpers.getFakeMsi()
- self.test_file_path = "test_msi.msi"
-
- def tearDown(self):
- # remove the hopefully written file
- os.remove(self.test_file_path)
-
- def test_read_and_write(self):
- reader = MsiReader()
- writer = MsiWriter(self.msi)
- writer.write(self.test_file_path)
- read_msi = reader.read(self.test_file_path)
-
- np.testing.assert_array_equal(self.msi.get_image(),
- read_msi.get_image(),
- "data array of msi stays same" +
- "after read and write")
- np.testing.assert_array_equal(
- self.msi.get_properties()["wavelengths"],
- read_msi.get_properties()["wavelengths"],
- "properties of msi stay same after read and write")
-
-
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_normalize.py b/Modules/Biophotonics/python/iMC/msi/test/test_normalize.py
deleted file mode 100644
index 72f2a844c6..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_normalize.py
+++ /dev/null
@@ -1,74 +0,0 @@
-'''
-Created on Aug 20, 2015
-
-@author: wirkert
-'''
-import unittest
-import numpy as np
-
-import msi.normalize as norm
-import msi.test.helpers as helpers
-
-
-class TestNormalize(unittest.TestCase):
-
- def setUp(self):
- self.specialmsi = helpers.getFakeMsi()
- # set one pixel to special values
- self.specialValue = np.arange(self.specialmsi.get_image().shape[-1]) * 2
- self.specialmsi.get_image()[2, 2, :] = self.specialValue
-
- def tearDown(self):
- pass
-
- def test_normalizeIQ(self):
- original_shape = self.specialmsi.get_image().shape # shape should stay
- # value 4.0 is in band 3
- desired_matrix = self.specialmsi.get_image() / 4.0
- # except for special value, where it is 8
- desired_matrix[2, 2, :] = self.specialmsi.get_image()[2, 2, :] / 6.0
- # the same after normalization
- iq_normalizer = norm.NormalizeIQ(3)
- iq_normalizer.normalize(self.specialmsi)
-
- self.assertEqual(self.specialmsi.get_image().shape, original_shape,
- "shape not changed by normalization")
- np.testing.assert_equal(self.specialmsi.get_image(),
- desired_matrix,
- "msi correctly normalized by iq")
-
- def test_normalizeMean(self):
- original_shape = self.specialmsi.get_image().shape # shape should stay
- desired_matrix = self.specialmsi.get_image() / 15.0
- desired_matrix[2, 2, :] = self.specialmsi.get_image()[2, 2, :] / 20.0
- # the same after normalization
- mean_normalizer = norm.NormalizeMean()
- mean_normalizer.normalize(self.specialmsi)
-
- self.assertEqual(self.specialmsi.get_image().shape, original_shape,
- "shape not changed by normalization")
- np.testing.assert_equal(self.specialmsi.get_image(),
- desired_matrix,
- "msi correctly normalized by mean")
-
- def test_normalizeMean_with_masked_elemnets(self):
- original_shape = self.specialmsi.get_image().shape # shape should stay
- # set mask so it masks the special value
- mask = np.zeros_like(self.specialmsi.get_image())
- mask [2, 2, :] = 1
- mask = mask.astype(bool)
- masked_msi_image = np.ma.MaskedArray(self.specialmsi.get_image(),
- mask=mask)
- self.specialmsi.set_image(masked_msi_image)
- desired_matrix = masked_msi_image / 15.0
- # the same after normalization
- mean_normalizer = norm.NormalizeMean()
- mean_normalizer.normalize(self.specialmsi)
-
- self.assertEqual(self.specialmsi.get_image().shape, original_shape,
- "shape not changed by normalization")
- np.testing.assert_equal(self.specialmsi.get_image(),
- desired_matrix,
- "msi correctly normalized by mean")
- np.testing.assert_equal(mask, self.specialmsi.get_image().mask)
-
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_nrrdreader.py b/Modules/Biophotonics/python/iMC/msi/test/test_nrrdreader.py
deleted file mode 100644
index da5083a125..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_nrrdreader.py
+++ /dev/null
@@ -1,31 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Mon Aug 10 16:43:31 2015
-
-@author: wirkert
-"""
-
-import unittest
-from msi.io.nrrdreader import NrrdReader
-import numpy as np
-
-
-class TestNrrdReader(unittest.TestCase):
-
- def setUp(self):
- self.nrrdReader = NrrdReader()
- self.msi = self.nrrdReader.read('./msi/data/testMsi.nrrd')
-
- def test_read_does_not_crash(self):
- # if we got this far, at least an image was read.
- self.assertTrue(len(self.msi.get_image().shape) == 3,
- "read image has correct basic shape dimensions")
- self.assertTrue(self.msi.get_image().shape[-1] == 5,
- "read image has correct number of image stacks")
- self.assertTrue(np.array_equal(self.msi.get_image()[2, 2, :],
- np.array([1, 2, 3, 4, 5])),
- "read image contains correct data")
-
- def test_read_non_existing_image_returns_exception(self):
- with self.assertRaises(RuntimeError):
- self.nrrdReader.read("./msi/data/asdf.nrrd")
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_nrrdwriter.py b/Modules/Biophotonics/python/iMC/msi/test/test_nrrdwriter.py
deleted file mode 100644
index c442b76159..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_nrrdwriter.py
+++ /dev/null
@@ -1,54 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug 13 09:52:47 2015
-
-@author: wirkert
-"""
-
-import unittest
-import os
-import numpy as np
-
-import msi.msimanipulations as msimani
-from msi.io.nrrdreader import NrrdReader
-from msi.io.nrrdwriter import NrrdWriter
-from msi.test import helpers
-
-
-class TestNrrdWriter(unittest.TestCase):
-
- def setUp(self):
- # setup file and the path where it shall be written to
- self.msi = helpers.getFakeMsi()
- self.fileUriToWrite = "testfile.nrrd"
-
- def tearDown(self):
- # remove the hopefully written file
- os.remove(self.fileUriToWrite)
-
- def test_imageWriterCreatesFile(self):
- writer = NrrdWriter(self.msi)
- writer.write(self.fileUriToWrite)
- self.assertTrue(os.path.isfile(self.fileUriToWrite),
- "file was written to disk")
-
- def test_imageWriterCreatesCorrectFile(self):
-
- writer = NrrdWriter(self.msi)
- writer.write(self.fileUriToWrite)
-
- reader = NrrdReader()
- msi = reader.read(self.fileUriToWrite)
- self.assertTrue(msi == helpers.getFakeMsi(),
- "image correctly written and read")
-
- def test_write_one_d_image_works(self):
- writer = NrrdWriter(self.msi)
- msimani.calculate_mean_spectrum(self.msi)
- writer.write(self.fileUriToWrite)
-
- reader = NrrdReader()
- msi = reader.read(self.fileUriToWrite)
- np.testing.assert_array_equal(msi.get_image(),
- np.array([1, 2, 3, 4, 5]),
- "1d image correctly written and read")
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_spectrometerreader.py b/Modules/Biophotonics/python/iMC/msi/test/test_spectrometerreader.py
deleted file mode 100644
index b993a434bf..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_spectrometerreader.py
+++ /dev/null
@@ -1,47 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 7 18:02:08 2015
-
-@author: wirkert
-"""
-
-import unittest
-
-from msi.io.spectrometerreader import SpectrometerReader
-
-
-class TestSpectrometer(unittest.TestCase):
-
- def setUp(self):
- self.exampleFileName = "./msi/data/Transmission_15-49-35-978_filter700nm.txt"
- self.reader = SpectrometerReader()
-
- def tearDown(self):
- pass
-
- def test_create(self):
- self.assertTrue(True, "Created empty reader during setup")
-
- def test_read_spectrum(self):
- msi = self.reader.read(self.exampleFileName)
-
- self.assertAlmostEqual(msi.get_image()[0],
- 70.50,
- msg="first spectral element is read correctly")
- self.assertAlmostEqual(msi.get_image()[-1],
- 68.13,
- msg="last sprectral element is read correctly")
- self.assertTrue(msi.get_image().size == 2048,
- "correct number of elements read")
-
- def test_read_wavelengths(self):
- msi = self.reader.read(self.exampleFileName)
-
- self.assertAlmostEqual(msi.get_wavelengths()[0],
- 187.255 * 10 ** -9,
- msg="first wavelength element is read correctly")
- self.assertAlmostEqual(msi.get_wavelengths()[-1],
- 1103.852 * 10 ** -9,
- msg="last wavelength element is read correctly")
- self.assertTrue(msi.get_wavelengths().size == 2048,
- "correct number of elements read")
diff --git a/Modules/Biophotonics/python/iMC/msi/test/test_tiffwriter.py b/Modules/Biophotonics/python/iMC/msi/test/test_tiffwriter.py
deleted file mode 100644
index a2e880b80c..0000000000
--- a/Modules/Biophotonics/python/iMC/msi/test/test_tiffwriter.py
+++ /dev/null
@@ -1,40 +0,0 @@
-
-import unittest
-import os
-
-from msi.io.tiffwriter import TiffWriter
-from msi.io.tiffreader import TiffReader
-from msi.test import helpers
-
-
-class TestTiffWriter(unittest.TestCase):
-
- def setUp(self):
- # setup file and the path where it shall be written to
- self.msi = helpers.getFakeMsi()
- self.msi.set_image(self.msi.get_image())
- self.fileUriToWrite = os.path.join(os.getcwd(), "testfiles")
-
- def tearDown(self):
- # remove the hopefully written files
- folder, file_prefix = os.path.split(self.fileUriToWrite)
- image_files = [f for f in os.listdir(folder) if
- os.path.isfile(os.path.join(folder, f))]
- image_files = [f for f in image_files if f.startswith(file_prefix)]
- # expand to full path
- image_files = [os.path.join(folder, f) for f in image_files]
- for f in image_files:
- os.remove(f)
-
- def test_imageWriterCreatesFile(self):
- writer = TiffWriter(self.msi, convert_to_nm=False)
- writer.write(self.fileUriToWrite)
-
- def test_imageWriterCreatesCorrectFile(self):
- writer = TiffWriter(self.msi, convert_to_nm=False)
- writer.write(self.fileUriToWrite)
-
- reader = TiffReader(shift_bits=0)
- msi = reader.read(self.fileUriToWrite)
- self.assertTrue(msi == helpers.getFakeMsi(),
- "image correctly written and read")
diff --git a/Modules/Biophotonics/python/iMC/regression/__init__.py b/Modules/Biophotonics/python/iMC/regression/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/regression/domain_adaptation.py b/Modules/Biophotonics/python/iMC/regression/domain_adaptation.py
deleted file mode 100644
index 316f378aa9..0000000000
--- a/Modules/Biophotonics/python/iMC/regression/domain_adaptation.py
+++ /dev/null
@@ -1,88 +0,0 @@
-'''
-Created on Oct 20, 2015
-
-@author: wirkert
-'''
-
-import numpy as np
-from sklearn.cross_validation import KFold
-from sklearn.grid_search import GridSearchCV
-from sklearn.linear_model.logistic import LogisticRegressionCV
-from sklearn.ensemble.forest import RandomForestClassifier
-
-
-def prepare_data_for_weights_estimation(X_s, X_t):
- nr_s = X_s.shape[0]
- nr_t = X_t.shape[0]
- source_labels = np.zeros(nr_s)
- target_labels = np.ones(nr_t)
- X_all = np.concatenate((X_s, X_t))
- all_labels = np.concatenate((source_labels, target_labels))
- return X_all, all_labels
-
-
-def estimate_weights_random_forests(X_s, X_t, X_w):
-
- X_all, all_labels = prepare_data_for_weights_estimation(X_s, X_t)
- # train logistic regression
- kf = KFold(X_all.shape[0], 10, shuffle=True)
- param_grid_rf = [
- {"n_estimators": np.array([500]),
- "max_depth": np.array([6]),
- # "max_features": np.array([1, 2, 4, 8, 16]),
- "min_samples_leaf": np.array([100])}]
- rf = GridSearchCV(RandomForestClassifier(50, max_depth=10,
- class_weight="auto", n_jobs=-1),
- param_grid_rf, cv=kf, n_jobs=-1)
- rf = RandomForestClassifier(100, max_depth=6, min_samples_leaf=200,
- class_weight="auto", n_jobs=-1)
- rf.fit(X_all, all_labels)
- # print "best parameters for rf weights determination: ", rf.best_estimator_
- probas = rf.predict_proba(X_w)
- weights = probas[:, 1] / probas[:, 0]
- return weights
-
-
-def estimate_weights_logistic_regresssion(X_s, X_t):
- """ estimate a logistic regressor to predict the probability of a sample
- to be generated by one class or the other.
- If one class is over or under represented weights will be adapted.
-
- Parameters:
- X_s: samples from the source domain
- X_t: samples from the target domain
-
- Returns:
- weigths for X_s """
- X_all, all_labels = prepare_data_for_weights_estimation(X_s, X_t)
-
- kf = KFold(X_all.shape[0], 10, shuffle=True)
- best_lr = LogisticRegressionCV(class_weight="auto",
- Cs=np.logspace(4, 8, 10),
- fit_intercept=False)
- best_lr.fit(X_all, all_labels)
-
- weights = X_s.shape[0] / X_t.shape[0] * np.exp(np.dot(X_s, best_lr.coef_.T)
- + best_lr.intercept_)
- return weights
-
-
-def resample(X, y, w, nr_samples=None):
- """bootstrapping: resample with replacement according to weights
-
- Returns:
- (X_new, w_new): the chosen samples and the new weights.
- by design these new weights are all equal to 1."""
- if (nr_samples is None):
- nr_samples = X.shape[0]
- w = w / np.sum(w) # normalize
- # create index array with samples to draw:
- total_nr_samples = X.shape[0] # nr total samples
- chosen_samples = np.random.choice(total_nr_samples,
- size=nr_samples,
- replace=True, p=np.squeeze(w))
- if y.ndim == 1:
- y_chosen = y[chosen_samples]
- else:
- y_chosen = y[chosen_samples, :]
- return X[chosen_samples, :], y_chosen, np.ones(nr_samples)
diff --git a/Modules/Biophotonics/python/iMC/regression/estimation.py b/Modules/Biophotonics/python/iMC/regression/estimation.py
deleted file mode 100644
index 7b84e88974..0000000000
--- a/Modules/Biophotonics/python/iMC/regression/estimation.py
+++ /dev/null
@@ -1,130 +0,0 @@
-
-
-"""
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-"""
-'''
-Created on Oct 21, 2015
-
-@author: wirkert
-'''
-
-import math
-import logging
-import time
-
-import tensorflow as tf
-import numpy as np
-import SimpleITK as sitk
-
-from regression.tensorflow_estimator import multilayer_perceptron, cnn
-import msi.imgmani as imgmani
-
-
-def SAMDistance(x, y):
- return math.acos(np.dot(x, y) / (np.linalg.norm(x) * np.linalg.norm(y)))
-
-
-def estimate_image(msi, regressor):
- """given an Msi and an regressor estimate the parmaeters for this image
-
- Paramters:
- msi: multi spectral image
- regressor: regressor, must implement the predict method"""
-
- # estimate parameters
- collapsed_msi = imgmani.collapse_image(msi.get_image())
- # in case of nan values: set to 0
- collapsed_msi[np.isnan(collapsed_msi)] = 0.
- collapsed_msi[np.isinf(collapsed_msi)] = 0.
-
- start = time.time()
- estimated_parameters = regressor.predict(collapsed_msi)
- end = time.time()
- estimation_time = end - start
- logging.info("time necessary for estimating image parameters: " +
- str(estimation_time) + "s")
- # restore shape
- feature_dimension = 1
- if len(estimated_parameters.shape) > 1:
- feature_dimension = estimated_parameters.shape[-1]
-
- estimated_paramters_as_image = np.reshape(
- estimated_parameters, (msi.get_image().shape[0],
- msi.get_image().shape[1],
- feature_dimension))
- # save as sitk nrrd.
- sitk_img = sitk.GetImageFromArray(estimated_paramters_as_image,
- isVector=True)
- return sitk_img, estimation_time
-
-
-def estimate_image_tensorflow(msi, model_checkpoint_dir):
- # estimate parameters
- collapsed_msi = imgmani.collapse_image(msi.get_image())
- # in case of nan values: set to 0
- collapsed_msi[np.isnan(collapsed_msi)] = 0.
- collapsed_msi[np.isinf(collapsed_msi)] = 0.
-
-
- tf.reset_default_graph()
-
- keep_prob = tf.placeholder("float")
- nr_wavelengths = len(msi.get_wavelengths())
- x = tf.placeholder("float", [None, nr_wavelengths, 1, 1])
-
- x_test_image = np.reshape(msi.get_image(), [-1, nr_wavelengths, 1, 1])
-
- # Construct the desired model
- # pred, regularizers = multilayer_perceptron(x, nr_wavelengths, 100, 1,
- # keep_prob)
- pred = cnn(x, 1, keep_prob)
-
- # Initializing the variables
- init = tf.initialize_all_variables()
-
- saver = tf.train.Saver()
-
- with tf.Session() as sess:
- sess.run(tf.initialize_all_variables())
- # restore model:
- ckpt = tf.train.get_checkpoint_state(model_checkpoint_dir)
-
- if ckpt and ckpt.model_checkpoint_path:
- saver.restore(sess, ckpt.model_checkpoint_path)
-
- start = time.time()
- estimated_parameters = pred.eval({x: x_test_image,
- keep_prob:1.0})
- end = time.time()
- estimation_time = end - start
- logging.info("time necessary for estimating image parameters: " +
- str(estimation_time) + "s")
- # restore shape
- feature_dimension = 1
- if len(estimated_parameters.shape) > 1:
- feature_dimension = estimated_parameters.shape[-1]
-
- estimated_paramters_as_image = np.reshape(
- estimated_parameters, (msi.get_image().shape[0],
- msi.get_image().shape[1],
- feature_dimension))
- # save as sitk nrrd.
- sitk_img = sitk.GetImageFromArray(estimated_paramters_as_image,
- isVector=True)
-
- return sitk_img, estimation_time
-
-
-def standard_score(estimator, X, y):
- """our standard scoring method is the median absolute error"""
- return np.median(np.abs(estimator.predict(X) - y))
-
diff --git a/Modules/Biophotonics/python/iMC/regression/linear.py b/Modules/Biophotonics/python/iMC/regression/linear.py
deleted file mode 100644
index dcd96977a7..0000000000
--- a/Modules/Biophotonics/python/iMC/regression/linear.py
+++ /dev/null
@@ -1,95 +0,0 @@
-'''
-Created on Oct 19, 2015
-
-@author: wirkert
-'''
-
-import numpy as np
-from scipy.interpolate import interp1d
-
-from mc.usuag import get_haemoglobin_extinction_coefficients
-
-class LinearSaO2Unmixing(object):
- '''
- classdocs
- '''
-
- def __init__(self):
- # oxygenated haemoglobin extinction coefficients
- eHb02 = 0
- eHb = 0
-
- # oxygenated haemoglobin extinction coefficients
- eHbO2 = np.array([34772.8,
- 27840.93333,
- 23748.8 ,
- 21550.8 ,
- 21723.46667,
- 28064.8 ,
- 39131.73333,
- 45402.93333,
- 42955.06667,
- 40041.73333,
- 42404.4 ,
- 36333.6 ,
- 22568.26667,
- 6368.933333,
- 1882.666667,
- 1019.333333,
- 664.6666667,
- 473.3333333,
- 376.5333333,
- 327.2 ,
- 297.0666667],)
- # deoxygenated haemoglobin extinction coefficients
- eHb = [18031.73333 ,
- 15796.8 ,
- 17365.33333 ,
- 21106.53333 ,
- 26075.06667 ,
- 32133.2 ,
- 39072.66667 ,
- 46346.8 ,
- 51264 ,
- 50757.33333 ,
- 45293.33333 ,
- 36805.46667 ,
- 26673.86667 ,
- 17481.73333 ,
- 10210.13333 ,
- 7034 ,
- 5334.533333 ,
- 4414.706667 ,
- 3773.96 ,
- 3257.266667 ,
- 2809.866667]
- nr_total_wavelengths = len(eHb)
- # to account for scattering losses we allow a constant offset
- scattering = np.ones(nr_total_wavelengths)
- # put eHbO2, eHb and scattering term in one measurement matrix
- self.H = np.vstack((eHbO2, eHb, scattering)).T
- self.lsq_solution_matrix = np.dot(np.linalg.inv(np.dot(self.H.T,
- self.H)),
- self.H.T)
-
-
- def fit(self, X, y, weights=None):
- """only implemented to fit to the standard sklearn framework."""
- pass
-
- def predict(self, X):
- """predict like in sklearn:
-
- Parameters:
- X: nrsamples x nr_features matrix of samples to predict for
- regression
-
- Returns:
- y: array of shape [nr_samples] with values for predicted
- oxygenation """
- # do least squares estimation
- oxy_test, deoxy, s = np.dot(self.lsq_solution_matrix, X.T)
- # calculate oxygenation = oxygenated blood / total blood
- saO2 = oxy_test / (oxy_test + deoxy)
-
- return np.clip(saO2, 0., 1.)
diff --git a/Modules/Biophotonics/python/iMC/regression/preprocessing.py b/Modules/Biophotonics/python/iMC/regression/preprocessing.py
deleted file mode 100644
index 494f7a82db..0000000000
--- a/Modules/Biophotonics/python/iMC/regression/preprocessing.py
+++ /dev/null
@@ -1,94 +0,0 @@
-'''
-Created on Oct 26, 2015
-
-@author: wirkert
-'''
-
-import numpy as np
-import pandas as pd
-from sklearn.preprocessing import Normalizer
-
-
-def preprocess2(df, nr_samples=None, snr=None, movement_noise_sigma=None,
- magnification=None, bands_to_sortout=None):
-
- # first set 0 reflectances to nan
- df["reflectances"] = df["reflectances"].replace(to_replace=0.,
- value=np.nan)
- # remove nan
- df.dropna(inplace=True)
-
- # extract nr_samples samples from data
- if nr_samples is not None:
- df = df.sample(nr_samples)
-
- # get reflectance and oxygenation
- X = df.reflectances
- if bands_to_sortout is not None and bands_to_sortout.size > 0:
- X.drop(X.columns[bands_to_sortout], axis=1, inplace=True)
- snr = np.delete(snr, bands_to_sortout)
- X = X.values
- y = df.layer0[["sao2", "vhb"]]
-
- # do data magnification
- if magnification is not None:
- X_temp = X
- y_temp = y
- for i in range(magnification - 1):
- X = np.vstack((X, X_temp))
- y = pd.concat([y, y_temp])
-
- # add noise to reflectances
- camera_noise = 0.
- if snr is not None:
- sigmas = X / snr
- noises = np.random.normal(loc=0., scale=1, size=X.shape)
- camera_noise = sigmas*noises
-
- movement_noise = 0.
- if movement_noise_sigma is not None:
- nr_bands = X.shape[1]
- nr_samples = X.shape[0]
- # we assume no correlation between neighboring bands
- CORRELATION_COEFFICIENT = 0.0
- movement_variance = movement_noise_sigma ** 2
- movement_variances = np.ones(nr_bands) * movement_variance
- movement_covariances = np.ones(nr_bands-1) * CORRELATION_COEFFICIENT * \
- movement_variance
- movement_covariance_matrix = np.diag(movement_variances) + \
- np.diag(movement_covariances, -1) + \
- np.diag(movement_covariances, 1)
- # percentual sample errors
- sample_errors_p = np.random.multivariate_normal(mean=np.zeros(nr_bands),
- cov=movement_covariance_matrix,
- size=nr_samples)
- # errors w.r.t. the curve height.
- movement_noise = X * sample_errors_p
-
- X += camera_noise + movement_noise
-
- X = np.clip(X, 0.00001, 1.)
- # do normalizations
- X = normalize(X)
- return X, y
-
-
-def preprocess(batch, nr_samples=None, snr=None, movement_noise_sigma=None,
- magnification=None, bands_to_sortout=None):
- X, y = preprocess2(batch, nr_samples, snr, movement_noise_sigma,
- magnification, bands_to_sortout)
-
- return X, y["sao2"]
-
-
-def normalize(X):
- # normalize reflectances
- normalizer = Normalizer(norm='l1')
- X = normalizer.transform(X)
- # reflectances to absorption
- absorptions = -np.log(X)
- X = absorptions
- # get rid of sorted out bands
- normalizer = Normalizer(norm='l2')
- X = normalizer.transform(X)
- return X
diff --git a/Modules/Biophotonics/python/iMC/regression/tensorflow_dataset.py b/Modules/Biophotonics/python/iMC/regression/tensorflow_dataset.py
deleted file mode 100644
index 4bc2065aac..0000000000
--- a/Modules/Biophotonics/python/iMC/regression/tensorflow_dataset.py
+++ /dev/null
@@ -1,83 +0,0 @@
-"""Functions for downloading and reading ipcai data."""
-from __future__ import print_function
-
-import os
-
-import numpy
-import pandas as pd
-
-from regression.preprocessing import preprocess
-
-
-class DataSet(object):
- def __init__(self, images, labels, fake_data=False):
- if fake_data:
- self._num_examples = 10000
- else:
- assert images.shape[0] == labels.shape[0], (
- "images.shape: %s labels.shape: %s" % (images.shape,
- labels.shape))
- self._num_examples = images.shape[0]
- images = images.astype(numpy.float32)
- self._images = images
- self._labels = labels
- if self._labels.ndim == 1:
- self._labels = self._labels[:, numpy.newaxis]
- self._epochs_completed = 0
- self._index_in_epoch = 0
-
- @property
- def images(self):
- return self._images
-
- @property
- def labels(self):
- return self._labels
-
- @property
- def num_examples(self):
- return self._num_examples
-
- @property
- def epochs_completed(self):
- return self._epochs_completed
-
- def next_batch(self, batch_size, fake_data=False):
- """Return the next `batch_size` examples from this data set."""
- if fake_data:
- fake_image = [1.0 for _ in xrange(784)]
- fake_label = 0
- return [fake_image for _ in xrange(batch_size)], [
- fake_label for _ in xrange(batch_size)]
- start = self._index_in_epoch
- self._index_in_epoch += batch_size
- if self._index_in_epoch > self._num_examples:
- # Finished epoch
- self._epochs_completed += 1
- # Shuffle the data
- perm = numpy.arange(self._num_examples)
- numpy.random.shuffle(perm)
- self._images = self._images[perm]
- self._labels = self._labels[perm]
-
- # Start next epoch
- start = 0
- self._index_in_epoch = batch_size
- assert batch_size <= self._num_examples
- end = self._index_in_epoch
- return self._images[start:end], self._labels[start:end]
-
-
-def read_data_set(dataframe_filename, fake_data=False):
-
- if fake_data:
- data_set = DataSet([], [], fake_data=True)
- return data_set
-
- df_data_set = pd.read_csv(os.path.join(dir, dataframe_filename),
- header=[0, 1])
-
- data_set_images, data_set_labels = preprocess(df_data_set, snr=10.)
- data_set_labels = data_set_labels.values
- data_set = DataSet(data_set_images, data_set_labels)
- return data_set
diff --git a/Modules/Biophotonics/python/iMC/regression/tensorflow_estimator.py b/Modules/Biophotonics/python/iMC/regression/tensorflow_estimator.py
deleted file mode 100644
index b5025563ec..0000000000
--- a/Modules/Biophotonics/python/iMC/regression/tensorflow_estimator.py
+++ /dev/null
@@ -1,88 +0,0 @@
-
-
-import tensorflow as tf
-
-
-def weight_variable(shape):
- initial = tf.truncated_normal(shape, stddev=0.1)
- return tf.Variable(initial)
-
-
-def bias_variable(shape):
- initial = tf.constant(0.1, shape=shape)
- return tf.Variable(initial)
-
-
-def conv2d(x, W, padding='SAME'):
- return tf.nn.conv2d(x, W, strides=[1, 1, 1, 1], padding=padding)
-
-
-def max_pool1d(x, poolsize=2):
- return tf.nn.max_pool(x, ksize=[1, poolsize, 1, 1],
- strides=[1, poolsize, 1, 1], padding='SAME')
-
-
-def add_cnn_layer(input, n_inputs, n_outputs, kernel_size, padding='SAME'):
- #w = weight_variable([n_inputs, n_outputs])
- #b = bias_variable([n_outputs])
- W = weight_variable([kernel_size, 1, n_inputs, n_outputs])
- b = bias_variable([n_outputs])
- # Hidden layer with RELU activation
- #new_layer = tf.nn.relu(tf.add(tf.matmul(input, w), b))
- h_conv = tf.nn.relu(conv2d(input, W, padding=padding) + b)
- # Add dropout regularization
- #new_layer_with_dropout = tf.nn.dropout(new_layer, keep_prob)
- h_pool = max_pool1d(h_conv)
- return h_pool, W
-
-
-def add_fully_connected_layer(_X, n_inputs, n_outputs, keep_prob):
- W = weight_variable([n_inputs, n_outputs])
- b = bias_variable([n_outputs])
- # Hidden layer with RELU activation
- new_layer = tf.nn.relu(tf.add(tf.matmul(_X, W), b))
- # Add dropout regularization
- new_layer_with_dropout = tf.nn.dropout(new_layer, keep_prob)
-
- return new_layer_with_dropout, W
-
-
-# this is my exemplary convolutional network
-def cnn(_X, n_classes, keep_prob):
- # two convolutional layers
- layer_1, _ = add_cnn_layer(_X, 1, 32, 3, padding='VALID')
- layer_2, _ = add_cnn_layer(layer_1, 32, 32, 2, padding='VALID')
- # flatten last one to be able to apply it to fully connected layer
- final_number_of_dimensions = 1*32
- layer_2_flat = tf.reshape(layer_2, [-1, final_number_of_dimensions])
-
- # fully connected layer to bring information together
- fc_dim = 5
- h_fc1_drop, _ = add_fully_connected_layer(layer_2_flat,
- final_number_of_dimensions,
- fc_dim, keep_prob)
-
- # return linear output layer
- W_fc2 = weight_variable([fc_dim, n_classes])
- b_fc2 = bias_variable([n_classes])
- return tf.matmul(h_fc1_drop, W_fc2) + b_fc2
-
-
-# and this is the simpler multilayer perceptron
-def multilayer_perceptron(x, n_bands, n_hidden, n_classes, keep_prob):
- flattend_input = tf.reshape(x, [-1, n_bands])
- layer_1, W_1 = add_fully_connected_layer(flattend_input, n_bands, n_hidden,
- keep_prob)
- layer_2, W_2 = add_fully_connected_layer(layer_1, n_hidden, n_hidden,
- keep_prob)
- last_hidden_layer, W_3 = add_fully_connected_layer(layer_2, n_hidden, n_hidden,
- keep_prob)
-
- W_out = weight_variable([n_hidden, n_classes])
- b_out = bias_variable([n_classes])
-
- regularizers = (tf.nn.l2_loss(W_1) + tf.nn.l2_loss(W_2) +
- tf.nn.l2_loss(W_3) + tf.nn.l2_loss(W_out))
-
- return tf.matmul(last_hidden_layer, W_out) + b_out, regularizers
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/basic_checks/__init__.py b/Modules/Biophotonics/python/iMC/scripts/basic_checks/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/scripts/basic_checks/script_evaluate_color_checkerboard.py b/Modules/Biophotonics/python/iMC/scripts/basic_checks/script_evaluate_color_checkerboard.py
deleted file mode 100644
index fcf5bea72e..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/basic_checks/script_evaluate_color_checkerboard.py
+++ /dev/null
@@ -1,266 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 14 11:09:18 2015
-
-@author: wirkert
-"""
-
-
-import Image
-import ImageEnhance
-import logging
-import datetime
-import copy
-
-from scipy.interpolate import interp1d
-from sklearn.preprocessing import normalize
-from sklearn.metrics import r2_score
-
-from msi.io.nrrdreader import NrrdReader
-import msi.normalize as norm
-from ipcai2016.tasks_common import *
-import commons
-from ipcai2016 import tasks_mc
-import msi.plot as msiplot
-from msi.io.spectrometerreader import SpectrometerReader
-from msi.normalize import standard_normalizer
-from msi.io.tiffringreader import TiffRingReader
-
-TiffRingReader.RESIZE_FACTOR = 0.5
-
-sc = commons.ScriptCommons()
-
-sc.add_dir("COLORCHECKER_DATA",
- os.path.join(sc.get_dir("DATA_FOLDER"), "colorchecker_laparoscope"))
-
-sc.add_dir("COLORCHECKER_RESULTS",
- os.path.join(sc.get_dir("RESULTS_FOLDER"),
- "colorchecker_laparoscope"))
-
-sc.add_dir("FLAT_FOLDER",
- os.path.join(sc.get_dir("DATA_FOLDER"),
- "colorchecker_laparoscope_flatfield"))
-
-sc.add_dir("SPECTROMETER_REFERENCE_DATA",
- os.path.join(sc.get_dir("DATA_FOLDER"),
- "spectrometer_reflectance_new"))
-
-sc.add_dir("FILTER_TRANSMISSIONS",
- os.path.join(sc.get_dir("DATA_FOLDER"),
- "filter_transmissions"))
-
-
-class CheckColorCheckerBoards(luigi.Task):
- image_name = luigi.Parameter()
-
- def requires(self):
- return Flatfield(flatfield_folder=sc.get_full_dir("FLAT_FOLDER")), \
- SingleMultispectralImage(image=self.image_name), \
- Dark(dark_folder=sc.get_full_dir("DARK_FOLDER")), \
- SpectrometerToSpectrocam(spectrometer_measurement=
- os.path.join(sc.get_full_dir("SPECTROMETER_REFERENCE_DATA"),
- os.path.split(self.image_name)[1][0:8] + ".txt"))
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("COLORCHECKER_RESULTS"),
- os.path.split(self.image_name)[1] +
- "_" + "_color_check" + ".png"))
-
- def run(self):
-
- print "... read data"
-
- segmentation_file = os.path.join(
- sc.get_full_dir("COLORCHECKER_DATA"), "seg.tiff")
- segmentation_file2 = os.path.join(
- sc.get_full_dir("COLORCHECKER_DATA"), "seg2.tiff")
-
- nrrd_reader = NrrdReader()
- tiff_ring_reader = TiffRingReader()
- # read the flatfield
- flat = nrrd_reader.read(self.input()[0].path)
- dark = nrrd_reader.read(self.input()[2].path)
- # read the msi
- nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
- msi, segmentation = tiff_ring_reader.read(self.input()[1].path,
- nr_filters,
- segmentation=segmentation_file)
- msi_copy = copy.deepcopy(msi) # copy to be able to apply both
- # segmentations
- msimani.apply_segmentation(msi, segmentation)
- msi2, segmentation2 = tiff_ring_reader.read(self.input()[1].path,
- nr_filters,
- segmentation=segmentation_file2)
- msimani.apply_segmentation(msi2, segmentation2)
-
- msimani.apply_segmentation(msi_copy, segmentation + segmentation2)
-
- # read the spectrometer measurement
- msi_spectrometer = nrrd_reader.read(self.input()[3].path)
-
- # correct by flatfield and dark image
- #msimani.image_correction(msi, flat, dark)
- #msimani.image_correction(msi2, flat, dark)
- #msimani.image_correction(msi_copy, flat, dark)
- msimani.dark_correction(msi, dark)
- msimani.dark_correction(msi2, dark)
- msimani.dark_correction(msi_copy, dark)
-
- # create artificial rgb
- rgb_image = msi_copy.get_image()[:, :, [2, 3, 1]]
- rgb_image /= np.max(rgb_image)
- rgb_image *= 255.
-
- # preprocess the image
- # sortout unwanted bands
- print "... apply normalizations"
- # normalize to get rid of lighting intensity
- norm.standard_normalizer.normalize(msi)
- norm.standard_normalizer.normalize(msi2)
-
- print "... plot"
-
- # plot of the rgb image
- rgb_image = rgb_image.astype(np.uint8)
- im = Image.fromarray(rgb_image, 'RGB')
- enh_brightness = ImageEnhance.Brightness(im)
- im = enh_brightness.enhance(2.)
- plotted_image = np.array(im)
-
- plt.figure()
- f, (ax_rgb, ax_spectra) = plt.subplots(1, 2)
- plot_image(plotted_image, ax_rgb, title="false rgb")
-
- msiplot.plotMeanError(msi, ax_spectra)
- msiplot.plotMeanError(msi2, ax_spectra)
-
- standard_normalizer.normalize(msi_spectrometer)
- msiplot.plot(msi_spectrometer, ax_spectra)
-
- mean_spectrometer = msi_spectrometer.get_image()
- mean_msi = msimani.calculate_mean_spectrum(msi).get_image()
- mean_msi2 = msimani.calculate_mean_spectrum(msi2).get_image()
- r2_msi = r2_score(mean_spectrometer, mean_msi)
- r2_msi2 = r2_score(mean_spectrometer, mean_msi2)
-
- ax_spectra.legend(["spectrocam 1 r2: " + str(r2_msi),
- "spectrocam 2 r2: " + str(r2_msi2), "spectrometer"],
- bbox_to_anchor=(0., 1.02, 1., .102), loc=3,
- ncol=2, mode="expand", borderaxespad=0.,
- fontsize=5)
-
- plt.savefig(self.output().path,
- dpi=250, bbox_inches='tight')
-
-
-class CameraQEFile(luigi.Task):
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("DATA_FOLDER"),
- "camera_quantum_efficiency.csv"))
-
-
-class SpectrometerToSpectrocam(luigi.Task):
-
- spectrometer_measurement = luigi.Parameter()
-
- def requires(self):
- # all wavelengths must have been measured for transmission and stored in
- # wavelength.txt files (e.g. 470.txt)
- filenames = ((sc.other["RECORDED_WAVELENGTHS"] * 10**9).astype(int)).astype(str)
- filenames = map(lambda name: tasks_mc.FilterTransmission(os.path.join(sc.get_full_dir("FILTER_TRANSMISSIONS"),
- name) + ".txt"),
- filenames)
-
- return tasks_mc.SpectrometerFile(self.spectrometer_measurement), \
- filenames, CameraQEFile()
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- os.path.split(self.spectrometer_measurement)[1] +
- "_spectrocam.nrrd"))
-
- def run(self):
- # load spectrometer measurement
- spectrometer_reader = SpectrometerReader()
- spectrometer_msi = spectrometer_reader.read(self.input()[0].path)
-
- # the wavelengths recorded by the spectrometer
- spectrometer_wavelengths = spectrometer_msi.get_wavelengths()
-
- spectrometer_white = spectrometer_reader.read(os.path.join(
- sc.get_full_dir("DATA_FOLDER"), "spectrometer_whitebalance",
- "white_IL_1_OO_20ms.txt"))
- spectrometer_dark = spectrometer_reader.read(os.path.join(
- sc.get_full_dir("DATA_FOLDER"), "spectrometer_whitebalance",
- "dark_1_OO_20ms.txt"))
- msimani.dark_correction(spectrometer_white, spectrometer_dark)
- white_interpolator = interp1d(spectrometer_white.get_wavelengths(),
- spectrometer_white.get_image(),
- bounds_error=False, fill_value=0.)
- white_interpolated = white_interpolator(spectrometer_wavelengths)
-
- camera_qe = pd.read_csv(self.input()[2].path)
- camera_qe_interpolator = interp1d(camera_qe["wavelengths"] * 10**-9,
- camera_qe["quantum efficiency"],
- bounds_error=False,
- fill_value=0.)
- camera_qe_interpolated = \
- camera_qe_interpolator(spectrometer_wavelengths)
-
- # camera batch creation:
- new_reflectances = []
- for band in self.input()[1]:
- df_filter = pd.read_csv(band.path)
- interpolator = interp1d(df_filter["wavelengths"],
- df_filter["reflectances"],
- assume_sorted=False, bounds_error=False)
- # use this to create new reflectances
- interpolated_filter = interpolator(spectrometer_wavelengths)
- # if a wavelength cannot be interpolated, set it to 0
- interpolated_filter = np.nan_to_num(interpolated_filter)
- # account for cameras quantum efficiency
- interpolated_filter *= camera_qe_interpolated * white_interpolated
- # normalize band response
- #normalize(interpolated_filter.reshape(1, -1), norm='l1', copy=False)
- folded_reflectance = np.dot(spectrometer_msi.get_image(),
- interpolated_filter)
- new_reflectances.append(folded_reflectance)
- plt.plot(interpolated_filter)
- new_reflectances = np.array(new_reflectances).T
- spectrometer_msi.set_image(new_reflectances,
- wavelengths=sc.other["RECORDED_WAVELENGTHS"])
-
- # write it
- nrrd_writer = NrrdWriter(spectrometer_msi)
- nrrd_writer.write(self.output().path)
-
-if __name__ == '__main__':
-
- # create a folder for the results if necessary
- sc.set_root("/media/wirkert/data/Data/2020_Current_Works/")
- sc.create_folders()
-
- # root folder there the data lies
- logging.basicConfig(filename=os.path.join(sc.get_full_dir("LOG_FOLDER"),
- "color_checker" +
- str(datetime.datetime.now()) +
- '.log'), level=logging.INFO)
- luigi.interface.setup_interface_logging()
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- logger = logging.getLogger()
- logger.addHandler(ch)
-
- sch = luigi.scheduler.CentralPlannerScheduler()
- w = luigi.worker.Worker(scheduler=sch)
-
- files = get_image_files_from_folder(sc.get_full_dir("COLORCHECKER_DATA"),
- suffix="F0.tiff", fullpath=True)
-
- for f in files:
- main_task = CheckColorCheckerBoards(image_name=f)
- w.add(main_task)
-
- w.run()
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/commons.py b/Modules/Biophotonics/python/iMC/scripts/commons.py
deleted file mode 100644
index 48e060132c..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/commons.py
+++ /dev/null
@@ -1,97 +0,0 @@
-"""
-This file contains a singleton class which manages the paths set for evaluating
-the scripts.
-
-Also it contains some utility methods.
-"""
-
-import os
-
-import numpy as np
-
-
-class ScriptCommons(object):
- """
- The commonly shared paths to the data/log/results... folders.
- + additional commonly available data as recorded wavelengths
- this is a singleton pattern copied from
- http://python-3-patterns-idioms-test.readthedocs.org/en/latest/Singleton.html
- """
-
- class __ScriptCommons_Singleton:
-
- def __init__(self):
-
- self.root = os.path.join("..", "..")
-
- self.dirs = {"LOG_FOLDER": "log",
- "DATA_FOLDER": "data",
- "RESULTS_FOLDER": "results"}
-
- self.dirs["FLAT_FOLDER"] = os.path.join(self.dirs["DATA_FOLDER"],
- "flatfields")
- self.dirs["DARK_FOLDER"] = os.path.join(self.dirs["DATA_FOLDER"],
- "dark")
-
- self.dirs["INTERMEDIATES_FOLDER"] = os.path.join(
- self.dirs["RESULTS_FOLDER"], "intermediate")
-
- self.dirs["MC_DATA_FOLDER"] = os.path.join(
- self.dirs["INTERMEDIATES_FOLDER"], "mc_data")
-
- self.other = {"RECORDED_WAVELENGTHS": np.array([580, 470,
- 660, 560,
- 480, 511,
- 600, 700])
- * 10 ** -9}
-
- def create_folders(self):
- """
- Create all folders listed in self.folders if not existing
- """
- for f in self.dirs:
- create_folder_if_necessary(self.get_full_dir(f))
-
- def set_root(self, root):
- self.root = root
-
- def get_root(self):
- return self.root
-
- def add_dir(self, key, new_dir):
- """
- Add/replace a directory to the singletons list.
- Directories can be returned with get_dir and with their full path by
- calling get_full_dir
-
- :param key: the key under which it shall be retrievable
- :param new_dir: the directory to add to the list
- """
- self.dirs[key] = new_dir
-
- def get_dir(self, key):
- return self.dirs[key]
-
- def get_full_dir(self, key):
- return os.path.join(self.get_root(), self.get_dir(key))
-
- instance = None
-
- def __new__(cls): # __new__ always a classmethod
- if not ScriptCommons.instance:
- ScriptCommons.instance = ScriptCommons.__ScriptCommons_Singleton()
- return ScriptCommons.instance
-
- def __getattr__(self, name):
- return getattr(self.instance, name)
-
- def __setattr__(self, name):
- return setattr(self.instance, name)
-
-
-def create_folder_if_necessary(folder):
- """
- :param folder: create the folder folder if necessary (not already existing)
- """
- if not os.path.exists(folder):
- os.makedirs(folder)
diff --git a/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/__init__.py b/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/domain_adaptation_paths.py b/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/domain_adaptation_paths.py
deleted file mode 100644
index 23660eb1f1..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/domain_adaptation_paths.py
+++ /dev/null
@@ -1,18 +0,0 @@
-
-
-import os
-
-ROOT_FOLDER = "/media/wirkert/data/Data/2016_03_Domain_Adaptation"
-LOG_FOLDER = os.path.join(ROOT_FOLDER, "log")
-DATA_FOLDER = os.path.join(ROOT_FOLDER, "data")
-RESULTS_FOLDER = os.path.join(ROOT_FOLDER, "results")
-INTERMEDIATES_FOLDER = os.path.join(RESULTS_FOLDER, "intermediate")
-MC_DATA_FOLDER = os.path.join(INTERMEDIATES_FOLDER, "mc_data")
-
-
-def create_folder_if_necessary(folder):
- if not os.path.exists(folder):
- os.makedirs(folder)
-
-create_folder_if_necessary(INTERMEDIATES_FOLDER)
-create_folder_if_necessary(LOG_FOLDER)
diff --git a/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/script_analyze_da_in_silico.py b/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/script_analyze_da_in_silico.py
deleted file mode 100644
index f8d486e90a..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/domain_adaptation/script_analyze_da_in_silico.py
+++ /dev/null
@@ -1,364 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 14 11:09:18 2015
-
-@author: wirkert
-"""
-
-import os
-import logging
-import datetime
-
-import numpy as np
-import pandas as pd
-import luigi
-import matplotlib.pyplot as plt
-import seaborn as sns
-
-from regression.preprocessing import preprocess
-import domain_adaptation_paths as sp
-from ipcai2016 import tasks_mc
-from ipcai2016.script_analyze_ipcai_in_silico import w_standard, noise_levels, \
- evaluate_data, standard_plotting, NoisePlot
-# additionally we need the weights estimation functionality
-from regression.domain_adaptation import estimate_weights_random_forests
-
-
-class WeightedBatch(luigi.Task):
- which_source = luigi.Parameter()
- which_target = luigi.Parameter()
- noise = luigi.FloatParameter()
-
- def requires(self):
- return tasks_mc.CameraBatch(self.which_source), \
- tasks_mc.CameraBatch(self.which_target)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sp.ROOT_FOLDER,
- sp.RESULTS_FOLDER,
- "adapted_" +
- self.which_source +
- "_with_" + self.which_target +
- "_noise_" + str(self.noise) +
- ".txt"))
-
- def run(self):
- # get data
- df_source = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_target = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- # first extract X_source and X_target, preprocessed at standard noise
- # level
- X_source, y_source = preprocess(df_source, w_percent=w_standard)
- X_target, y_target = preprocess(df_target, w_percent=w_standard)
-
- # train a classifier to determine probability for specific class
- weights = estimate_weights_random_forests(X_source, X_target, X_source)
- # add weight to dataframe
- df_source["weights"] = weights
-
- # finally save the dataframe with the added weights
- df_source.to_csv(self.output().path, index=False)
-
-
-class DaNoisePlot(luigi.Task):
- """
- Very similar to NoisePlot in IPCAI in silico evaluation but with
- weighted data coming in.
- """
- which_train = luigi.Parameter()
- which_test = luigi.Parameter()
-
- def requires(self):
- # for each noise level we need to create the weights
- NecessaryBatches = map(lambda noise: WeightedBatch(self.which_train,
- self.which_test,
- noise),
- noise_levels)
- return NecessaryBatches(self.which_train, self.which_test), \
- tasks_mc.CameraBatch(self.which_test)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sp.ROOT_FOLDER,
- sp.RESULTS_FOLDER,
- sp.FINALS_FOLDER,
- "noise_da_plot_train_" +
- self.which_train +
- "_test_" + self.which_test +
- ".png"))
-
- def run(self):
- # get data
- df_train = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_test = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- df = evaluate_data(df_train, noise_levels, df_test, noise_levels)
- standard_plotting(df)
-
- # finally save the figure
- plt.savefig(self.output().path, dpi=500,
- bbox_inches='tight')
-
-
-class GeneratingDistributionPlot(luigi.Task):
- which_source = luigi.Parameter()
- which_target = luigi.Parameter()
-
- def requires(self):
- return WeightedBatch(self.which_source, self.which_target), \
- tasks_mc.CameraBatch(self.which_target)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sp.ROOT_FOLDER,
- sp.RESULTS_FOLDER,
- sp.FINALS_FOLDER,
- "generating_distribution_" +
- self.which_source +
- "_adapted_to_" +
- self.which_target +
- ".png"))
-
- def run(self):
- # get data
- df_source = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_target = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- # create dataframe suited for plotting
- # we do a weighted sampling with replacement to be able to create some
- # plots there the data distribution is visible.
- nr_samples = 100
- # first data weighted by domain adaptation
- df_source_adapted = df_source["layer0"].copy()
- df_source_adapted["weights"] = df_source["weights"]
- df_source_adapted["data"] = "adapted"
- df_source_adapted = df_source_adapted.sample(n=nr_samples, replace=True,
- weights="weights")
- # now original source data
- df_source = df_source["layer0"].copy()
- df_source["weights"] = 1 # we set the weights here to 1
- df_source["data"] = "source"
- df_source = df_source.sample(n=nr_samples, replace=True,
- weights="weights")
- # now the target data
- df_target = df_target["layer0"]
- df_target["weights"] = 1
- df_target["data"] = "target"
- df_target = df_target.sample(n=nr_samples, replace=True,
- weights="weights")
- # now merge all three dataframes to the dataframe used for the plotting
- df = pd.concat([df_source, df_source_adapted, df_target])
- # since we already sampled we can get rid of weights
- df.drop("weights", axis=1, inplace=True)
- # d to um
- df["d"] *= 10**6
- # vhb and sao2 to %
- df["vhb"] *= 100
- df["sao2"] *= 100
-
- # do some serious plotting
- g = sns.pairplot(df, vars=["vhb", "sao2", "d"],
- hue="data", markers=["o", "s", "D"])
-
- # tidy up plot
- g.add_legend()
-
- # finally save the figure
- plt.savefig(self.output().path, dpi=500,
- bbox_inches='tight')
-
-
-class WeightDistributionPlot(luigi.Task):
- which_source = luigi.Parameter()
- which_target = luigi.Parameter()
-
- def requires(self):
- return WeightedBatch(self.which_source, self.which_target)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sp.ROOT_FOLDER,
- sp.RESULTS_FOLDER,
- sp.FINALS_FOLDER,
- "weight_distribution_" +
- self.which_source +
- "_adapted_to_" +
- self.which_target +
- ".png"))
-
- def run(self):
- # get data
- df_source = pd.read_csv(self.input().path, header=[0, 1])
-
- df_source["weights"].plot.hist(bins=100)
- plt.axvline(x=1, ymin=0, ymax=df_source.shape[0])
- # TODO: add cumsum on top
-
- # finally save the figure
- plt.savefig(self.output().path, dpi=500,
- bbox_inches='tight')
-
-
-class FeatureDistributionPlot(luigi.Task):
- which_source = luigi.Parameter()
- which_target = luigi.Parameter()
-
- def requires(self):
- return WeightedBatch(self.which_source, self.which_target), \
- tasks_mc.CameraBatch(self.which_target)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sp.ROOT_FOLDER,
- sp.RESULTS_FOLDER,
- sp.FINALS_FOLDER,
- "feature_distribution_" +
- self.which_source +
- "_adapted_to_" +
- self.which_target +
- ".png"))
-
- def run(self):
- # get data
- df_source = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_target = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- df_f_source = format_dataframe_for_distribution_plotting(df_source)
- df_f_target = format_dataframe_for_distribution_plotting(df_target)
- df_f_adapted = format_dataframe_for_distribution_plotting(df_source,
- weights=df_source["weights"].values.squeeze())
-
- # build a combined df
- df_f_source["data"] = "source"
- df_f_target["data"] = "target"
- df_f_adapted["data"] = "adapted"
- df = pd.concat([df_f_source, df_f_target, df_f_adapted])
-
- # do the plotting
- grid = sns.FacetGrid(df, col="w", hue="data", col_wrap=3, size=1.5)
- grid.map(plt.plot, "bins", "frequency")
-
- # tidy up plot
- grid.fig.tight_layout(w_pad=1)
- grid.add_legend()
- grid.set(xticks=(0, 1))
-
- # finally save the figure
- plt.savefig(self.output().path, dpi=500)
-
-
-class DAvNormalPlot(luigi.Task):
- which_train = luigi.Parameter()
- which_test = luigi.Parameter()
- which_train_no_covariance_shift = luigi.Parameter()
-
- def requires(self):
- return WeightedBatch(self.which_train, self.which_test), \
- tasks_mc.CameraBatch(self.which_test), \
- tasks_mc.CameraBatch(self.which_train_no_covariance_shift)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sp.ROOT_FOLDER,
- sp.RESULTS_FOLDER,
- sp.FINALS_FOLDER,
- "da_v_normal_train_" +
- self.which_train +
- "_test_" + self.which_test +
- ".png"))
-
- def run(self):
- # get data
- df_train = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_test = pd.read_csv(self.input()[1].path, header=[0, 1])
- df_train_no_covariance_shift = pd.read_csv(self.input()[2].path,
- header=[0, 1])
-
- evaluation_setups = [EvaluationStruct("Proposed", rf)]
- # evaluate the different methods
- df_adapted = evaluate_data(df_train, noise_levels,
- df_test, noise_levels,
- evaluation_setups=evaluation_setups)
- df_adapted["data"] = "adapted"
- df_no_adaptation = evaluate_data(
- df_train.drop("weights", axis=1), noise_levels,
- df_test, noise_levels,
- evaluation_setups=evaluation_setups)
- df_no_adaptation["data"] = "source"
- df_no_covariance_shift = evaluate_data(
- df_train_no_covariance_shift, noise_levels,
- df_test, noise_levels,
- evaluation_setups=evaluation_setups)
- df_no_covariance_shift["data"] = "target"
- df = pd.concat([df_adapted, df_no_adaptation, df_no_covariance_shift])
-
- # plot it
- sns.boxplot(data=df, x="noise added [sigma %]", y="Errors", hue="data",
- hue_order=["source", "adapted", "target"], fliersize=0)
- # tidy up plot
- plt.ylim((0, 40))
- plt.legend(loc='upper left')
-
- # finally save the figure
- plt.savefig(self.output().path, dpi=500)
-
-
-def format_dataframe_for_distribution_plotting(df, weights=None):
- if weights is None:
- weights = np.ones(df.shape[0])
-
- bins = np.arange(0, 1, 0.01)
-
- # we're only interested in reflectance information
- df_formatted = df.loc[:, "reflectances"]
- # to [nm] for plotting
- df_formatted.rename(columns=lambda x: float(x)*10**9, inplace=True)
-
- # transform data to a histogram
- df_formatted = df_formatted.apply(lambda x:
- pd.Series(np.histogram(x, bins=bins,
- weights=weights,
- normed=True)[0]),
- axis=0)
- # convert to long form using bins as identifier
- df_formatted["bins"] = bins[1:]
- df_formatted = pd.melt(df_formatted, id_vars=["bins"],
- var_name="w", value_name="frequency")
-
- return df_formatted
-
-
-if __name__ == '__main__':
- logging.basicConfig(filename=os.path.join(sp.LOG_FOLDER,
- "da_in_silico_plots" +
- str(datetime.datetime.now()) +
- '.log'),
- level=logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- logger = logging.getLogger()
- logger.addHandler(ch)
- luigi.interface.setup_interface_logging()
-
- source_domain = "ipcai_revision_generic"
- target_domain = "ipcai_revision_colon_test"
-
- sch = luigi.scheduler.CentralPlannerScheduler()
- w = luigi.worker.Worker(scheduler=sch)
- # check how the graph looks with same domains for training and testing
- w.add(DaNoisePlot(which_train="ipcai_revision_colon_train",
- which_test="ipcai_revision_colon_test"))
- # check how the graph looks without domain adaptation
- w.add(NoisePlot(which_train=source_domain, which_test=target_domain))
- # Set a different testing domain to evaluate domain sensitivity
- w.add(DaNoisePlot(which_train=source_domain, which_test=target_domain))
-
- w.add(WeightDistributionPlot(which_source=source_domain,
- which_target=target_domain))
- w.add(FeatureDistributionPlot(which_source=source_domain,
- which_target=target_domain))
- # also plot distributions for equal domains to check for errors in data
- w.add(FeatureDistributionPlot(which_source="ipcai_revision_colon_mean_scattering_train",
- which_target="ipcai_revision_colon_mean_scattering_test"))
- # plot how the generating model data (e.g. sao2 and vhb) is distributed
- w.add(GeneratingDistributionPlot(which_source=source_domain,
- which_target=target_domain))
- w.add(DAvNormalPlot(which_train=source_domain, which_test=target_domain,
- which_train_no_covariance_shift="ipcai_revision_colon_train"))
- w.run()
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/__init__.py b/Modules/Biophotonics/python/iMC/scripts/ipcai2016/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_silico.py b/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_silico.py
deleted file mode 100644
index 0db37b69f9..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_silico.py
+++ /dev/null
@@ -1,335 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 14 11:09:18 2015
-
-@author: wirkert
-"""
-
-import os
-import logging
-import datetime
-from collections import namedtuple
-
-import matplotlib
-import numpy as np
-import pandas as pd
-from pandas import DataFrame
-import luigi
-import matplotlib.pyplot as plt
-from sklearn.ensemble.forest import RandomForestRegressor
-
-import tasks_mc
-from regression.preprocessing import preprocess, preprocess2
-from regression.linear import LinearSaO2Unmixing
-
-import commons
-
-sc = commons.ScriptCommons()
-
-sc.add_dir("IN_SILICO_RESULTS_PATH", os.path.join(sc.get_dir("RESULTS_FOLDER"),
- "in_silico"))
-
-sc.other["RECORDED_WAVELENGTHS"] = np.arange(470, 680, 10) * 10 ** -9
-
-w_standard = 10. # for this evaluation we add 10% noise
-
-font = {'family' : 'normal',
- 'size' : 20}
-
-matplotlib.rc('font', **font)
-
-
-# setup standard random forest
-rf = RandomForestRegressor(10, min_samples_leaf=10, max_depth=9, n_jobs=-1)
-EvaluationStruct = namedtuple("EvaluationStruct",
- "name regressor")
-# standard evaluation setup
-standard_evaluation_setups = [EvaluationStruct("Linear Beer-Lambert",
- LinearSaO2Unmixing())
- , EvaluationStruct("Proposed", rf)]
-
-# color palette
-my_colors = ["red", "green"]
-
-# standard noise levels
-noise_levels = np.array([1,2,3,4,5,6,7,8,9,10,
- 15,20,30,40,50,100,150,200]).astype("float")
-
-
-class TrainingSamplePlot(luigi.Task):
- which_train = luigi.Parameter()
- which_test = luigi.Parameter()
-
- def requires(self):
- return tasks_mc.CameraBatch(self.which_train), \
- tasks_mc.CameraBatch(self.which_test)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("IN_SILICO_RESULTS_PATH"),
- "sample_plot_train_" +
- self.which_train +
- "_test_" + self.which_test +
- ".pdf"))
-
- def run(self):
- # get data
- df_train = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_test = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- # for this plot we write a custom evaluation function as it is built
- # a little different
-
- # create a new dataframe which will hold all the generated errors
- df = pd.DataFrame()
-
- nr_training_samples = np.arange(10, 15010, 50).astype(int)
- # not very pythonic, don't care
- for n in nr_training_samples:
- X_test, y_test = preprocess(df_test, snr=w_standard)
- # only take n samples for training
- X_train, y_train = preprocess(df_train, nr_samples=n,
- snr=w_standard)
-
- regressor = rf
- regressor.fit(X_train, y_train)
- y_pred = regressor.predict(X_test)
- # save results to a dataframe
- errors = np.abs(y_pred - y_test)
- errors = errors.reshape(len(errors), 1)
- current_df = DataFrame(errors * 100,
- columns=["Errors"])
- current_df["Method"] = "Proposed"
- current_df["Number Samples"] = n / 10**3.
- df = pd.concat([df, current_df], ignore_index=True)
- logging.info(
- "Finished training classifier with {0} samples".format(
- str(n)))
-
- df = df.groupby("Number Samples").describe()
- # get the error description in the rows:
- df = df.unstack(-1)
- # get rid of multiindex by dropping "Error" level
- df.columns = df.columns.droplevel(0)
-
- plt.figure()
- plt.plot(df.index, df["50%"], color="green")
-
- # tidy up the plot
- plt.xlabel("number of training samples / 1000")
- plt.ylabel("absolute error [%]")
- plt.ylim((0, 20))
- plt.xlim((0, 15))
- plt.grid()
-
- # finally save the figure
- plt.savefig(self.output().path, mode="pdf", dpi=500,
- bbox_inches='tight')
-
-
-class VhbPlot(luigi.Task):
- which_train = luigi.Parameter()
- which_test = luigi.Parameter()
-
- def requires(self):
- return tasks_mc.CameraBatch(self.which_train), \
- tasks_mc.CameraBatch(self.which_test)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("IN_SILICO_RESULTS_PATH"),
- "vhb_noise_plot_train_" +
- self.which_train +
- "_test_" + self.which_test +
- ".pdf"))
-
- @staticmethod
- def preprocess_vhb(batch, nr_samples=None, snr=None,
- magnification=None, bands_to_sortout=None):
- """ For evaluating vhb we extract labels for vhb instead of sao2"""
- X, y = preprocess2(batch, nr_samples, snr,
- magnification, bands_to_sortout)
-
- return X, y["vhb"].values
-
- def run(self):
- # get data
- df_train = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_test = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- # for vhb we only evaluate the proposed method since the linear
- # beer-lambert is not applicable
- evaluation_setups = [EvaluationStruct("Proposed", rf)]
- df = evaluate_data(df_train, noise_levels, df_test, noise_levels,
- evaluation_setups=evaluation_setups,
- preprocessing=self.preprocess_vhb)
- standard_plotting(df, color_palette=["green"],
- xytext_position=(2, 3))
- plt.ylim((0, 4))
-
- # finally save the figure
- plt.savefig(self.output().path, dpi=500,
- bbox_inches='tight')
-
-
-class NoisePlot(luigi.Task):
- which_train = luigi.Parameter()
- which_test = luigi.Parameter()
-
- def requires(self):
- return tasks_mc.CameraBatch(self.which_train), \
- tasks_mc.CameraBatch(self.which_test)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("IN_SILICO_RESULTS_PATH"),
- "noise_plot_train_" +
- self.which_train +
- "_test_" + self.which_test +
- ".pdf"))
-
- def run(self):
- # get data
- df_train = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_test = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- df = evaluate_data(df_train, noise_levels, df_test, noise_levels)
- standard_plotting(df)
-
- # finally save the figure
- plt.savefig(self.output().path, mode="pdf", dpi=500,
- bbox_inches='tight')
-
-
-class WrongNoisePlot(luigi.Task):
- which_train = luigi.Parameter()
- which_test = luigi.Parameter()
- train_snr = luigi.FloatParameter()
-
- def requires(self):
- return tasks_mc.CameraBatch(self.which_train), \
- tasks_mc.CameraBatch(self.which_test)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("IN_SILICO_RESULTS_PATH"),
- str(self.train_snr) +
- "_wrong_noise_plot_train_" +
- self.which_train +
- "_test_" + self.which_test +
- ".pdf"))
-
- def run(self):
- # get data
- df_train = pd.read_csv(self.input()[0].path, header=[0, 1])
- df_test = pd.read_csv(self.input()[1].path, header=[0, 1])
-
- # do same as in NoisePlot but with standard noise input
- df = evaluate_data(df_train,
- np.ones_like(noise_levels) * self.train_snr,
- df_test, noise_levels)
- standard_plotting(df)
-
- # finally save the figure
- plt.savefig(self.output().path, mode="pdf", dpi=500,
- bbox_inches='tight')
-
-
-def evaluate_data(df_train, w_train, df_test, w_test,
- evaluation_setups=None, preprocessing=None):
- """ Our standard method to evaluate the data. It will fill a DataFrame df
- which saves the errors for each evaluated setup"""
- if evaluation_setups is None:
- evaluation_setups = standard_evaluation_setups
- if preprocessing is None:
- preprocessing = preprocess
- if ("weights" in df_train) and df_train["weights"].size > 0:
- weights = df_train["weights"].as_matrix().squeeze()
- else:
- weights = np.ones(df_train.shape[0])
-
- # create a new dataframe which will hold all the generated errors
- df = pd.DataFrame()
- for one_w_train, one_w_test in zip(w_train, w_test):
- # setup testing function
- X_test, y_test = preprocessing(df_test, snr=one_w_test)
- # extract noisy data
- X_train, y_train = preprocessing(df_train, snr=one_w_train)
- for e in evaluation_setups:
- regressor = e.regressor
- regressor.fit(X_train, y_train, weights)
- y_pred = regressor.predict(X_test)
- # save results to a dataframe
- errors = np.abs(y_pred - y_test)
- errors = errors.reshape(len(errors), 1)
- current_df = DataFrame(errors * 100,
- columns=["Errors"])
- current_df["Method"] = e.name
- current_df["SNR"] = int(one_w_test)
- df = pd.concat([df, current_df], ignore_index=True)
-
- return df
-
-
-def standard_plotting(df, color_palette=None, xytext_position=None):
- if color_palette is None:
- color_palette = my_colors
- if xytext_position is None:
- xytext_position = (2, 15)
-
- plt.figure()
-
- # group it by method and noise level and get description on the errors
- df_statistics = df.groupby(['Method', 'SNR']).describe()
- # get the error description in the rows:
- df_statistics = df_statistics.unstack(-1)
- # get rid of multiindex by dropping "Error" level
- df_statistics.columns = df_statistics.columns.droplevel(0)
-
- # iterate over methods to plot linegraphs with error tube
- # probably this can be done nicer, but no idea how exactly
-
- for color, method in zip(
- color_palette, df_statistics.index.get_level_values("Method").unique()):
- df_method = df_statistics.loc[method]
- plt.plot(df_method.index, df_method["50%"],
- color=color, label=method)
- plt.fill_between(df_method.index, df_method["25%"], df_method["75%"],
- facecolor=color, edgecolor=color,
- alpha=0.5)
- # tidy up the plot
- plt.ylim((0, 40))
- plt.gca().set_xticks(np.arange(0, 200, 10), minor=True)
- plt.xlabel("SNR")
- plt.ylabel("absolute error [%]")
- plt.grid()
- plt.legend()
-
-
-if __name__ == '__main__':
-
- sc.set_root("/media/wirkert/data/Data/2016_02_02_IPCAI/")
- sc.create_folders()
-
- logging.basicConfig(filename=os.path.join(sc.get_full_dir("LOG_FOLDER"),
- "in_silico_plots_" +
- str(datetime.datetime.now()) +
- '.log'),
- level=logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- logger = logging.getLogger()
- logger.addHandler(ch)
- luigi.interface.setup_interface_logging()
-
- train = "ipcai_revision_colon_mean_scattering_train"
- test = "ipcai_revision_colon_mean_scattering_test"
-
- sch = luigi.scheduler.CentralPlannerScheduler()
- w = luigi.worker.Worker(scheduler=sch)
- w.add(TrainingSamplePlot(which_train=train, which_test=test))
- w.add(NoisePlot(which_train=train, which_test=test))
- w.add(WrongNoisePlot(which_train=train, which_test=test, train_snr=10.))
- w.add(WrongNoisePlot(which_train=train, which_test=test, train_snr=50.))
- w.add(WrongNoisePlot(which_train=train, which_test=test, train_snr=200.))
- # Set a different testing domain to evaluate domain sensitivity
- w.add(NoisePlot(which_train=train,
- which_test="ipcai_revision_generic_mean_scattering_test"))
- w.add(VhbPlot(which_train=train, which_test=test))
- w.run()
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_vivo_liver.py b/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_vivo_liver.py
deleted file mode 100644
index 2f547afe3f..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_vivo_liver.py
+++ /dev/null
@@ -1,294 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 14 11:09:18 2015
-
-@author: wirkert
-"""
-
-
-import Image
-import ImageEnhance
-import logging
-import datetime
-
-import SimpleITK as sitk
-import matplotlib
-
-from msi.io.nrrdreader import NrrdReader
-import msi.normalize as norm
-from regression.estimation import estimate_image
-from tasks_common import *
-import commons
-from msi.io.tiffringreader import TiffRingReader
-
-TiffRingReader.RESIZE_FACTOR = 0.5
-
-sc = commons.ScriptCommons()
-
-sc.add_dir("LIVER_DATA",
- os.path.join(sc.get_dir("DATA_FOLDER"), "liver_images"))
-sc.add_dir("LIVER_RESULTS", os.path.join(sc.get_dir("RESULTS_FOLDER"), "liver"))
-
-sc.add_dir("FILTER_TRANSMISSIONS",
- os.path.join(sc.get_dir("DATA_FOLDER"),
- "filter_transmissions"))
-
-font = {'family' : 'normal',
- 'size' : 30}
-matplotlib.rc('font', **font)
-
-
-class ResultsFile(luigi.Task):
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("LIVER_RESULTS"),
- "results.csv"))
-
-
-class OxyAndVhbOverTimeTask(luigi.Task):
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("LIVER_RESULTS"),
- "liver_oxy_over_time.pdf"))
-
- def requires(self):
- return ResultsFile()
-
- def run(self):
- df = pd.read_csv(self.input().path, index_col=0)
- # determine times from start:
- image_name_strings = df["image name"].values
- time_strings = map(lambda s: s[
- s.find("2014-08-03_")+11:s.find("2014-08-03_")+19],
- image_name_strings)
- time_in_s = map(lambda s: int(s[0:2]) * 3600 +
- int(s[3:5]) * 60 +
- int(s[6:]), time_strings)
- df["time since drug delivery [s]"] = np.array(time_in_s) - time_in_s[0]
-
- # print oxy over time as scatterplot.
- ax = df.plot.scatter(x="time since drug delivery [s]",
- y="oxygenation mean [%]",
- s=100, alpha=0.5,
- fontsize=30)
- ax.set_xlim((-1, 70))
-
- plt.axvline(x=0, ymin=0, ymax=1, linewidth=2)
- plt.axvline(x=56, ymin=0, ymax=1, linewidth=2)
- ax.annotate('drug delivery', xy=(0, ax.get_ylim()[1]),
- xycoords='data', xytext=(0, 0),
- fontsize=30,
- textcoords='offset points')
- ax.annotate('porcine death', xy=(56, ax.get_ylim()[1]),
- xycoords='data', xytext=(-100, 0),
- fontsize=30,
- textcoords='offset points')
- ax.yaxis.label.set_size(30)
- ax.xaxis.label.set_size(30)
- plt.grid()
-
- df.to_csv(self.input().path)
-
- # create and save vhb plot
- plt.savefig(self.output().path,
- dpi=250, bbox_inches='tight', mode="pdf")
-
- # print vhb over time as scatterplot.
- ax = df.plot.scatter(x="time since drug delivery [s]",
- y="blood volume fraction mean [%]",
- s=100, alpha=0.5,
- fontsize=30)
- ax.set_xlim((-1, 70))
-
- plt.axvline(x=0, ymin=0, ymax=1, linewidth=2)
- plt.axvline(x=56, ymin=0, ymax=1, linewidth=2)
- ax.annotate('drug delivery', xy=(0, ax.get_ylim()[1]),
- xycoords='data', xytext=(0, 0),
- fontsize=30,
- textcoords='offset points')
- ax.annotate('porcine death', xy=(56, ax.get_ylim()[1]),
- xycoords='data', xytext=(-100, 0),
- fontsize=30,
- textcoords='offset points')
- ax.yaxis.label.set_size(30)
- ax.xaxis.label.set_size(30)
- plt.grid()
-
- plt.savefig(self.output().path + "_vhb_mean.pdf",
- dpi=250, bbox_inches='tight', mode="pdf")
-
-
-class IPCAICreateOxyImageTask(luigi.Task):
- image_name = luigi.Parameter()
- df_prefix = luigi.Parameter()
-
- def requires(self):
- return IPCAITrainRegressor(df_prefix=self.df_prefix), \
- Flatfield(flatfield_folder=sc.get_full_dir("FLAT_FOLDER")), \
- SingleMultispectralImage(image=os.path.join(
- sc.get_full_dir("LIVER_DATA"), self.image_name)), \
- Dark(dark_folder=sc.get_full_dir("DARK_FOLDER"))
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("LIVER_RESULTS"),
- self.image_name + "_" +
- self.df_prefix +
- "_oxy_summary" + ".png"))
-
- def run(self):
- nrrd_reader = NrrdReader()
- tiff_ring_reader = TiffRingReader()
- # read the flatfield
- flat = nrrd_reader.read(self.input()[1].path)
- dark = nrrd_reader.read(self.input()[3].path)
- # read the msi
- nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
- msi, segmentation = tiff_ring_reader.read(self.input()[2].path,
- nr_filters)
-
- # only take into account not saturated pixels.
- segmentation = np.max(msi.get_image(), axis=-1) < 2000.
-
- # read the regressor
- e_file = open(self.input()[0].path, 'r')
- e = pickle.load(e_file)
-
- # correct image setup
- position_filter_nr_in_string = self.image_name.find(" 2014") - 1
- filter_nr = int(self.image_name[
- position_filter_nr_in_string:position_filter_nr_in_string+1])
- original_order = np.arange(nr_filters)
- new_image_order = np.concatenate((
- original_order[nr_filters - filter_nr:],
- original_order[:nr_filters - filter_nr]))
- # resort msi to restore original order
- msimani.get_bands(msi, new_image_order)
- # correct by flatfield
- msimani.image_correction(msi, flat, dark)
-
- # create artificial rgb
- rgb_image = msi.get_image()[:, :, [2, 3, 1]]
- rgb_image /= np.max(rgb_image)
- rgb_image *= 255.
-
- # preprocess the image
- # sortout unwanted bands
- print "1"
- # zero values would lead to infinity logarithm, thus clip.
- msi.set_image(np.clip(msi.get_image(), 0.00001, 2. ** 64))
- # normalize to get rid of lighting intensity
- norm.standard_normalizer.normalize(msi)
- # transform to absorption
- msi.set_image(-np.log(msi.get_image()))
- # normalize by l2 for stability
- norm.standard_normalizer.normalize(msi, "l2")
- print "2"
- # estimate
- sitk_image, time = estimate_image(msi, e)
- image = sitk.GetArrayFromImage(sitk_image)
-
- plt.figure()
- print "3"
- rgb_image = rgb_image.astype(np.uint8)
- im = Image.fromarray(rgb_image, 'RGB')
- enh_brightness = ImageEnhance.Brightness(im)
- im = enh_brightness.enhance(5.)
- plotted_image = np.array(im)
- top_left_axis = plt.gca()
- top_left_axis.imshow(plotted_image, interpolation='nearest')
- top_left_axis.xaxis.set_visible(False)
- top_left_axis.yaxis.set_visible(False)
-
- plt.set_cmap("jet")
- print "4"
- # plot parametric maps
- # first oxygenation
- plt.figure()
- oxy_image = image[:, :, 0]
- segmentation[0, 0] = 1
- segmentation[0, 1] = 1
- oxy_image = np.ma.masked_array(oxy_image, ~segmentation)
- oxy_image[np.isnan(oxy_image)] = 0.
- oxy_image[np.isinf(oxy_image)] = 0.
- oxy_mean = np.mean(oxy_image)
- oxy_image[0, 0] = 0.0
- oxy_image[0, 1] = 1.
- plot_image(oxy_image[:, :], plt.gca())
- plt.savefig(self.output().path,
- dpi=250, bbox_inches='tight')
- # second blood volume fraction
- plt.figure()
- vhb_image = image[:, :, 1]
- vhb_image = np.ma.masked_array(vhb_image, ~segmentation)
- vhb_image[np.isnan(vhb_image)] = 0.
- vhb_image[np.isinf(vhb_image)] = 0.
- vhb_image[0, 0] = 0.0
- vhb_image[0, 1] = 0.1
- vhb_image = np.clip(vhb_image, 0.0, 0.1)
- vhb_mean = np.mean(vhb_image)
- plot_image(vhb_image, plt.gca())
- plt.savefig(self.output().path + "vhb.png",
- dpi=250, bbox_inches='tight')
-
- # store results summary in dataframe
- df_image_results = pd.DataFrame(data=np.expand_dims([self.image_name,
- oxy_mean * 100.,
- vhb_mean * 100.,
- time], 0),
- columns=["image name",
- "oxygenation mean [%]",
- "blood volume fraction mean [%]",
- "time to estimate"])
-
- results_file = os.path.join(sc.get_full_dir("LIVER_RESULTS"),
- "results.csv")
- if os.path.isfile(results_file):
- df_results = pd.read_csv(results_file, index_col=0)
- df_results = pd.concat((df_results, df_image_results)).reset_index(
- drop=True
- )
- else:
- df_results = df_image_results
-
- df_results.to_csv(results_file)
-
- print "5"
- plt.close("all")
-
-
-if __name__ == '__main__':
-
- # create a folder for the results if necessary
- sc.set_root("/media/wirkert/data/Data/2016_02_02_IPCAI/")
- sc.create_folders()
-
- # root folder there the data lies
- logging.basicConfig(filename=os.path.join(sc.get_full_dir("LOG_FOLDER"),
- "liver" +
- str(datetime.datetime.now()) +
- '.log'), level=logging.INFO)
- luigi.interface.setup_interface_logging()
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- logger = logging.getLogger()
- logger.addHandler(ch)
-
- sch = luigi.scheduler.CentralPlannerScheduler()
- w = luigi.worker.Worker(scheduler=sch)
-
- onlyfiles = get_image_files_from_folder(sc.get_full_dir("LIVER_DATA"))
-
- first_invivo_image_files = filter(lambda image_name: "0 2014" in image_name,
- onlyfiles)
-
- for f in first_invivo_image_files:
- main_task = IPCAICreateOxyImageTask(image_name=f,
- df_prefix="ipcai_revision_colon_mean_scattering_train")
- w.add(main_task)
-
- w.run()
-
- oxygenation_over_time_task = OxyAndVhbOverTimeTask()
- w.add(oxygenation_over_time_task)
- w.run()
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_vivo_small_bowel.py b/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_vivo_small_bowel.py
deleted file mode 100644
index 6ce3da2895..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_analyze_ipcai_in_vivo_small_bowel.py
+++ /dev/null
@@ -1,276 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 14 11:09:18 2015
-
-@author: wirkert
-"""
-
-import Image
-import ImageEnhance
-import logging
-import datetime
-
-import SimpleITK as sitk
-import matplotlib
-
-from msi.io.nrrdreader import NrrdReader
-import msi.normalize as norm
-from regression.estimation import estimate_image
-from tasks_common import *
-import commons
-from msi.io.tiffringreader import TiffRingReader
-
-TiffRingReader.RESIZE_FACTOR = 0.5
-
-sc = commons.ScriptCommons()
-
-
-sc.add_dir("SMALL_BOWEL_DATA",
- os.path.join(sc.get_dir("DATA_FOLDER"), "small_bowel_images"))
-
-sc.add_dir("SMALL_BOWEL_RESULT", os.path.join(sc.get_dir("RESULTS_FOLDER"),
- "small_bowel"))
-
-sc.add_dir("FILTER_TRANSMISSIONS",
- os.path.join(sc.get_dir("DATA_FOLDER"),
- "filter_transmissions"))
-
-font = {'family' : 'normal',
- 'size' : 25}
-matplotlib.rc('font', **font)
-
-
-class ResultsFile(luigi.Task):
-
- def output(self):
- return luigi.LocalTarget(os.path.join(
- sc.get_full_dir("SMALL_BOWEL_RESULT"), "results.csv"))
-
-
-class OxyOverTimeTask(luigi.Task):
-
- def output(self):
- return luigi.LocalTarget(os.path.join(
- sc.get_full_dir("SMALL_BOWEL_RESULT"),
- "colon_oxy_over_time.pdf"))
-
- def requires(self):
- return ResultsFile()
-
- def run(self):
- df = pd.read_csv(self.input().path, index_col=0)
-
- # determine times from start:
- image_name_strings = df["image name"].values
- time_strings = map(lambda s: s[
- s.find("2015-10-08_")+11:s.find("2015-10-08_")+19],
- image_name_strings)
- time_in_s = map(lambda s: int(s[0:2]) * 3600 +
- int(s[3:5]) * 60 +
- int(s[6:]), time_strings)
- df["time since first frame [s]"] = np.array(time_in_s) - time_in_s[0]
- df["time since applying first clip [s]"] = df["time since first frame [s]"] - 4
- # print oxy over time as scatterplot.
- plt.figure()
- ax = df.plot.scatter(x="time since applying first clip [s]",
- y="oxygenation mean [%]", fontsize=30,
- s=50, alpha=0.5)
- ax.set_xlim((-5, 600))
-
- plt.axvline(x=0, ymin=0, ymax=1, linewidth=2)
- plt.axvline(x=39, ymin=0, ymax=1, linewidth=2)
- plt.axvline(x=100, ymin=0, ymax=1, linewidth=2)
- plt.axvline(x=124, ymin=0, ymax=1, linewidth=2)
- ax.annotate('1', xy=(0, ax.get_ylim()[1]),
- fontsize=18,
- color="blue",
- xycoords='data', xytext=(-5, 0),
- textcoords='offset points')
- ax.annotate('2', xy=(39, ax.get_ylim()[1]),
- fontsize=18,
- color="blue",
- xycoords='data', xytext=(-5, 0),
- textcoords='offset points')
- ax.annotate('3', xy=(100, ax.get_ylim()[1]),
- fontsize=18,
- color="blue",
- xycoords='data', xytext=(-5, 0),
- textcoords='offset points')
- ax.annotate('4', xy=(124, ax.get_ylim()[1]),
- fontsize=18,
- color="blue",
- xycoords='data', xytext=(-5, 0),
- textcoords='offset points')
-
- plt.grid()
-
- df.to_csv(self.input().path)
-
- # save
- plt.savefig(self.output().path,
- dpi=250, bbox_inches='tight', mode="pdf")
-
-
-def plot_image(image, axis):
- im2 = axis.imshow(image, interpolation='nearest', alpha=1.0)
- # axis.set_title(title, fontsize=5)
- # divider = make_axes_locatable(axis)
- # cax = divider.append_axes("right", size="10%", pad=0.05)
- # cbar = plt.colorbar(im2, cax=cax)
- # cbar.ax.tick_params(labelsize=5)
- axis.xaxis.set_visible(False)
-
-
-class IPCAICreateOxyImageTask(luigi.Task):
- image_name = luigi.Parameter()
- df_prefix = luigi.Parameter()
-
- def requires(self):
- return IPCAITrainRegressor(df_prefix=self.df_prefix), \
- Flatfield(flatfield_folder=sc.get_full_dir("FLAT_FOLDER")), \
- SingleMultispectralImage(image=self.image_name), \
- Dark(dark_folder=sc.get_full_dir("DARK_FOLDER"))
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("SMALL_BOWEL_RESULT"),
- os.path.split(self.image_name)[1] +
- "_" + self.df_prefix +
- "_summary" + ".png"))
-
- def run(self):
- nrrd_reader = NrrdReader()
- tiff_ring_reader = TiffRingReader()
- # read the flatfield
- flat = nrrd_reader.read(self.input()[1].path)
- dark = nrrd_reader.read(self.input()[3].path)
- # read the msi
- nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
- msi, segmentation = tiff_ring_reader.read(self.input()[2].path,
- nr_filters)
- # only take into account not saturated pixels.
- segmentation = np.logical_and(segmentation,
- (np.max(msi.get_image(),
- axis=-1) < 1000.))
-
- # read the regressor
- e_file = open(self.input()[0].path, 'r')
- e = pickle.load(e_file)
-
- # correct image setup
- filter_nr = int(self.image_name[-6:-5])
- original_order = np.arange(nr_filters)
- new_image_order = np.concatenate((
- original_order[nr_filters - filter_nr:],
- original_order[:nr_filters - filter_nr]))
- # resort msi to restore original order
- msimani.get_bands(msi, new_image_order)
- # correct by flatfield
- msimani.image_correction(msi, flat, dark)
-
- # create artificial rgb
- rgb_image = msi.get_image()[:, :, [2, 3, 1]]
- rgb_image /= np.max(rgb_image)
- rgb_image *= 255.
-
- # preprocess the image
- # sortout unwanted bands
- print "1"
- # zero values would lead to infinity logarithm, thus clip.
- msi.set_image(np.clip(msi.get_image(), 0.00001, 2. ** 64))
- # normalize to get rid of lighting intensity
- norm.standard_normalizer.normalize(msi)
- # transform to absorption
- msi.set_image(-np.log(msi.get_image()))
- # normalize by l2 for stability
- norm.standard_normalizer.normalize(msi, "l2")
- print "2"
- # estimate
- sitk_image, time = estimate_image(msi, e)
- image = sitk.GetArrayFromImage(sitk_image)
-
- plt.figure()
- print "3"
- rgb_image = rgb_image.astype(np.uint8)
- im = Image.fromarray(rgb_image, 'RGB')
- enh_brightness = ImageEnhance.Brightness(im)
- im = enh_brightness.enhance(10.)
- plotted_image = np.array(im)
- top_left_axis = plt.gca()
- top_left_axis.imshow(plotted_image, interpolation='nearest')
- top_left_axis.xaxis.set_visible(False)
- top_left_axis.yaxis.set_visible(False)
-
- plt.set_cmap("jet")
- print "4"
- # plot parametric maps
- segmentation[0, 0] = 1
- segmentation[0, 1] = 1
- oxy_image = np.ma.masked_array(image[:, :, 0], ~segmentation)
- oxy_image[np.isnan(oxy_image)] = 0.
- oxy_image[np.isinf(oxy_image)] = 0.
- oxy_mean = np.mean(oxy_image)
- oxy_image[0, 0] = 0.0
- oxy_image[0, 1] = 1.
-
- plot_image(oxy_image[:, :], plt.gca())
-
- df_image_results = pd.DataFrame(data=np.expand_dims([self.image_name,
- oxy_mean * 100.,
- time], 0),
- columns=["image name",
- "oxygenation mean [%]",
- "time to estimate"])
-
- results_file = os.path.join(sc.get_full_dir("SMALL_BOWEL_RESULT"),
- "results.csv")
- if os.path.isfile(results_file):
- df_results = pd.read_csv(results_file, index_col=0)
- df_results = pd.concat((df_results, df_image_results)).reset_index(
- drop=True
- )
- else:
- df_results = df_image_results
-
- df_results.to_csv(results_file)
-
- plt.savefig(self.output().path,
- dpi=250, bbox_inches='tight')
- plt.close("all")
-
-
-if __name__ == '__main__':
-
- # create a folder for the results if necessary
- sc.set_root("/media/wirkert/data/Data/2016_02_02_IPCAI/")
- sc.create_folders()
-
- # root folder there the data lies
- logging.basicConfig(filename=os.path.join(sc.get_full_dir("LOG_FOLDER"),
- "small_bowel_images" +
- str(datetime.datetime.now()) +
- '.log'),
- level=logging.INFO)
- luigi.interface.setup_interface_logging()
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- logger = logging.getLogger()
- logger.addHandler(ch)
-
- sch = luigi.scheduler.CentralPlannerScheduler()
- w = luigi.worker.Worker(scheduler=sch)
-
-
- # determine files to process
- files = get_image_files_from_folder(sc.get_full_dir("SMALL_BOWEL_DATA"),
- suffix="F0.tiff", fullpath=True)
-
- for f in files:
- main_task = IPCAICreateOxyImageTask(image_name=f,
- df_prefix="ipcai_revision_colon_mean_scattering_te")
- w.add(main_task)
- w.run()
-
- oxygenation_over_time_task = OxyOverTimeTask()
- w.add(oxygenation_over_time_task)
- w.run()
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_calculate_spectra.py b/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_calculate_spectra.py
deleted file mode 100644
index 5ceb764c33..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/script_calculate_spectra.py
+++ /dev/null
@@ -1,123 +0,0 @@
-'''
-Created on Sep 9, 2015
-
-@author: wirkert
-'''
-
-
-import logging
-import datetime
-import os
-import time
-
-import numpy as np
-import luigi
-
-import commons
-import mc.factories as mcfac
-from mc.sim import SimWrapper
-from mc.create_spectrum import create_spectrum
-
-# parameter setting
-NR_BATCHES = 100
-NR_ELEMENTS_IN_BATCH = 1000
-# the wavelengths to be simulated
-WAVELENGHTS = np.arange(450, 720, 2) * 10 ** -9
-NR_PHOTONS = 10 ** 6
-
-# experiment configuration
-MCI_FILENAME = "./temp.mci"
-MCO_FILENAME = "temp.mco"
-# this path definitly needs to be adapted by you
-PATH_TO_MCML = "/home/wirkert/workspace/monteCarlo/gpumcml/fast-gpumcml/"
-EXEC_MCML = "gpumcml.sm_20"
-
-
-sc = commons.ScriptCommons()
-
-
-class CreateSpectraTask(luigi.Task):
- df_prefix = luigi.Parameter()
- batch_nr = luigi.IntParameter()
- nr_samples = luigi.IntParameter()
- factory = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("MC_DATA_FOLDER"),
- self.df_prefix + "_" +
- str(self.batch_nr) + ".txt"))
-
- def run(self):
- start = time.time()
- # setup simulation wrapper
- sim_wrapper = SimWrapper()
- sim_wrapper.set_mci_filename(MCI_FILENAME)
- sim_wrapper.set_mcml_executable(os.path.join(PATH_TO_MCML, EXEC_MCML))
- # setup model
- tissue_model = self.factory.create_tissue_model()
- tissue_model.set_mci_filename(sim_wrapper.mci_filename)
- tissue_model.set_mco_filename(MCO_FILENAME)
- tissue_model.set_nr_photons(NR_PHOTONS)
- # setup array in which data shall be stored
- batch = self.factory.create_batch_to_simulate()
- batch.create_parameters(self.nr_samples)
- # dataframe created by batch:
- df = batch.df
- # add reflectance column to dataframe
- for w in WAVELENGHTS:
- df["reflectances", w] = np.NAN
-
- # for each instance of our tissue model
- for i in range(df.shape[0]):
- # set the desired element in the dataframe to be simulated
- tissue_model.set_dataframe_row(df.loc[i, :])
- logging.info("running simulation " + str(i) + " for\n" +
- str(tissue_model))
- reflectances = create_spectrum(tissue_model, sim_wrapper,
- WAVELENGHTS)
- # store in dataframe
- for r, w in zip(reflectances, WAVELENGHTS):
- df["reflectances", w][i] = r
-
- # clean up temporarily created files
- os.remove(MCI_FILENAME)
- created_mco_file = os.path.join(PATH_TO_MCML, MCO_FILENAME)
- if os.path.isfile(created_mco_file):
- os.remove(created_mco_file)
- # save the created output
- f = open(self.output().path, 'w')
- df.to_csv(f)
-
- end = time.time()
- logging.info("time for creating batch of mc data: %.f s" %
- (end - start))
-
-
-if __name__ == '__main__':
-
- # create a folder for the results if necessary
- sc.set_root("/media/wirkert/data/Data/2016_02_02_IPCAI/")
- sc.create_folders()
-
- logging.basicConfig(filename=os.path.join(sc.get_full_dir("LOG_FOLDER"),
- "calculate_spectra" +
- str(datetime.datetime.now()) +
- '.log'),
- level=logging.INFO)
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- logger = logging.getLogger()
- logger.addHandler(ch)
- luigi.interface.setup_interface_logging()
-
- sch = luigi.scheduler.CentralPlannerScheduler()
- w = luigi.worker.Worker(scheduler=sch)
- BATCH_NUMBERS = np.arange(0, NR_BATCHES, 1)
- for i in BATCH_NUMBERS:
- colon_task = CreateSpectraTask("ipcai_revision_generic_mean_scattering",
- i,
- NR_ELEMENTS_IN_BATCH,
- mcfac.GenericMeanScatteringFactory())
- w.add(colon_task)
- w.run()
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/tasks_common.py b/Modules/Biophotonics/python/iMC/scripts/ipcai2016/tasks_common.py
deleted file mode 100644
index 7df698175c..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/tasks_common.py
+++ /dev/null
@@ -1,166 +0,0 @@
-
-import os
-import pickle
-
-import numpy as np
-import pandas as pd
-import luigi
-from sklearn.ensemble.forest import RandomForestRegressor
-import matplotlib.pylab as plt
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-
-import tasks_mc
-import commons
-from msi.msi import Msi
-from msi.io.nrrdwriter import NrrdWriter
-import msi.msimanipulations as msimani
-from regression.preprocessing import preprocess2
-from msi.io.tiffringreader import TiffRingReader
-
-sc = commons.ScriptCommons()
-
-"""
-Collection of functions and luigi.Task s which are used by more than one script
-"""
-
-
-def get_image_files_from_folder(folder,
- prefix="", suffix=".tiff", fullpath=False):
- # small helper function to get all the image files in a folder
- # it will only return files which end with suffix.
- # if fullpath==True it will return the full path of the file, otherwise
- # only the filename
- # get all filenames
- image_files = [f for f in os.listdir(folder) if
- os.path.isfile(os.path.join(folder, f))]
- image_files.sort()
- image_files = [f for f in image_files if f.endswith(suffix)]
- image_files = [f for f in image_files if f.startswith(prefix)]
- if fullpath: # expand to full path if wished
- image_files = [os.path.join(folder, f) for f in image_files]
- return image_files
-
-
-def plot_image(image, axis=None, title=None, cmap=None):
- if axis is None:
- axis = plt.gca()
- if cmap is None:
- im = axis.imshow(image, interpolation='nearest', alpha=1.0)
- else:
- im = axis.imshow(image, interpolation='nearest', alpha=1.0,
- cmap=cmap)
- divider = make_axes_locatable(axis)
- cax = divider.append_axes("right", size="20%", pad=0.05)
- cbar = plt.colorbar(im, cax=cax)
-
- axis.xaxis.set_visible(False)
- axis.yaxis.set_visible(False)
- if title is not None:
- axis.set_title(title)
-
-
-class IPCAITrainRegressor(luigi.Task):
- df_prefix = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- "reg_small_bowel_" +
- self.df_prefix))
-
- def requires(self):
- return tasks_mc.SpectroCamBatch(self.df_prefix)
-
- def run(self):
- # extract data from the batch
- df_train = pd.read_csv(self.input().path, header=[0, 1])
-
- X, y = preprocess2(df_train, snr=10.)
- # train regressor
- reg = RandomForestRegressor(10, min_samples_leaf=10, max_depth=9,
- n_jobs=-1)
- # reg = KNeighborsRegressor(algorithm="auto")
- # reg = LinearRegression()
- # reg = sklearn.svm.SVR(kernel="rbf", degree=3, C=100., gamma=10.)
- # reg = LinearSaO2Unmixing()
- reg.fit(X, y.values)
- # reg = LinearSaO2Unmixing()
- # save regressor
- regressor_file = self.output().open('w')
- pickle.dump(reg, regressor_file)
- regressor_file.close()
-
-
-class SingleMultispectralImage(luigi.Task):
-
- image = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(self.image)
-
-
-class Flatfield(luigi.Task):
-
- flatfield_folder = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- "flatfield.nrrd"))
-
- def run(self):
- tiff_ring_reader = TiffRingReader()
- nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
-
- # analyze all the first image files
- image_files = get_image_files_from_folder(self.flatfield_folder)
- image_files = filter(lambda image_name: "F0" in image_name, image_files)
-
- # helper function to take maximum of two images
- def maximum_of_two_images(image_1, image_name_2):
- image_2 = tiff_ring_reader.read(os.path.join(self.flatfield_folder,
- image_name_2),
- nr_filters)[0].get_image()
- return np.maximum(image_1, image_2)
-
- # now reduce to maximum of all the single images
- flat_maximum = reduce(lambda x, y: maximum_of_two_images(x, y),
- image_files, 0)
- msi = Msi(image=flat_maximum)
- msi.set_wavelengths(sc.other["RECORDED_WAVELENGTHS"])
-
- # write flatfield as nrrd
- writer = NrrdWriter(msi)
- writer.write(self.output().path)
-
-
-class Dark(luigi.Task):
- dark_folder = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- "dark" +
- ".nrrd"))
-
- def run(self):
- tiff_ring_reader = TiffRingReader()
- nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
-
- # analyze all the first image files
- image_files = get_image_files_from_folder(self.dark_folder,
- suffix="F0.tiff")
-
- # returns the mean dark image vector of all inputted dark image
- # overly complicated TODO SW: make this simple code readable.
- dark_means = map(lambda image_name:
- msimani.calculate_mean_spectrum(
- tiff_ring_reader.read(os.path.join(self.dark_folder, image_name),
- nr_filters)[0]),
- image_files)
- dark_means_sum = reduce(lambda x, y: x+y.get_image(), dark_means, 0)
- final_dark_mean = dark_means_sum / len(dark_means)
-
- msi = Msi(image=final_dark_mean)
- msi.set_wavelengths(sc.other["RECORDED_WAVELENGTHS"])
-
- # write flatfield as nrrd
- writer = NrrdWriter(msi)
- writer.write(self.output().path)
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/tasks_mc.py b/Modules/Biophotonics/python/iMC/scripts/ipcai2016/tasks_mc.py
deleted file mode 100644
index c3771dfd9d..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai2016/tasks_mc.py
+++ /dev/null
@@ -1,155 +0,0 @@
-'''
-Created on Sep 10, 2015
-
-@author: wirkert
-'''
-
-
-
-import os
-
-import pandas as pd
-import numpy as np
-import luigi
-from scipy.interpolate import interp1d
-from sklearn.preprocessing import normalize
-
-import commons
-import mc.dfmanipulations as dfmani
-from msi.io.spectrometerreader import SpectrometerReader
-
-sc = commons.ScriptCommons()
-
-
-class SpectrometerFile(luigi.Task):
- input_file = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(self.input_file)
-
-
-class FilterTransmission(luigi.Task):
- input_file = luigi.Parameter()
-
- def requires(self):
- return SpectrometerFile(self.input_file)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- "processed_transmission" + os.path.split(self.input_file)[1]))
-
- def run(self):
- reader = SpectrometerReader()
- filter_transmission = reader.read(self.input().path)
- # filter high and low _wavelengths
- wavelengths = filter_transmission.get_wavelengths()
- fi_image = filter_transmission.get_image()
- fi_image[wavelengths < 450 * 10 ** -9] = 0.0
- fi_image[wavelengths > 720 * 10 ** -9] = 0.0
- # filter elements farther away than +- 30nm
- file_name = os.path.split(self.input_file)[1]
- name_to_float = float(os.path.splitext(file_name)[0])
- fi_image[wavelengths < (name_to_float - 30) * 10 ** -9] = 0.0
- fi_image[wavelengths > (name_to_float + 30) * 10 ** -9] = 0.0
- # elements < 0 are set to 0.
- fi_image[fi_image < 0.0] = 0.0
-
- # write it to a dataframe
- df = pd.DataFrame()
- df["wavelengths"] = wavelengths
- df["reflectances"] = fi_image
- df.to_csv(self.output().path, index=False)
-
-
-class JoinBatches(luigi.Task):
- df_prefix = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- self.df_prefix + "_" +
- "all" + ".txt"))
-
- def run(self):
- # get all files in the search path
- files = [f for f in os.listdir(sc.get_full_dir("MC_DATA_FOLDER"))
- if os.path.isfile(os.path.join(sc.get_full_dir("MC_DATA_FOLDER"), f))]
- # from these get only those who start with correct batch prefix
- df_file_names = [os.path.join(sc.get_full_dir("MC_DATA_FOLDER"), f)
- for f in files if f.startswith(self.df_prefix)]
- # load these files
- dfs = [pd.read_csv(f, header=[0, 1]) for f in df_file_names]
- # now join them to one batch
- joined_df = pd.concat(dfs, ignore_index=True)
- # write it
- joined_df.to_csv(self.output().path, index=False)
-
-
-class CameraBatch(luigi.Task):
- """takes a batch of reference data and converts it to the spectra
- processed by a camera with the specified wavelengths assuming a 10nm FWHM"""
- df_prefix = luigi.Parameter()
-
- def requires(self):
- return JoinBatches(self.df_prefix)
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- self.df_prefix +
- "_all_virtual_camera.txt"))
-
- def run(self):
- # load dataframe
- df = pd.read_csv(self.input().path, header=[0, 1])
- # camera batch creation:
- dfmani.fold_by_sliding_average(df, 6)
- dfmani.interpolate_wavelengths(df, sc.other["RECORDED_WAVELENGTHS"])
- # write it
- df.to_csv(self.output().path, index=False)
-
-
-class SpectroCamBatch(luigi.Task):
- """
- Same as CameraBatch in purpose but adapts the batch to our very specific
- SpectroCam set-up.
- """
- df_prefix = luigi.Parameter()
-
- def requires(self):
- # all wavelengths must have been measured for transmission and stored in
- # wavelength.txt files (e.g. 470.txt)
- filenames = ((sc.other["RECORDED_WAVELENGTHS"] * 10**9).astype(int)).astype(str)
- filenames = map(lambda name: FilterTransmission(os.path.join(sc.get_full_dir("FILTER_TRANSMISSIONS"),
- name +
- ".txt")),
- filenames)
-
- return JoinBatches(self.df_prefix), filenames
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("INTERMEDIATES_FOLDER"),
- self.df_prefix +
- "_all_spectrocam.txt"))
-
- def run(self):
- # load dataframe
- df = pd.read_csv(self.input()[0].path, header=[0, 1])
- # camera batch creation:
- new_reflectances = []
- for band in self.input()[1]:
- df_filter = pd.read_csv(band.path)
- interpolator = interp1d(df_filter["wavelengths"],
- df_filter["reflectances"],
- assume_sorted=False, bounds_error=False)
- # use this to create new reflectances
- interpolated_filter = interpolator(df["reflectances"].
- columns.astype(float))
- # normalize band response
- normalize(interpolated_filter.reshape(1, -1), norm='l1', copy=False)
- folded_reflectance = np.dot(df["reflectances"].values,
- interpolated_filter)
- new_reflectances.append(folded_reflectance)
- new_reflectances = np.array(new_reflectances).T
- dfmani.switch_reflectances(df, sc.other["RECORDED_WAVELENGTHS"],
- new_reflectances)
- # write it
- df.to_csv(self.output().path, index=False)
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/__init__.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_image_hdf5.h5_list.txt b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_image_hdf5.h5_list.txt
deleted file mode 100644
index 1a0f78a1b1..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_image_hdf5.h5_list.txt
+++ /dev/null
@@ -1 +0,0 @@
-ipcai_image_hdf5.h5
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_solver.prototxt b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_solver.prototxt
deleted file mode 100644
index d76ba8c7f1..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_solver.prototxt
+++ /dev/null
@@ -1,24 +0,0 @@
-# The train/test net protocol buffer definition
-train_net: "ipcai_train.prototxt"
-test_net: "ipcai_test.prototxt"
-# test_iter specifies how many forward passes the test should carry out.
-# In the case of MNIST, we have test batch size 100 and 100 test iterations,
-# covering the full 10,000 testing images.
-test_iter: 100
-# Carry out testing every 500 training iterations.
-test_interval: 500
-# The base learning rate, momentum and the weight decay of the network.
-base_lr: 0.01
-momentum: 0.0
-weight_decay: 0.0005
-# The learning rate policy
-lr_policy: "inv"
-gamma: 0.0001
-power: 0.75
-# Display every 100 iterations
-display: 1000
-# The maximum number of iterations
-max_iter: 10000
-# snapshot intermediate results
-snapshot: 5000
-snapshot_prefix: "snapshot"
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test.prototxt b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test.prototxt
deleted file mode 100644
index 72534d20a0..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test.prototxt
+++ /dev/null
@@ -1,77 +0,0 @@
-layer {
- name: "data"
- type: "HDF5Data"
- top: "data"
- top: "label"
- hdf5_data_param {
- source: "ipcai_test_hdf5.h5_list.txt"
- batch_size: 50
- }
-}
-layer {
- name: "fc1"
- type: "InnerProduct"
- bottom: "data"
- top: "fc1"
- inner_product_param {
- num_output: 25
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "relu1"
- type: "ReLU"
- bottom: "fc1"
- top: "fc1"
-}
-layer {
- name: "fc2"
- type: "InnerProduct"
- bottom: "fc1"
- top: "fc2"
- inner_product_param {
- num_output: 25
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "relu2"
- type: "ReLU"
- bottom: "fc2"
- top: "fc2"
-}
-layer {
- name: "score"
- type: "InnerProduct"
- bottom: "fc2"
- top: "score"
- inner_product_param {
- num_output: 1
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "loss"
- type: "EuclideanLoss"
- bottom: "score"
- bottom: "label"
- top: "loss"
-}
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test_hdf5.h5_list.txt b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test_hdf5.h5_list.txt
deleted file mode 100644
index 691abad4da..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test_hdf5.h5_list.txt
+++ /dev/null
@@ -1 +0,0 @@
-ipcai_test_hdf5.h5
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test_image.prototxt b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test_image.prototxt
deleted file mode 100644
index 6bc1620c4f..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_test_image.prototxt
+++ /dev/null
@@ -1,70 +0,0 @@
-
-layer {
- name: "data"
- type: "HDF5Data"
- top: "data"
- hdf5_data_param {
- source: "ipcai_image_hdf5.h5_list.txt"
- batch_size: 1263612
- }
-}
-layer {
- name: "fc1"
- type: "InnerProduct"
- bottom: "data"
- top: "fc1"
- inner_product_param {
- num_output: 25
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "relu1"
- type: "ReLU"
- bottom: "fc1"
- top: "fc1"
-}
-layer {
- name: "fc2"
- type: "InnerProduct"
- bottom: "fc1"
- top: "fc2"
- inner_product_param {
- num_output: 25
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "relu2"
- type: "ReLU"
- bottom: "fc2"
- top: "fc2"
-}
-layer {
- name: "score"
- type: "InnerProduct"
- bottom: "fc2"
- top: "score"
- inner_product_param {
- num_output: 1
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_train.prototxt b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_train.prototxt
deleted file mode 100644
index d79b65aa90..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_train.prototxt
+++ /dev/null
@@ -1,77 +0,0 @@
-layer {
- name: "data"
- type: "HDF5Data"
- top: "data"
- top: "label"
- hdf5_data_param {
- source: "ipcai_train_hdf5.h5_list.txt"
- batch_size: 100
- }
-}
-layer {
- name: "fc1"
- type: "InnerProduct"
- bottom: "data"
- top: "fc1"
- inner_product_param {
- num_output: 25
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "relu1"
- type: "ReLU"
- bottom: "fc1"
- top: "fc1"
-}
-layer {
- name: "fc2"
- type: "InnerProduct"
- bottom: "fc1"
- top: "fc2"
- inner_product_param {
- num_output: 25
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "relu2"
- type: "ReLU"
- bottom: "fc2"
- top: "fc2"
-}
-layer {
- name: "score"
- type: "InnerProduct"
- bottom: "fc2"
- top: "score"
- inner_product_param {
- num_output: 1
- weight_filler {
- type: "xavier"
- }
- bias_filler {
- type: "constant"
- value: 0.1
- }
- }
-}
-layer {
- name: "loss"
- type: "EuclideanLoss"
- bottom: "score"
- bottom: "label"
- top: "loss"
-}
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_train_hdf5.h5_list.txt b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_train_hdf5.h5_list.txt
deleted file mode 100644
index d4b8316827..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/ipcai_train_hdf5.h5_list.txt
+++ /dev/null
@@ -1 +0,0 @@
-ipcai_train_hdf5.h5
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_create_hdf5_database.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_create_hdf5_database.py
deleted file mode 100644
index 3c416e3446..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_create_hdf5_database.py
+++ /dev/null
@@ -1,29 +0,0 @@
-import h5py, os
-import pandas as pd
-
-from regression.preprocessing import preprocess
-
-
-def create_hdf5(path_to_simulation_results, hdf5_name):
-
- df = pd.read_csv(path_to_simulation_results, header=[0, 1])
-
- X, y = preprocess(df, snr=10.)
- y = y.values
-
- with h5py.File(hdf5_name,'w') as H:
- H.create_dataset('data', data=X ) # note the name X given to the dataset!
- H.create_dataset('label', data=y ) # note the name y given to the dataset!
- with open(hdf5_name + '_list.txt','w') as L:
- L.write(hdf5_name) # list all h5 files you are going to use
-
-
-data_root = "/media/wirkert/data/Data/2016_02_02_IPCAI/results/intermediate"
-
-TRAIN_IMAGES = os.path.join(data_root,
- "ipcai_revision_colon_mean_scattering_train_all_spectrocam.txt")
-TEST_IMAGES = os.path.join(data_root,
- "ipcai_revision_colon_mean_scattering_test_all_spectrocam.txt")
-
-create_hdf5(TRAIN_IMAGES, "ipcai_train_hdf5.h5")
-create_hdf5(TEST_IMAGES, "ipcai_test_hdf5.h5")
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_create_lmdb_database.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_create_lmdb_database.py
deleted file mode 100644
index ad0160c8ce..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_create_lmdb_database.py
+++ /dev/null
@@ -1,52 +0,0 @@
-
-import os
-
-import pandas as pd
-import lmdb
-import caffe
-
-from regression.preprocessing import preprocess
-
-
-def create_lmdb(path_to_simulation_results, lmdb_name):
-
- df = pd.read_csv(path_to_simulation_results, header=[0, 1])
-
- X, y = preprocess(df, snr=10.)
- y = y.values * 1000
-
- # We need to prepare the database for the size. We'll set it 10 times
- # greater than what we theoretically need. There is little drawback to
- # setting this too big. If you still run into problem after raising
- # this, you might want to try saving fewer entries in a single
- # transaction.
- map_size = X.nbytes * 10
-
- env = lmdb.open(lmdb_name, map_size=map_size)
-
- with env.begin(write=True) as txn:
- # txn is a Transaction object
- for i in range(X.shape[0]):
- datum = caffe.proto.caffe_pb2.Datum()
- datum.channels = X.shape[1]
- datum.height = 1
- datum.width = 1
- datum.data = X[i].tobytes() # or .tostring() if numpy < 1.9
- datum.label = int(y[i])
- str_id = '{:08}'.format(i)
-
- # The encode is only essential in Python 3
- txn.put(str_id.encode('ascii'), datum.SerializeToString())
-
-
-data_root = "/media/wirkert/data/Data/2016_02_02_IPCAI/results/intermediate"
-
-TRAIN_IMAGES = os.path.join(data_root,
- "ipcai_revision_colon_mean_scattering_train_all_spectrocam.txt")
-TEST_IMAGES = os.path.join(data_root,
- "ipcai_revision_colon_mean_scattering_test_all_spectrocam.txt")
-
-create_lmdb(TRAIN_IMAGES, "ipcai_train_lmdb")
-create_lmdb(TEST_IMAGES, "ipcai_test_lmdb")
-
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_test_pretrained_model.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_test_pretrained_model.py
deleted file mode 100644
index 688ad933ec..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_test_pretrained_model.py
+++ /dev/null
@@ -1,26 +0,0 @@
-
-import time
-
-import caffe
-
-from ipcai2016.tasks_common import plot_image
-
-model_def = 'ipcai_test_image.prototxt'
-model_weights = 'snapshot_iter_100000.caffemodel'
-
-net = caffe.Net(model_def, # defines the structure of the model
- model_weights, # contains the trained weights
- caffe.TEST) # use test mode (e.g., don't perform dropout)
-
-### perform classification
-
-start = time.time()
-output = net.forward()
-end = time.time()
-estimation_time = end - start
-
-print "time necessary for estimating image parameters: " + str(estimation_time) + "s"
-
-image = output['score'].reshape(1029,1228)
-
-plot_image(image)
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_train_caffe.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_train_caffe.py
deleted file mode 100644
index c269272502..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_caffe/script_train_caffe.py
+++ /dev/null
@@ -1,83 +0,0 @@
-from pylab import *
-
-import caffe
-from caffe import layers as L, params as P
-
-
-def ipcai(database, batch_size):
- # our version of LeNet: a series of linear and simple nonlinear transformations
- n = caffe.NetSpec()
-
- n.data, n.label = L.HDF5Data(batch_size=batch_size, source=database, ntop=2)
-
- n.fc1 = L.InnerProduct(n.data, num_output=25, weight_filler=dict(type='xavier'),
- bias_filler=dict(type='constant', value=0.1))
- n.relu1 = L.ReLU(n.fc1, in_place=True)
- n.fc2 = L.InnerProduct(n.relu1, num_output=25, weight_filler=dict(type='xavier'),
- bias_filler=dict(type='constant', value=0.1))
- n.relu2 = L.ReLU(n.fc2, in_place=True)
- n.score = L.InnerProduct(n.relu2, num_output=1, weight_filler=dict(type='xavier'),
- bias_filler=dict(type='constant', value=0.1))
- n.loss = L.EuclideanLoss(n.score, n.label)
-
- return n.to_proto()
-
-with open('ipcai_train.prototxt', 'w') as f:
- f.write(str(ipcai('ipcai_train_hdf5.h5_list.txt', 100)))
-
-with open('ipcai_test.prototxt', 'w') as f:
- f.write(str(ipcai('ipcai_test_hdf5.h5_list.txt', 50)))
-
-caffe.set_device(0)
-caffe.set_mode_gpu()
-
-### load the solver and create train and test nets
-solver = None # ignore this workaround for lmdb data (can't instantiate two solvers on the same data)
-solver = caffe.SGDSolver('ipcai_solver.prototxt')
-
-# each output is (batch size, feature dim, spatial dim)
-print [(k, v.data.shape) for k, v in solver.net.blobs.items()]
-
-# just print the weight sizes (we'll omit the biases)
-print [(k, v[0].data.shape) for k, v in solver.net.params.items()]
-
-solver.net.forward() # train net
-print solver.test_nets[0].forward() # test net (there can be more than one)
-
-niter = 100000
-test_interval = 1000
-# losses will also be stored in the log
-train_loss = zeros(niter)
-test_acc = zeros(int(np.ceil(niter / test_interval)))
-output = zeros((niter, 8, 10))
-
-# the main solver loop
-for it in range(niter):
- solver.step(1) # SGD by Caffe
-
- # store the train loss
- train_loss[it] = solver.net.blobs['loss'].data
-
- # store the output on the first test batch
- # (start the forward pass at fc1 to avoid loading new data)
- solver.test_nets[0].forward(start='fc1')
- output[it] = solver.test_nets[0].blobs['score'].data[:8]
-
- # run a full test every so often
- # (Caffe can also do this for us and write to a log, but we show here
- # how to do it directly in Python, where more complicated things are easier.)
- if it % test_interval == 0:
- print 'Iteration', it, 'testing...'
- mean = 0.
- for i in range(100):
- solver.test_nets[0].forward()
- mean += np.sum(np.abs(np.squeeze(solver.test_nets[0].blobs['score'].data)
- - solver.test_nets[0].blobs['label'].data))
- mean = mean / 5000
- test_acc[it // test_interval] = mean * 100. # %
-
-print "final testing accuracy: ", test_acc[-1]
-
-
-print solver.test_nets[0].blobs['score'].data
-print solver.test_nets[0].blobs['label'].data
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/__init__.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/input_data.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/input_data.py
deleted file mode 100644
index d1d0d28e2b..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/input_data.py
+++ /dev/null
@@ -1,144 +0,0 @@
-"""Functions for downloading and reading MNIST data."""
-from __future__ import print_function
-import gzip
-import os
-import urllib
-import numpy
-SOURCE_URL = 'http://yann.lecun.com/exdb/mnist/'
-def maybe_download(filename, work_directory):
- """Download the data from Yann's website, unless it's already here."""
- if not os.path.exists(work_directory):
- os.mkdir(work_directory)
- filepath = os.path.join(work_directory, filename)
- if not os.path.exists(filepath):
- filepath, _ = urllib.urlretrieve(SOURCE_URL + filename, filepath)
- statinfo = os.stat(filepath)
- print('Succesfully downloaded', filename, statinfo.st_size, 'bytes.')
- return filepath
-def _read32(bytestream):
- dt = numpy.dtype(numpy.uint32).newbyteorder('>')
- return numpy.frombuffer(bytestream.read(4), dtype=dt)
-def extract_images(filename):
- """Extract the images into a 4D uint8 numpy array [index, y, x, depth]."""
- print('Extracting', filename)
- with gzip.open(filename) as bytestream:
- magic = _read32(bytestream)
- if magic != 2051:
- raise ValueError(
- 'Invalid magic number %d in MNIST image file: %s' %
- (magic, filename))
- num_images = _read32(bytestream)
- rows = _read32(bytestream)
- cols = _read32(bytestream)
- buf = bytestream.read(rows * cols * num_images)
- data = numpy.frombuffer(buf, dtype=numpy.uint8)
- data = data.reshape(num_images, rows, cols, 1)
- return data
-def dense_to_one_hot(labels_dense, num_classes=10):
- """Convert class labels from scalars to one-hot vectors."""
- num_labels = labels_dense.shape[0]
- index_offset = numpy.arange(num_labels) * num_classes
- labels_one_hot = numpy.zeros((num_labels, num_classes))
- labels_one_hot.flat[index_offset + labels_dense.ravel()] = 1
- return labels_one_hot
-def extract_labels(filename, one_hot=False):
- """Extract the labels into a 1D uint8 numpy array [index]."""
- print('Extracting', filename)
- with gzip.open(filename) as bytestream:
- magic = _read32(bytestream)
- if magic != 2049:
- raise ValueError(
- 'Invalid magic number %d in MNIST label file: %s' %
- (magic, filename))
- num_items = _read32(bytestream)
- buf = bytestream.read(num_items)
- labels = numpy.frombuffer(buf, dtype=numpy.uint8)
- if one_hot:
- return dense_to_one_hot(labels)
- return labels
-class DataSet(object):
- def __init__(self, images, labels, fake_data=False):
- if fake_data:
- self._num_examples = 10000
- else:
- assert images.shape[0] == labels.shape[0], (
- "images.shape: %s labels.shape: %s" % (images.shape,
- labels.shape))
- self._num_examples = images.shape[0]
- # Convert shape from [num examples, rows, columns, depth]
- # to [num examples, rows*columns] (assuming depth == 1)
- assert images.shape[3] == 1
- images = images.reshape(images.shape[0],
- images.shape[1] * images.shape[2])
- # Convert from [0, 255] -> [0.0, 1.0].
- images = images.astype(numpy.float32)
- images = numpy.multiply(images, 1.0 / 255.0)
- self._images = images
- self._labels = labels
- self._epochs_completed = 0
- self._index_in_epoch = 0
- @property
- def images(self):
- return self._images
- @property
- def labels(self):
- return self._labels
- @property
- def num_examples(self):
- return self._num_examples
- @property
- def epochs_completed(self):
- return self._epochs_completed
- def next_batch(self, batch_size, fake_data=False):
- """Return the next `batch_size` examples from this data set."""
- if fake_data:
- fake_image = [1.0 for _ in xrange(784)]
- fake_label = 0
- return [fake_image for _ in xrange(batch_size)], [
- fake_label for _ in xrange(batch_size)]
- start = self._index_in_epoch
- self._index_in_epoch += batch_size
- if self._index_in_epoch > self._num_examples:
- # Finished epoch
- self._epochs_completed += 1
- # Shuffle the data
- perm = numpy.arange(self._num_examples)
- numpy.random.shuffle(perm)
- self._images = self._images[perm]
- self._labels = self._labels[perm]
- # Start next epoch
- start = 0
- self._index_in_epoch = batch_size
- assert batch_size <= self._num_examples
- end = self._index_in_epoch
- return self._images[start:end], self._labels[start:end]
-def read_data_sets(train_dir, fake_data=False, one_hot=False):
- class DataSets(object):
- pass
- data_sets = DataSets()
- if fake_data:
- data_sets.train = DataSet([], [], fake_data=True)
- data_sets.validation = DataSet([], [], fake_data=True)
- data_sets.test = DataSet([], [], fake_data=True)
- return data_sets
- TRAIN_IMAGES = 'train-images-idx3-ubyte.gz'
- TRAIN_LABELS = 'train-labels-idx1-ubyte.gz'
- TEST_IMAGES = 't10k-images-idx3-ubyte.gz'
- TEST_LABELS = 't10k-labels-idx1-ubyte.gz'
- VALIDATION_SIZE = 5000
- local_file = maybe_download(TRAIN_IMAGES, train_dir)
- train_images = extract_images(local_file)
- local_file = maybe_download(TRAIN_LABELS, train_dir)
- train_labels = extract_labels(local_file, one_hot=one_hot)
- local_file = maybe_download(TEST_IMAGES, train_dir)
- test_images = extract_images(local_file)
- local_file = maybe_download(TEST_LABELS, train_dir)
- test_labels = extract_labels(local_file, one_hot=one_hot)
- validation_images = train_images[:VALIDATION_SIZE]
- validation_labels = train_labels[:VALIDATION_SIZE]
- train_images = train_images[VALIDATION_SIZE:]
- train_labels = train_labels[VALIDATION_SIZE:]
- data_sets.train = DataSet(train_images, train_labels)
- data_sets.validation = DataSet(validation_images, validation_labels)
- data_sets.test = DataSet(test_images, test_labels)
- return data_sets
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/input_ipcai_data.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/input_ipcai_data.py
deleted file mode 100644
index 65429d72ad..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/input_ipcai_data.py
+++ /dev/null
@@ -1,103 +0,0 @@
-"""Functions for downloading and reading ipcai data."""
-from __future__ import print_function
-
-import os
-
-import numpy
-import pandas as pd
-
-from regression.preprocessing import preprocess
-
-
-class DataSet(object):
- def __init__(self, images, labels, fake_data=False):
- if fake_data:
- self._num_examples = 10000
- else:
- assert images.shape[0] == labels.shape[0], (
- "images.shape: %s labels.shape: %s" % (images.shape,
- labels.shape))
- self._num_examples = images.shape[0]
- images = images.astype(numpy.float32)
- self._images = images
- self._labels = labels
- if self._labels.ndim == 1:
- self._labels = self._labels[:, numpy.newaxis]
- self._epochs_completed = 0
- self._index_in_epoch = 0
-
- @property
- def images(self):
- return self._images
-
- @property
- def labels(self):
- return self._labels
-
- @property
- def num_examples(self):
- return self._num_examples
-
- @property
- def epochs_completed(self):
- return self._epochs_completed
-
- def next_batch(self, batch_size, fake_data=False):
- """Return the next `batch_size` examples from this data set."""
- if fake_data:
- fake_image = [1.0 for _ in xrange(784)]
- fake_label = 0
- return [fake_image for _ in xrange(batch_size)], [
- fake_label for _ in xrange(batch_size)]
- start = self._index_in_epoch
- self._index_in_epoch += batch_size
- if self._index_in_epoch > self._num_examples:
- # Finished epoch
- self._epochs_completed += 1
- # Shuffle the data
- perm = numpy.arange(self._num_examples)
- numpy.random.shuffle(perm)
- self._images = self._images[perm]
- self._labels = self._labels[perm]
-
- # Start next epoch
- start = 0
- self._index_in_epoch = batch_size
- assert batch_size <= self._num_examples
- end = self._index_in_epoch
- return self._images[start:end], self._labels[start:end]
-
-
-def read_data_sets(dir, fake_data=False):
-
- class DataSets(object):
- pass
- data_sets = DataSets()
- if fake_data:
- data_sets.train = DataSet([], [], fake_data=True)
- data_sets.validation = DataSet([], [], fake_data=True)
- data_sets.test = DataSet([], [], fake_data=True)
- return data_sets
-
- TRAIN_IMAGES = "ipcai_revision_colon_mean_scattering_train_all_spectrocam.txt"
- TEST_IMAGES = "ipcai_revision_colon_mean_scattering_test_all_spectrocam.txt"
-
- df_train = pd.read_csv(os.path.join(dir, TRAIN_IMAGES), header=[0, 1])
- df_test = pd.read_csv(os.path.join(dir, TEST_IMAGES), header=[0, 1])
-
- train_images, train_labels = preprocess(df_train, snr=10.)
- test_images, test_labels = preprocess(df_test, snr=10.)
-
- train_labels = train_labels.values
- test_labels = test_labels.values
-
- VALIDATION_SIZE = 1
-
- validation_images = train_images[:VALIDATION_SIZE]
- validation_labels = train_labels[:VALIDATION_SIZE]
- train_images = train_images[VALIDATION_SIZE:]
- train_labels = train_labels[VALIDATION_SIZE:]
- data_sets.train = DataSet(train_images, train_labels)
- data_sets.validation = DataSet(validation_images, validation_labels)
- data_sets.test = DataSet(test_images, test_labels)
- return data_sets
\ No newline at end of file
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/script_train_tensorflow_model.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/script_train_tensorflow_model.py
deleted file mode 100644
index ee85401f73..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_tensorflow/script_train_tensorflow_model.py
+++ /dev/null
@@ -1,270 +0,0 @@
-
-import Image
-import ImageEnhance
-import logging
-import datetime
-
-import SimpleITK as sitk
-import tensorflow as tf
-
-from regression.tensorflow_estimator import multilayer_perceptron, cnn
-from regression.tensorflow_dataset import read_data_set
-from ipcai2016.tasks_common import *
-import commons
-from msi.io.nrrdreader import NrrdReader
-import msi.normalize as norm
-from regression.estimation import estimate_image_tensorflow
-
-sc = commons.ScriptCommons()
-sc.set_root("/media/wirkert/data/Data/2016_02_02_IPCAI/")
-sc.create_folders()
-
-ipcai_dir = sc.get_full_dir("INTERMEDIATES_FOLDER")
-
-sc.add_dir("SMALL_BOWEL_DATA",
- os.path.join(sc.get_dir("DATA_FOLDER"), "small_bowel_images"))
-
-sc.add_dir("TENSORFLOW_DATA",
- os.path.join(sc.get_dir("INTERMEDIATES_FOLDER"), "TensorflowModels"))
-
-sc.add_dir("SMALL_BOWEL_RESULT", os.path.join(sc.get_dir("RESULTS_FOLDER"),
- "small_bowel_tensorflow"))
-
-sc.add_dir("FILTER_TRANSMISSIONS",
- os.path.join(sc.get_dir("DATA_FOLDER"),
- "filter_transmissions"))
-
-
-
-def plot_image(image, axis):
- im2 = axis.imshow(image, interpolation='nearest', alpha=1.0)
- axis.xaxis.set_visible(False)
-
-
-class TensorFlowCreateOxyImageTask(luigi.Task):
- image_name = luigi.Parameter()
- df_prefix = luigi.Parameter()
- df_test_prefix = luigi.Parameter()
-
- def requires(self):
- return TensorflowTrainRegressor(df_prefix=self.df_prefix,
- df_test_prefix=self.df_test_prefix), \
- Flatfield(flatfield_folder=sc.get_full_dir("FLAT_FOLDER")), \
- SingleMultispectralImage(image=self.image_name), \
- Dark(dark_folder=sc.get_full_dir("DARK_FOLDER"))
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("SMALL_BOWEL_RESULT"),
- os.path.split(self.image_name)[1] +
- "_" + self.df_prefix +
- "_summary" + ".png"))
-
-
- def run(self):
- nrrd_reader = NrrdReader()
- tiff_ring_reader = TiffRingReader()
- # read the flatfield
- flat = nrrd_reader.read(self.input()[1].path)
- dark = nrrd_reader.read(self.input()[3].path)
- # read the msi
- nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
- msi, segmentation = tiff_ring_reader.read(self.input()[2].path,
- nr_filters, resize_factor=0.5)
- # only take into account not saturated pixels.
- segmentation = np.logical_and(segmentation,
- (np.max(msi.get_image(),
- axis=-1) < 1000.))
-
- # correct image setup
- filter_nr = int(self.image_name[-6:-5])
- original_order = np.arange(nr_filters)
- new_image_order = np.concatenate((
- original_order[nr_filters - filter_nr:],
- original_order[:nr_filters - filter_nr]))
- # resort msi to restore original order
- msimani.get_bands(msi, new_image_order)
- # correct by flatfield
- msimani.image_correction(msi, flat, dark)
-
- # create artificial rgb
- rgb_image = msi.get_image()[:, :, [2, 3, 1]]
- rgb_image /= np.max(rgb_image)
- rgb_image *= 255.
-
- # preprocess the image
- # sortout unwanted bands
- print "1"
- # zero values would lead to infinity logarithm, thus clip.
- msi.set_image(np.clip(msi.get_image(), 0.00001, 2. ** 64))
- # normalize to get rid of lighting intensity
- norm.standard_normalizer.normalize(msi)
- # transform to absorption
- msi.set_image(-np.log(msi.get_image()))
- # normalize by l2 for stability
- norm.standard_normalizer.normalize(msi, "l2")
- print "2"
- # estimate
- path = sc.get_full_dir("TENSORFLOW_DATA")
- sitk_image, time = estimate_image_tensorflow(msi, path)
- image = sitk.GetArrayFromImage(sitk_image)
-
- plt.figure()
- print "3"
- rgb_image = rgb_image.astype(np.uint8)
- im = Image.fromarray(rgb_image, 'RGB')
- enh_brightness = ImageEnhance.Brightness(im)
- im = enh_brightness.enhance(10.)
- plotted_image = np.array(im)
- top_left_axis = plt.gca()
- top_left_axis.imshow(plotted_image, interpolation='nearest')
- top_left_axis.xaxis.set_visible(False)
- top_left_axis.yaxis.set_visible(False)
-
- plt.set_cmap("jet")
- print "4"
- # plot parametric maps
- segmentation[0, 0] = 1
- segmentation[0, 1] = 1
- oxy_image = np.ma.masked_array(image[:, :], ~segmentation)
- oxy_image[np.isnan(oxy_image)] = 0.
- oxy_image[np.isinf(oxy_image)] = 0.
- oxy_mean = np.mean(oxy_image)
- oxy_image[0, 0] = 0.0
- oxy_image[0, 1] = 1.
-
- plot_image(oxy_image[:, :], plt.gca())
-
- df_image_results = pd.DataFrame(data=np.expand_dims([self.image_name,
- oxy_mean * 100.,
- time], 0),
- columns=["image name",
- "oxygenation mean [%]",
- "time to estimate"])
-
- results_file = os.path.join(sc.get_full_dir("SMALL_BOWEL_RESULT"),
- "results.csv")
- if os.path.isfile(results_file):
- df_results = pd.read_csv(results_file, index_col=0)
- df_results = pd.concat((df_results, df_image_results)).reset_index(
- drop=True
- )
- else:
- df_results = df_image_results
-
- df_results.to_csv(results_file)
-
- plt.savefig(self.output().path,
- dpi=250, bbox_inches='tight')
- plt.close("all")
-
-
-class TensorflowTrainRegressor(luigi.Task):
- df_prefix = luigi.Parameter()
- df_test_prefix = luigi.Parameter()
-
- def output(self):
- return luigi.LocalTarget(os.path.join(sc.get_full_dir("TENSORFLOW_DATA"),
- "model.ckpt"))
-
- def requires(self):
- return tasks_mc.SpectroCamBatch(self.df_prefix), \
- tasks_mc.SpectroCamBatch(self.df_test_prefix)
-
- def run(self):
- # extract data from the batch
- tensorflow_dataset = read_data_set(self.input()[0].path)
- test_dataset = read_data_set(self.input()[1].path)
-
- # train regressor
- # Construct the desired model
-
- # Network Parameters
- nr_filters = len(sc.other["RECORDED_WAVELENGTHS"])
- x = tf.placeholder("float", [None, nr_filters, 1, 1])
- # Construct the desired model
- keep_prob = tf.placeholder("float")
- # pred, regularizers = multilayer_perceptron(x, nr_filters, 100, 1,
- # keep_prob)
- pred = cnn(x, 1, keep_prob)
- # define parameters
- learning_rate = 0.0001
- training_epochs = 300
- batch_size = 100
- display_step = 1
-
- # Define loss and optimizer
-
- y = tf.placeholder("float", [None, 1])
- cost = tf.reduce_mean(tf.square(pred - y))
- optimizer = tf.train.AdamOptimizer(learning_rate=learning_rate).minimize(cost)
-
- # Initializing the variables
- init = tf.initialize_all_variables()
-
- saver = tf.train.Saver() # defaults to saving all variables
-
- # Launch the graph
- with tf.Session() as sess:
- sess.run(init)
-
- # Training cycle
- for epoch in range(training_epochs):
- avg_cost = 0.
- total_batch = int(tensorflow_dataset.num_examples/batch_size)
- # Loop over all batches
- for i in range(total_batch):
- batch_xs, batch_ys = tensorflow_dataset.next_batch(batch_size)
- # Fit training using batch data
- x_image = np.reshape(batch_xs, [-1, nr_filters, 1, 1])
- sess.run(optimizer, feed_dict={x: x_image, y: batch_ys,
- keep_prob: 0.75})
- # Compute average loss
- avg_cost += sess.run(cost, feed_dict={x: x_image, y: batch_ys,
- keep_prob: 1.0})/total_batch
- # Display logs per epoch step
- if epoch % display_step == 0:
- print "Epoch:", '%04d' % (epoch+1), "cost=", "{:.9f}".format(avg_cost)
-
- # Test model
- accuracy = tf.reduce_mean(tf.cast(tf.abs(pred-y), "float"))
- x_test_image = np.reshape(test_dataset.images, [-1, nr_filters, 1, 1])
- print "Mean testing error:", accuracy.eval({x: x_test_image,
- y: test_dataset.labels,
- keep_prob:1.0})
-
- print "Optimization Finished!"
- saver.save(sess, self.output().path)
-
-
-if __name__ == '__main__':
-
- # create a folder for the results if necessary
- sc.set_root("/media/wirkert/data/Data/2016_02_02_IPCAI/")
- sc.create_folders()
-
- # root folder there the data lies
- logging.basicConfig(filename=os.path.join(sc.get_full_dir("LOG_FOLDER"),
- "small_bowel_images" +
- str(datetime.datetime.now()) +
- '.log'),
- level=logging.INFO)
- luigi.interface.setup_interface_logging()
- ch = logging.StreamHandler()
- ch.setLevel(logging.INFO)
- logger = logging.getLogger()
- logger.addHandler(ch)
-
- sch = luigi.scheduler.CentralPlannerScheduler()
- w = luigi.worker.Worker(scheduler=sch)
-
- # determine files to process
- files = get_image_files_from_folder(sc.get_full_dir("SMALL_BOWEL_DATA"),
- suffix="F0.tiff", fullpath=True)
-
- for f in files:
- main_task = TensorFlowCreateOxyImageTask(image_name=f,
- df_prefix="ipcai_revision_colon_mean_scattering_train",
- df_test_prefix="ipcai_revision_colon_mean_scattering_test")
- w.add(main_task)
- w.run()
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/__init__.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/input_icai_data.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/input_icai_data.py
deleted file mode 100644
index 4aaf742da7..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/input_icai_data.py
+++ /dev/null
@@ -1,110 +0,0 @@
-"""
-This tutorial introduces logistic regression using Theano and stochastic
-gradient descent.
-
-Logistic regression is a probabilistic, linear classifier. It is parametrized
-by a weight matrix :math:`W` and a bias vector :math:`b`. Classification is
-done by projecting data points onto a set of hyperplanes, the distance to
-which is used to determine a class membership probability.
-
-Mathematically, this can be written as:
-
-.. math::
- P(Y=i|x, W,b) &= softmax_i(W x + b) \\
- &= \frac {e^{W_i x + b_i}} {\sum_j e^{W_j x + b_j}}
-
-
-The output of the model or prediction is then done by taking the argmax of
-the vector whose i'th element is P(Y=i|x).
-
-.. math::
-
- y_{pred} = argmax_i P(Y=i|x,W,b)
-
-
-This tutorial presents a stochastic gradient descent optimization method
-suitable for large datasets.
-
-
-References:
-
- - textbooks: "Pattern Recognition and Machine Learning" -
- Christopher M. Bishop, section 4.3.2
-
-"""
-
-from __future__ import print_function
-
-import os
-
-import numpy
-import pandas as pd
-import numpy as np
-
-import theano
-import theano.tensor as T
-
-from regression.preprocessing import preprocess
-
-__docformat__ = 'restructedtext en'
-
-
-def create_dataset(path_to_simulation_results):
-
- df = pd.read_csv(path_to_simulation_results, header=[0, 1])
-
- X, y = preprocess(df, snr=10.)
- y = y.values
- return X, y
-
-
-
-def load_data(data_root):
- ''' Loads the dataset
-
- :type dataset: string
- :param dataset: the path to the dataset (here MNIST)
- '''
-
- TRAIN_IMAGES = os.path.join(data_root,
- "ipcai_revision_colon_mean_scattering_train_all_spectrocam.txt")
- TEST_IMAGES = os.path.join(data_root,
- "ipcai_revision_colon_mean_scattering_test_all_spectrocam.txt")
-
- train_set = create_dataset(TRAIN_IMAGES)
- valid_set = create_dataset(TEST_IMAGES)
- test_set = (np.load("sample_image.npy"), np.array([0]))
-
- def shared_dataset(data_xy, borrow=True):
- """ Function that loads the dataset into shared variables
-
- The reason we store our dataset in shared variables is to allow
- Theano to copy it into the GPU memory (when code is run on GPU).
- Since copying data into the GPU is slow, copying a minibatch everytime
- is needed (the default behaviour if the data is not in a shared
- variable) would lead to a large decrease in performance.
- """
- data_x, data_y = data_xy
- shared_x = theano.shared(numpy.asarray(data_x,
- dtype=theano.config.floatX),
- borrow=borrow)
- shared_y = theano.shared(numpy.asarray(data_y,
- dtype=theano.config.floatX),
- borrow=borrow)
- # When storing data on the GPU it has to be stored as floats
- # therefore we will store the labels as ``floatX`` as well
- # (``shared_y`` does exactly that). But during our computations
- # we need them as ints (we use labels as index, and if they are
- # floats it doesn't make sense) therefore instead of returning
- # ``shared_y`` we will have to cast it to int. This little hack
- # lets ous get around this issue
- return shared_x, shared_y
-
- test_set_x, test_set_y = shared_dataset(test_set, 0)
- valid_set_x, valid_set_y = shared_dataset(valid_set)
- train_set_x, train_set_y = shared_dataset(train_set)
-
- rval = [(train_set_x, train_set_y), (valid_set_x, valid_set_y),
- (test_set_x, test_set_y)]
- return rval
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/logistic_sgd.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/logistic_sgd.py
deleted file mode 100644
index 6ef9f732b3..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/logistic_sgd.py
+++ /dev/null
@@ -1,176 +0,0 @@
-"""
-This tutorial introduces logistic regression using Theano and stochastic
-gradient descent.
-
-Logistic regression is a probabilistic, linear classifier. It is parametrized
-by a weight matrix :math:`W` and a bias vector :math:`b`. Classification is
-done by projecting data points onto a set of hyperplanes, the distance to
-which is used to determine a class membership probability.
-
-Mathematically, this can be written as:
-
-.. math::
- P(Y=i|x, W,b) &= softmax_i(W x + b) \\
- &= \frac {e^{W_i x + b_i}} {\sum_j e^{W_j x + b_j}}
-
-
-The output of the model or prediction is then done by taking the argmax of
-the vector whose i'th element is P(Y=i|x).
-
-.. math::
-
- y_{pred} = argmax_i P(Y=i|x,W,b)
-
-
-This tutorial presents a stochastic gradient descent optimization method
-suitable for large datasets.
-
-
-References:
-
- - textbooks: "Pattern Recognition and Machine Learning" -
- Christopher M. Bishop, section 4.3.2
-
-"""
-
-from __future__ import print_function
-
-import numpy
-
-import theano
-import theano.tensor as T
-
-
-__docformat__ = 'restructedtext en'
-
-
-class LogisticRegression(object):
- """Multi-class Logistic Regression Class
-
- The logistic regression is fully described by a weight matrix :math:`W`
- and bias vector :math:`b`. Classification is done by projecting data
- points onto a set of hyperplanes, the distance to which is used to
- determine a class membership probability.
- """
-
- def __init__(self, input, n_in, n_out):
- """ Initialize the parameters of the logistic regression
-
- :type input: theano.tensor.TensorType
- :param input: symbolic variable that describes the input of the
- architecture (one minibatch)
-
- :type n_in: int
- :param n_in: number of input units, the dimension of the space in
- which the datapoints lie
-
- :type n_out: int
- :param n_out: number of output units, the dimension of the space in
- which the labels lie
-
- """
- # start-snippet-1
- # initialize with 0 the weights W as a matrix of shape (n_in, n_out)
- self.W = theano.shared(
- value=numpy.zeros(
- (n_in, n_out),
- dtype=theano.config.floatX
- ),
- name='W',
- borrow=True
- )
- # initialize the biases b as a vector of n_out 0s
- self.b = theano.shared(
- value=numpy.zeros(
- (n_out,),
- dtype=theano.config.floatX
- ),
- name='b',
- borrow=True
- )
-
- # symbolic expression for computing the matrix of class-membership
- # probabilities
- # Where:
- # W is a matrix where column-k represent the separation hyperplane for
- # class-k
- # x is a matrix where row-j represents input training sample-j
- # b is a vector where element-k represent the free parameter of
- # hyperplane-k
- #self.p_y_given_x = T.nnet.softmax(T.dot(input, self.W) + self.b)
- self.p_y_given_x = T.max(T.dot(input, self.W) + self.b, axis = 1)
-
-
- # symbolic description of how to compute prediction as class whose
- # probability is maximal
- self.y_pred = self.p_y_given_x
- #self.y_pred = self.p_y_given_x
- # end-snippet-1
-
- # parameters of the model
- self.params = [self.W, self.b]
-
- # keep track of model input
- self.input = input
-
- def negative_log_likelihood(self, y):
- """Return the mean of the negative log-likelihood of the prediction
- of this model under a given target distribution.
-
- .. math::
-
- \frac{1}{|\mathcal{D}|} \mathcal{L} (\theta=\{W,b\}, \mathcal{D}) =
- \frac{1}{|\mathcal{D}|} \sum_{i=0}^{|\mathcal{D}|}
- \log(P(Y=y^{(i)}|x^{(i)}, W,b)) \\
- \ell (\theta=\{W,b\}, \mathcal{D})
-
- :type y: theano.tensor.TensorType
- :param y: corresponds to a vector that gives for each example the
- correct label
-
- Note: we use the mean instead of the sum so that
- the learning rate is less dependent on the batch size
- """
- # start-snippet-2
- # y.shape[0] is (symbolically) the number of rows in y, i.e.,
- # number of examples (call it n) in the minibatch
- # T.arange(y.shape[0]) is a symbolic vector which will contain
- # [0,1,2,... n-1] T.log(self.p_y_given_x) is a matrix of
- # Log-Probabilities (call it LP) with one row per example and
- # one column per class LP[T.arange(y.shape[0]),y] is a vector
- # v containing [LP[0,y[0]], LP[1,y[1]], LP[2,y[2]], ...,
- # LP[n-1,y[n-1]]] and T.mean(LP[T.arange(y.shape[0]),y]) is
- # the mean (across minibatch examples) of the elements in v,
- # i.e., the mean log-likelihood across the minibatch.
- theano.printing.Print('p_y_given_x')(self.p_y_given_x)
- theano.printing.Print('y')(y)
- return T.mean(T.square(self.p_y_given_x - y))
- #return -T.mean(T.log(self.p_y_given_x)[T.arange(y.shape[0]), y])
- # end-snippet-2
-
- def errors(self, y):
- """Return a float representing the number of errors in the minibatch
- over the total number of examples of the minibatch ; zero one
- loss over the size of the minibatch
-
- :type y: theano.tensor.TensorType
- :param y: corresponds to a vector that gives for each example the
- correct label
- """
-
- # check if y has same dimension of y_pred
- if y.ndim != self.y_pred.ndim:
- raise TypeError(
- 'y should have the same shape as self.y_pred',
- ('y', y.type, 'y_pred', self.y_pred.type)
- )
- # check if y is of the correct datatype
- if y.dtype.startswith('float'):
- # the T.neq operator returns a vector of 0s and 1s, where 1
- # represents a mistake in prediction
- return T.mean(T.abs_(self.y_pred - y))
- else:
- raise NotImplementedError()
-
-
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/script_train_theano_model.py b/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/script_train_theano_model.py
deleted file mode 100644
index 32c2a7045e..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/ipcai_to_theano/script_train_theano_model.py
+++ /dev/null
@@ -1,445 +0,0 @@
-
-
-"""
-This tutorial introduces the multilayer perceptron using Theano.
-
- A multilayer perceptron is a logistic regressor where
-instead of feeding the input to the logistic regression you insert a
-intermediate layer, called the hidden layer, that has a nonlinear
-activation function (usually tanh or sigmoid) . One can use many such
-hidden layers making the architecture deep. The tutorial will also tackle
-the problem of MNIST digit classification.
-
-.. math::
-
- f(x) = G( b^{(2)} + W^{(2)}( s( b^{(1)} + W^{(1)} x))),
-
-References:
-
- - textbooks: "Pattern Recognition and Machine Learning" -
- Christopher M. Bishop, section 5
-
-"""
-
-from __future__ import print_function
-
-import os
-import sys
-import timeit
-import time
-
-import numpy
-import numpy as np
-import matplotlib.pylab as plt
-import theano
-import theano.tensor as T
-
-
-from logistic_sgd import LogisticRegression
-from input_icai_data import load_data
-from ipcai2016.tasks_common import plot_image
-
-#theano.config.compute_test_value = 'warn'
-#theano.config.mode = "FAST_COMPILE"
-#theano.config.exception_verbosity='high'
-
-__docformat__ = 'restructedtext en'
-
-
-# start-snippet-1
-class HiddenLayer(object):
- def __init__(self, rng, input, n_in, n_out, W=None, b=None,
- activation=T.tanh):
- """
- Typical hidden layer of a MLP: units are fully-connected and have
- sigmoidal activation function. Weight matrix W is of shape (n_in,n_out)
- and the bias vector b is of shape (n_out,).
-
- NOTE : The nonlinearity used here is tanh
-
- Hidden unit activation is given by: tanh(dot(input,W) + b)
-
- :type rng: numpy.random.RandomState
- :param rng: a random number generator used to initialize weights
-
- :type input: theano.tensor.dmatrix
- :param input: a symbolic tensor of shape (n_examples, n_in)
-
- :type n_in: int
- :param n_in: dimensionality of input
-
- :type n_out: int
- :param n_out: number of hidden units
-
- :type activation: theano.Op or function
- :param activation: Non linearity to be applied in the hidden
- layer
- """
- self.input = input
- # end-snippet-1
-
- # `W` is initialized with `W_values` which is uniformely sampled
- # from sqrt(-6./(n_in+n_hidden)) and sqrt(6./(n_in+n_hidden))
- # for tanh activation function
- # the output of uniform if converted using asarray to dtype
- # theano.config.floatX so that the code is runable on GPU
- # Note : optimal initialization of weights is dependent on the
- # activation function used (among other things).
- # For example, results presented in [Xavier10] suggest that you
- # should use 4 times larger initial weights for sigmoid
- # compared to tanh
- # We have no info for other function, so we use the same as
- # tanh.
- if W is None:
- W_values = numpy.asarray(
- rng.uniform(
- low=-numpy.sqrt(6. / (n_in + n_out)),
- high=numpy.sqrt(6. / (n_in + n_out)),
- size=(n_in, n_out)
- ),
- dtype=theano.config.floatX
- )
- if activation == theano.tensor.nnet.sigmoid:
- W_values *= 4
-
- W = theano.shared(value=W_values, name='W', borrow=True)
-
- if b is None:
- b_values = 0.1+numpy.zeros((n_out,), dtype=theano.config.floatX)
- b = theano.shared(value=b_values, name='b', borrow=True)
-
- self.W = W
- self.b = b
-
- lin_output = T.dot(input, self.W) + self.b
- self.output = (
- lin_output if activation is None
- else activation(lin_output)
- )
- # parameters of the model
- self.params = [self.W, self.b]
-
-
-# start-snippet-2
-class MLP(object):
- """Multi-Layer Perceptron Class
-
- A multilayer perceptron is a feedforward artificial neural network model
- that has one layer or more of hidden units and nonlinear activations.
- Intermediate layers usually have as activation function tanh or the
- sigmoid function (defined here by a ``HiddenLayer`` class) while the
- top layer is a softmax layer (defined here by a ``LogisticRegression``
- class).
- """
-
- def __init__(self, rng, input, n_in, n_hidden, n_out):
- """Initialize the parameters for the multilayer perceptron
-
- :type rng: numpy.random.RandomState
- :param rng: a random number generator used to initialize weights
-
- :type input: theano.tensor.TensorType
- :param input: symbolic variable that describes the input of the
- architecture (one minibatch)
-
- :type n_in: int
- :param n_in: number of input units, the dimension of the space in
- which the datapoints lie
-
- :type n_hidden: int
- :param n_hidden: number of hidden units
-
- :type n_out: int
- :param n_out: number of output units, the dimension of the space in
- which the labels lie
-
- """
-
- # Since we are dealing with a one hidden layer MLP, this will translate
- # into a HiddenLayer with a tanh activation function connected to the
- # LogisticRegression layer; the activation function can be replaced by
- # sigmoid or any other nonlinear function
- self.hiddenLayer1 = HiddenLayer(
- rng=rng,
- input=input,
- n_in=n_in,
- n_out=n_hidden,
- activation=T.nnet.relu
- )
-
- self.hiddenLayer2 = HiddenLayer(
- rng=rng,
- input=self.hiddenLayer1.output,
- n_in=n_hidden,
- n_out=n_hidden,
- activation=T.nnet.relu
- )
-
- # The logistic regression layer gets as input the hidden units
- # of the hidden layer
- self.logRegressionLayer = LogisticRegression(
- input=self.hiddenLayer2.output,
- n_in=n_hidden,
- n_out=n_out
- )
- # end-snippet-2 start-snippet-3
- # L1 norm ; one regularization option is to enforce L1 norm to
- # be small
- self.L1 = (
- abs(self.hiddenLayer1.W).sum()
- + abs(self.hiddenLayer2.W).sum()
- + abs(self.logRegressionLayer.W).sum()
- )
-
- # square of L2 norm ; one regularization option is to enforce
- # square of L2 norm to be small
- self.L2_sqr = (
- (self.hiddenLayer1.W ** 2).sum()
- + (self.hiddenLayer2.W ** 2).sum()
- + (self.logRegressionLayer.W ** 2).sum()
- )
-
- # negative log likelihood of the MLP is given by the negative
- # log likelihood of the output of the model, computed in the
- # logistic regression layer
- self.negative_log_likelihood = (
- self.logRegressionLayer.negative_log_likelihood
- )
- # same holds for the function computing the number of errors
- self.errors = self.logRegressionLayer.errors
-
- self.y_pred = self.logRegressionLayer.y_pred
-
- # the parameters of the model are the parameters of the two layer it is
- # made out of
- self.params = self.hiddenLayer1.params +\
- self.hiddenLayer2.params +\
- self.logRegressionLayer.params
- # end-snippet-3
-
- # keep track of model input
- self.input = input
-
-
-def test_mlp(learning_rate=0.001, L1_reg=0.0001, L2_reg=0.0001, n_epochs=1000,
- dataset="/media/wirkert/data/Data/2016_02_02_IPCAI/results/intermediate",
- batch_size=20, n_hidden=25,
- do_timing_test=False):
- """
- Demonstrate stochastic gradient descent optimization for a multilayer
- perceptron
-
- This is demonstrated on MNIST.
-
- :type learning_rate: float
- :param learning_rate: learning rate used (factor for the stochastic
- gradient
-
- :type L1_reg: float
- :param L1_reg: L1-norm's weight when added to the cost (see
- regularization)
-
- :type L2_reg: float
- :param L2_reg: L2-norm's weight when added to the cost (see
- regularization)
-
- :type n_epochs: int
- :param n_epochs: maximal number of epochs to run the optimizer
-
- :type dataset: string
- :param dataset: the path of the MNIST dataset file from
- http://www.iro.umontreal.ca/~lisa/deep/data/mnist/mnist.pkl.gz
-
-
- """
-
- datasets = load_data(dataset)
-
- train_set_x, train_set_y = datasets[0]
- valid_set_x, valid_set_y = datasets[1]
- test_set_x, test_set_y = datasets[2]
-
- # compute number of minibatches for training and validation
- n_train_batches = train_set_x.get_value(borrow=True).shape[0] // batch_size
- n_valid_batches = valid_set_x.get_value(borrow=True).shape[0] // batch_size
-
- ######################
- # BUILD ACTUAL MODEL #
- ######################
- print('... building the model')
-
- # allocate symbolic variables for the data
- index = T.lscalar() # index to a [mini]batch
- x = T.matrix('x') # the data is presented as rasterized images
- x.tag.test_value = np.zeros((5000, 8)).astype('float32')
- y = T.vector('y') # the labels are presented as 1D vector of
- # [int] labels
- y.tag.test_value = np.ones(5000).astype('float32')
-
- rng = numpy.random.RandomState(1234)
-
- # construct the MLP class
- classifier = MLP(
- rng=rng,
- input=x,
- n_in=8,
- n_hidden=n_hidden,
- n_out=1
- )
-
- # start-snippet-4
- # the cost we minimize during training is the negative log likelihood of
- # the model plus the regularization terms (L1 and L2); cost is expressed
- # here symbolically
- cost = (
- classifier.negative_log_likelihood(y)
- + L1_reg * classifier.L1
- + L2_reg * classifier.L2_sqr
- )
- # end-snippet-4
-
- # compiling a Theano function that computes the mistakes that are made
- # by the model on a minibatch
- test_model = theano.function(
- inputs=[],
- outputs=classifier.y_pred,
- givens={
- x: test_set_x
- }
- )
-
- validate_model = theano.function(
- inputs=[index],
- outputs=classifier.errors(y),
- givens={
- x: valid_set_x[index * batch_size:(index + 1) * batch_size],
- y: valid_set_y[index * batch_size:(index + 1) * batch_size]
- }
- )
-
- # start-snippet-5
- # compute the gradient of cost with respect to theta (sorted in params)
- # the resulting gradients will be stored in a list gparams
- gparams = [T.grad(cost, param) for param in classifier.params]
-
- # specify how to update the parameters of the model as a list of
- # (variable, update expression) pairs
-
- # given two lists of the same length, A = [a1, a2, a3, a4] and
- # B = [b1, b2, b3, b4], zip generates a list C of same size, where each
- # element is a pair formed from the two lists :
- # C = [(a1, b1), (a2, b2), (a3, b3), (a4, b4)]
- updates = [
- (param, param - learning_rate * gparam)
- for param, gparam in zip(classifier.params, gparams)
- ]
-
- # compiling a Theano function `train_model` that returns the cost, but
- # in the same time updates the parameter of the model based on the rules
- # defined in `updates`
- train_model = theano.function(
- inputs=[index],
- outputs=cost,
- updates=updates,
- givens={
- x: train_set_x[index * batch_size: (index + 1) * batch_size],
- y: train_set_y[index * batch_size: (index + 1) * batch_size]
- }
- )
- # end-snippet-5
-
- ###############
- # TRAIN MODEL #
- ###############
- print('... training')
-
- # early-stopping parameters
- patience = 10000 # look as this many examples regardless
- patience_increase = 2 # wait this much longer when a new best is
- # found
- improvement_threshold = 0.995 # a relative improvement of this much is
- # considered significant
- validation_frequency = min(n_train_batches, patience // 2)
- # go through this many
- # minibatche before checking the network
- # on the validation set; in this case we
- # check every epoch
-
- best_validation_loss = numpy.inf
- best_iter = 0
- test_score = 0.
- start_time = timeit.default_timer()
-
- epoch = 0
- done_looping = False
-
- while (epoch < n_epochs):# and (not done_looping):
- epoch = epoch + 1
- for minibatch_index in range(n_train_batches):
-
- minibatch_avg_cost = train_model(minibatch_index)
- # iteration number
- iter = (epoch - 1) * n_train_batches + minibatch_index
-
- if (iter + 1) % validation_frequency == 0:
- # compute zero-one loss on validation set
- validation_losses = [validate_model(i) for i
- in range(n_valid_batches)]
- this_validation_loss = numpy.mean(validation_losses)
-
- print(
- 'epoch %i, minibatch %i/%i, validation error %f %%' %
- (
- epoch,
- minibatch_index + 1,
- n_train_batches,
- this_validation_loss * 100.
- )
- )
-
- # if we got the best validation score until now
- if this_validation_loss < best_validation_loss:
- #improve patience if loss improvement is good enough
- if (
- this_validation_loss < best_validation_loss *
- improvement_threshold
- ):
- patience = max(patience, iter * patience_increase)
-
- best_validation_loss = this_validation_loss
- best_iter = iter
-
- if do_timing_test:
- # test it on the test set
- start = time.time()
- test_predictions = test_model()
- end = time.time()
- estimation_time = end - start
- print("time necessary for estimating image parameters: " +
- str(estimation_time) + "s")
- print(test_predictions.shape)
-
- if patience <= iter:
- done_looping = True
- #break
-
- end_time = timeit.default_timer()
- print(('Optimization complete. Best validation score of %f %% '
- 'obtained at iteration %i, with test performance %f %%') %
- (best_validation_loss * 100., best_iter + 1, test_score * 100.))
- print(('The code for file ' +
- os.path.split(__file__)[1] +
- ' ran for %.2fm' % ((end_time - start_time) / 60.)), file=sys.stderr)
-
- test_predictions = test_model()
- image = test_predictions.reshape(1029,1228)
- image[0, 0] = 0.0
- image[0, 1] = 1.
- image = np.clip(image, 0., 1.)
- plot_image(image)
- plt.savefig("sample_image.png",
- dpi=250, bbox_inches='tight')
-
-if __name__ == '__main__':
- test_mlp()
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/spielewiese/__init__.py b/Modules/Biophotonics/python/iMC/scripts/spielewiese/__init__.py
deleted file mode 100644
index e69de29bb2..0000000000
diff --git a/Modules/Biophotonics/python/iMC/scripts/spielewiese/monte_carlo_single_photon.py b/Modules/Biophotonics/python/iMC/scripts/spielewiese/monte_carlo_single_photon.py
deleted file mode 100644
index 05f0afc7dd..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/spielewiese/monte_carlo_single_photon.py
+++ /dev/null
@@ -1,203 +0,0 @@
-from collections import OrderedDict
-import numpy as np
-
-import theano
-from theano.ifelse import ifelse
-import theano.tensor as T
-import theano.tensor.inplace as inplace
-#from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
-from theano.tensor.shared_randomstreams import RandomStreams
-import time
-
-
-#theano.config.compute_test_value = 'warn'
-#theano.config.exception_verbosity='high'
-#theano.config.profile=True
-#theano.config.mode = "FAST_RUN"
-#theano.config.mode = "FAST_COMPILE"
-#theano.config.scan.allow_gc =True
-#theano.config.scan.allow_output_prealloc =False
-#theano.optimizer_excluding="more_mem"
-
-# initializing
-rng = RandomStreams(seed=234)
-photons = 10**6
-SHELL_MAX = 101
-
-
-mu_a = T.scalar('mu_a')
-# provide Theano with a default test-value
-mu_a.tag.test_value = 2.
-mu_s = T.scalar('mu_s')
-mu_s.tag.test_value = 20.
-microns_per_shell = T.scalar('microns_per_shell')
-microns_per_shell.tag.test_value = 50.
-
-albedo = mu_s / (mu_s + mu_a)
-shells_per_mfp = 1e4/microns_per_shell/(mu_a+mu_s)
-
-heat = theano.shared(np.zeros(SHELL_MAX, dtype=theano.config.floatX))
-
-x = T.scalar('x')
-x.tag.test_value = 0
-
-y = T.scalar('y')
-y.tag.test_value = 0
-
-z = T.scalar('z')
-z.tag.test_value = 0
-
-u = T.scalar('u')
-u.tag.test_value = 0
-
-v = T.scalar('v')
-v.tag.test_value = 0
-
-w = T.scalar('w')
-w.tag.test_value = 1
-
-weight = T.scalar('weight')
-weight.tag.test_value = 1
-
-
-def one_run(my_x, my_y, my_z,
- my_u, my_v, my_w,
- my_weight,
- my_heat, my_albedo, my_microns_per_shell):
-
- # move
- random = rng.uniform(low=0.00003, high=1.)
- t = -T.log(random)
-
- x_moved = my_x + my_u*t
- y_moved = my_y + my_v*t
- z_moved = my_z + my_w*t
-
- # absorb
- shell = T.cast(T.sqrt(T.sqr(x_moved) + T.sqr(y_moved) + T.sqr(z_moved))
- * my_microns_per_shell, 'int32')
- shell = T.clip(shell, 0, SHELL_MAX-1)
-
- new_weight = my_weight * my_albedo
-
- # new direction
- xi1 = rng.uniform(low=-1., high=1.)
- xi2 = rng.uniform(low=-1., high=1.)
- xi_norm = T.sqrt(T.sqr(xi1) + T.sqr(xi2))
-
- t_xi = rng.uniform(low=0.000000001, high=1.)
-
- # rescale xi12 to fit t_xi as norm
- xi1 = xi1/xi_norm * T.sqr(t_xi)
- xi2 = xi2/xi_norm * T.sqr(t_xi)
-
- u_new_direction = 2. * t_xi - 1.
- v_new_direction = xi1 * T.sqrt((1. - T.sqr(u_new_direction)) / t_xi)
- w_new_direction = xi2 * T.sqrt((1. - T.sqr(u_new_direction)) / t_xi)
-
- # roulette
- weight_for_starting_roulette = 0.001
- CHANCE = 0.1
- partakes_roulette = T.switch(T.lt(new_weight, weight_for_starting_roulette),
- 1,
- 0)
- roulette = rng.uniform(low=0., high=1.)
- loses_roulette = T.gt(roulette, CHANCE)
- # if roulette decides to terminate the photon: set weight to 0
- weight_after_roulette = ifelse(T.and_(partakes_roulette, loses_roulette),
- 0.,
- new_weight)
- # if partakes in roulette but does not get terminated
- weight_after_roulette = ifelse(T.and_(partakes_roulette, T.invert(loses_roulette)),
- weight_after_roulette / CHANCE,
- weight_after_roulette)
-
- new_heat = (1.0 - my_albedo) * my_weight
- heat_i = my_heat[shell]
-
- return (x_moved, y_moved, z_moved,\
- u_new_direction, v_new_direction, w_new_direction,\
- weight_after_roulette),\
- OrderedDict({my_heat: T.inc_subtensor(heat_i, new_heat)})
-
-
-# one_photon_results, one_photon_updates = theano.scan(fn=one_run,
-# outputs_info=[T.zeros_like(x),
-# T.zeros_like(y),
-# T.zeros_like(z),
-# T.zeros_like(u),
-# T.zeros_like(v),
-# T.ones_like(w),
-# T.ones_like(weight)],
-# non_sequences=[heat,
-# albedo,
-# microns_per_shell],
-# n_steps=100,
-# strict=True)
-#
-# final_one_photon_heat_result = one_photon_updates[heat]
-
-# heat_for_one_photon = theano.function(inputs=[x, y, z,
-# u, v, w,
-# weight,
-# mu_a, mu_s, microns_per_shell],
-# outputs=final_one_photon_heat_result,
-# updates=one_photon_updates)
-
-
-def all_runs(my_x, my_y, my_z,
- my_u, my_v, my_w,
- my_weight,
- my_heat,
- my_albedo, my_microns_per_shell):
- my_one_photon_results, my_one_photon_updates = theano.scan(fn=one_run,
- outputs_info=[T.zeros_like(my_x),
- T.zeros_like(my_y),
- T.zeros_like(my_z),
- T.zeros_like(my_u),
- T.zeros_like(my_v),
- T.ones_like(my_w),
- T.ones_like(my_weight)],
- non_sequences=[my_heat,
- my_albedo,
- my_microns_per_shell],
- n_steps=10,
- strict=True)
- return {my_heat: my_one_photon_updates[my_heat]}
-
-
-all_photon_results, all_photon_updates = theano.scan(fn=all_runs,
- outputs_info=None,
- non_sequences=[x, y, z,
- u, v, w,
- weight,
- heat,
- albedo, microns_per_shell],
- n_steps=10,
- strict=True)
-
-
-heat_for_all_photons = theano.function(inputs=[x, y, z,
- u, v, w,
- weight,
- mu_a, mu_s, microns_per_shell],
- outputs=all_photon_updates[heat],
- updates=all_photon_updates)
-
-
-
-
-
-start = time.time()
-
-print("start simulation")
-
-print(heat_for_all_photons(0., 0., 0.,
- 0., 0., 1.,
- 1.,
- 2., 20., 50.))
-
-end = time.time()
-print("end simulation after: " + str(end - start) + " seconds")
-
-
diff --git a/Modules/Biophotonics/python/iMC/scripts/spielewiese/spielewiese.py b/Modules/Biophotonics/python/iMC/scripts/spielewiese/spielewiese.py
deleted file mode 100644
index 871864547f..0000000000
--- a/Modules/Biophotonics/python/iMC/scripts/spielewiese/spielewiese.py
+++ /dev/null
@@ -1,130 +0,0 @@
-from collections import OrderedDict
-import numpy as np
-
-import theano
-import theano.tensor as T
-from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
-#from theano.tensor.shared_randomstreams import RandomStreams
-import time
-
-#theano.config.compute_test_value = 'warn'
-#theano.config.exception_verbosity='high'
-# initializing
-rng = RandomStreams(seed=234)
-photons = 10**6
-SHELL_MAX = 101
-
-mu_a = T.scalar('mu_a')
-# provide Theano with a default test-value
-mu_a.tag.test_value = 2.
-mu_s = T.scalar('mu_s')
-mu_s.tag.test_value = 20.
-microns_per_shell = T.scalar('microns_per_shell')
-microns_per_shell.tag.test_value = 50.
-
-albedo = mu_s / (mu_s + mu_a)
-shells_per_mfp = 1e4/microns_per_shell/(mu_a+mu_s)
-
-
-
-
-finished = theano.shared(np.array(0, dtype='int8'))
-
-xyz = theano.shared(np.zeros((photons,3), dtype=theano.config.floatX))
-
-uvw_np = np.zeros((photons,3), dtype=theano.config.floatX)
-uvw_np[:,2] = 1. # w = 1
-uvw = theano.shared(uvw_np)
-
-#weights_np = np.ones((photons,1), dtype=theano.config.floatX)
-weight = theano.shared(np.ones((photons,1), dtype=theano.config.floatX))
-
-heat_np = np.zeros((SHELL_MAX,1), dtype=theano.config.floatX)
-heat = theano.shared(heat_np)
-
-
-
-
-
-
-
-
-# while sum alive > 0
-
-def l2_norm_along_columns(A):
- A_normed = T.sqrt(T.sum(T.sqr(A), axis=1))
- A_normed = A_normed.reshape((photons, 1))
- return A_normed
-
-# move
-random = rng.uniform((photons,1), low=0.00003, high=1.)
-t = -T.log(random)
-t = T.addbroadcast(t, 1)
-
-xyz_moved = xyz + uvw*t
-#theano.printing.Print('xyz_moved')(xyz_moved)
-
-# absorb
-shells = T.cast(l2_norm_along_columns(xyz_moved) * shells_per_mfp,
- 'int32')
-shells = T.clip(shells, 0, SHELL_MAX-1)
-new_heats = (1.0 - albedo) * weight
-new_weight = weight * albedo
-theano.printing.Print('shells')(shells)
-
-# new direction
-xi12 = rng.uniform((photons,2), low=-1., high=1.)
-xi_norm = l2_norm_along_columns(xi12)
-
-t_xi = rng.uniform((photons,1), low=0.000000001, high=1.)
-t_xi = T.addbroadcast(t_xi, 1)
-
-# rescale xi12 to fit t_xi as norm
-xi12 = xi12/xi_norm * T.sqr(t_xi)
-
-u_new_direction = 2. * t_xi - 1.
-vw_new_direction = xi12 * T.sqrt((1. - T.sqr(u_new_direction)) / t_xi)
-uvw_new_direction = T.concatenate([u_new_direction, vw_new_direction], axis=1)
-
-#theano.printing.Print('t_xi')(t_xi)
-#theano.printing.Print('vw')(vw_new_direction)
-#theano.printing.Print('uvw')(uvw_new_direction)
-# roulette
-weight_for_starting_roulette = 0.001
-CHANCE = 0.1
-partakes_roulette = T.switch(T.lt(new_weight, weight_for_starting_roulette),
- 1,
- 0)
-roulette = rng.uniform((photons,1), low=0., high=1.)
-loses_roulette = T.gt(roulette, CHANCE)
-# if roulette decides to ter+minate the photon: set weight to 0
-weight_after_roulette = T.switch(T.and_(partakes_roulette, loses_roulette),
- 0.,
- new_weight)
-# if partakes in roulette but does not get terminated
-weight_after_roulette = T.switch(T.and_(partakes_roulette, T.invert(loses_roulette)),
- weight_after_roulette / CHANCE,
- weight_after_roulette)
-#theano.printing.Print('new weight')(new_weight)
-#theano.printing.Print('partakes_roulette')(partakes_roulette)
-#theano.printing.Print('loses_roulette')(loses_roulette)
-#theano.printing.Print('weight_after_roulette')(weight_after_roulette)
-
-
-one_cycle = theano.function(inputs=[mu_a, mu_s, microns_per_shell],
- outputs=[shells, new_heats],
- updates=OrderedDict({xyz: xyz_moved, uvw: uvw_new_direction,
- weight: weight_after_roulette,
- finished: T.allclose(weight, 0.)}))
-
-
-start = time.time()
-print("start simulation")
-
-while not finished.get_value():
- new_shells, new_heats = one_cycle(2, 20, 50)
-
-end = time.time()
-print("end simulation after: " + str(end - start) + " seconds")
-
-
diff --git a/Modules/Biophotonics/python/iMC/setup.py b/Modules/Biophotonics/python/iMC/setup.py
deleted file mode 100644
index 9e04fc9ca8..0000000000
--- a/Modules/Biophotonics/python/iMC/setup.py
+++ /dev/null
@@ -1,23 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug 7 18:41:50 2015
-
-@author: wirkert
-"""
-
-from setuptools import setup, find_packages
-
-setup(name='MITK-MSI',
- version='0.1',
- description='Multi spectral imaging (MSI) utilities',
- author='Sebastian Wirkert',
- author_email='s.wirkert@dkfz-heidelberg.de',
- license='BSD',
- packages=find_packages(exclude=['test*']),
- package_dir={},
- package_data={'data': ['*.txt', '*.mci', '*.nrrd']},
- install_requires=['numpy>=1.10.2', 'scipy', 'scikit-learn>=0.17',
- 'SimpleITK>=0.9.0', 'subprocess32',
- 'pypng', 'pandas>0.17', 'libtiff'],
- entry_points={} # for scripts, add later
- )
diff --git a/Modules/Biophotonics/python/iMC/tox.ini b/Modules/Biophotonics/python/iMC/tox.ini
deleted file mode 100644
index 51e0c9f594..0000000000
--- a/Modules/Biophotonics/python/iMC/tox.ini
+++ /dev/null
@@ -1,9 +0,0 @@
-# content of: tox.ini , put in same dir as setup.py
-[tox]
-envlist = py27
-[testenv]
-deps=discover # install pytest in the venvs
-install_command=pip install -f http://www.simpleitk.org/SimpleITK/resources/software.html --trusted-host www.simpleitk.org {opts} {packages}
-#changedir=tests
-commands=discover
-
diff --git a/Modules/Biophotonics/python/iMC/tutorials/Monte Carlo Spectra Generation - Basic tutorial.ipynb b/Modules/Biophotonics/python/iMC/tutorials/Monte Carlo Spectra Generation - Basic tutorial.ipynb
deleted file mode 100644
index e5ea2b6e52..0000000000
--- a/Modules/Biophotonics/python/iMC/tutorials/Monte Carlo Spectra Generation - Basic tutorial.ipynb
+++ /dev/null
@@ -1,1018 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# Creating and manipulating monte carlo spectra using MITK-MSI\n",
- "\n",
- "In this tutorial we will learn how to\n",
- "1. create reflectance spectra from examplary tissues\n",
- "2. how to analyse and visualize the created spectra\n",
- "3. how to manipulate them\n",
- "\n",
- "The MITK-MSI software provides a wrapper to the popular MCML approach to simulate how light travels through tissue. This wrapper can be found in mc/sim.py.\n",
- "In this tutorial we will utilize our tissue model which uses this wrapper to create the reflectance spectra.\n",
- "\n",
- "As a prerequisit, you need a MCML monte carlo simulation which uses the format specified [here](http://omlc.org/software/mc/).\n",
- "I tested this software with the GPU accelerated version which can be found [here](https://code.google.com/archive/p/gpumcml/)."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": [
- "# 1.1 create spectra - setup simulation environment\n",
- "\n",
- "# some necessary imports\n",
- "import logging\n",
- "import numpy as np\n",
- "import os\n",
- "# everything related to the simulation wrapper\n",
- "from mc import sim\n",
- "# the factories create batches (tissue samples) and suited tissue models\n",
- "from mc import factories\n",
- "# function which runs simulations for each wavelength\n",
- "from mc.create_spectrum import create_spectrum\n",
- "\n",
- "# Where does your monte carlo simulation executable resides in?\n",
- "MCML_EXECUTABLE = \"/home/wirkert/workspace/monteCarlo/gpumcml/fast-gpumcml/gpumcml.sm_20\"\n",
- "# The MCML needs a simulation input file, where shall it be created?\n",
- "MCI_FILENAME = \"./temp.mci\"\n",
- "# filename of the file with the simulation results. Due to a bug in GPUMCML will always\n",
- "# be created in the same folder as the MCML executable\n",
- "MCO_FILENAME = \"temp.mco\"\n",
- "# The wavelengths for which we want to run our simulation\n",
- "WAVELENGTHS = np.arange(450, 720, 2) * 10 ** -9\n",
- "\n",
- "# we want to create standard colonic tissue as specified in the IPCAI 2016 publication\n",
- "# \"Robust Near Real-Time Estimation of Physiological Parameters from Megapixel\n",
- "# Multispectral Images with Inverse Monte Carlo and Random Forest Regression\"\n",
- "factory = factories.ColonMuscleMeanScatteringFactory()\n",
- "# if you want to create data from the generic tissue mentioned in the paper, choose:\n",
- "#factory = factories.GenericMeanScatteringFactory()\n",
- "\n",
- "# create a simulation wrapper\n",
- "# the simulation wrapper wraps the mcml executable in python code\n",
- "sim_wrapper = sim.SimWrapper()\n",
- "# our simulation needs to know where the input file for the simulation\n",
- "# shall resign (will be automatically created)\n",
- "sim_wrapper.set_mci_filename(MCI_FILENAME)\n",
- "# also it needs to know where the simulation executable shall lie in\n",
- "sim_wrapper.set_mcml_executable(MCML_EXECUTABLE)\n",
- "\n",
- "# create the tissue model\n",
- "# it is responsible for writing the simulation input file\n",
- "tissue_model = factory.create_tissue_model()\n",
- "# tell it where the input file shall lie in\n",
- "tissue_model.set_mci_filename(sim_wrapper.mci_filename)\n",
- "# also set the output filename\n",
- "tissue_model.set_mco_filename(MCO_FILENAME)\n",
- "# tell it how much photons shall be simulated. Will be set to 10**6 by standard,\n",
- "# this is just an example\n",
- "tissue_model.set_nr_photons(10**6)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/html": [
- "<div>\n",
- "<table border=\"1\" class=\"dataframe\">\n",
- " <thead>\n",
- " <tr>\n",
- " <th></th>\n",
- " <th colspan=\"7\" halign=\"left\">layer0</th>\n",
- " <th colspan=\"7\" halign=\"left\">layer1</th>\n",
- " <th colspan=\"7\" halign=\"left\">layer2</th>\n",
- " </tr>\n",
- " <tr>\n",
- " <th></th>\n",
- " <th>vhb</th>\n",
- " <th>sao2</th>\n",
- " <th>a_mie</th>\n",
- " <th>b_mie</th>\n",
- " <th>d</th>\n",
- " <th>n</th>\n",
- " <th>g</th>\n",
- " <th>vhb</th>\n",
- " <th>sao2</th>\n",
- " <th>a_mie</th>\n",
- " <th>...</th>\n",
- " <th>d</th>\n",
- " <th>n</th>\n",
- " <th>g</th>\n",
- " <th>vhb</th>\n",
- " <th>sao2</th>\n",
- " <th>a_mie</th>\n",
- " <th>b_mie</th>\n",
- " <th>d</th>\n",
- " <th>n</th>\n",
- " <th>g</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
- " <tr>\n",
- " <th>0</th>\n",
- " <td>0.003780</td>\n",
- " <td>0.447583</td>\n",
- " <td>2425.900882</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000907</td>\n",
- " <td>1.36</td>\n",
- " <td>0.872626</td>\n",
- " <td>0.068985</td>\n",
- " <td>0.447583</td>\n",
- " <td>912.591151</td>\n",
- " <td>...</td>\n",
- " <td>0.000503</td>\n",
- " <td>1.36</td>\n",
- " <td>0.948700</td>\n",
- " <td>0.034427</td>\n",
- " <td>0.447583</td>\n",
- " <td>3150.494032</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000454</td>\n",
- " <td>1.38</td>\n",
- " <td>0.804610</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>1</th>\n",
- " <td>0.021198</td>\n",
- " <td>0.184410</td>\n",
- " <td>3022.116532</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000782</td>\n",
- " <td>1.36</td>\n",
- " <td>0.930268</td>\n",
- " <td>0.063804</td>\n",
- " <td>0.184410</td>\n",
- " <td>10.000000</td>\n",
- " <td>...</td>\n",
- " <td>0.000735</td>\n",
- " <td>1.36</td>\n",
- " <td>0.830601</td>\n",
- " <td>0.028247</td>\n",
- " <td>0.184410</td>\n",
- " <td>3101.261499</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000430</td>\n",
- " <td>1.38</td>\n",
- " <td>0.813056</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>2</th>\n",
- " <td>0.052096</td>\n",
- " <td>0.307445</td>\n",
- " <td>1171.322758</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000897</td>\n",
- " <td>1.36</td>\n",
- " <td>0.924933</td>\n",
- " <td>0.021053</td>\n",
- " <td>0.307445</td>\n",
- " <td>1433.788625</td>\n",
- " <td>...</td>\n",
- " <td>0.000738</td>\n",
- " <td>1.36</td>\n",
- " <td>0.807348</td>\n",
- " <td>0.006614</td>\n",
- " <td>0.307445</td>\n",
- " <td>1002.536901</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000485</td>\n",
- " <td>1.38</td>\n",
- " <td>0.943837</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>3</th>\n",
- " <td>0.076799</td>\n",
- " <td>0.471304</td>\n",
- " <td>1599.038671</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000878</td>\n",
- " <td>1.36</td>\n",
- " <td>0.900637</td>\n",
- " <td>0.084504</td>\n",
- " <td>0.471304</td>\n",
- " <td>3228.771326</td>\n",
- " <td>...</td>\n",
- " <td>0.000605</td>\n",
- " <td>1.36</td>\n",
- " <td>0.905222</td>\n",
- " <td>0.043674</td>\n",
- " <td>0.471304</td>\n",
- " <td>1810.114303</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000504</td>\n",
- " <td>1.38</td>\n",
- " <td>0.868953</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>4</th>\n",
- " <td>0.053123</td>\n",
- " <td>0.108137</td>\n",
- " <td>3524.480885</td>\n",
- " <td>1.286</td>\n",
- " <td>0.001001</td>\n",
- " <td>1.36</td>\n",
- " <td>0.833434</td>\n",
- " <td>0.095382</td>\n",
- " <td>0.108137</td>\n",
- " <td>1988.134950</td>\n",
- " <td>...</td>\n",
- " <td>0.000643</td>\n",
- " <td>1.36</td>\n",
- " <td>0.920940</td>\n",
- " <td>0.031201</td>\n",
- " <td>0.108137</td>\n",
- " <td>1731.751283</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000542</td>\n",
- " <td>1.38</td>\n",
- " <td>0.906191</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>5</th>\n",
- " <td>0.009147</td>\n",
- " <td>0.866703</td>\n",
- " <td>372.754799</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000943</td>\n",
- " <td>1.36</td>\n",
- " <td>0.841274</td>\n",
- " <td>0.094915</td>\n",
- " <td>0.866703</td>\n",
- " <td>1660.695761</td>\n",
- " <td>...</td>\n",
- " <td>0.000505</td>\n",
- " <td>1.36</td>\n",
- " <td>0.856969</td>\n",
- " <td>0.009274</td>\n",
- " <td>0.866703</td>\n",
- " <td>1991.390563</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000439</td>\n",
- " <td>1.38</td>\n",
- " <td>0.813544</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>6</th>\n",
- " <td>0.082903</td>\n",
- " <td>0.206032</td>\n",
- " <td>2314.415411</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000663</td>\n",
- " <td>1.36</td>\n",
- " <td>0.884492</td>\n",
- " <td>0.038608</td>\n",
- " <td>0.206032</td>\n",
- " <td>459.458466</td>\n",
- " <td>...</td>\n",
- " <td>0.000573</td>\n",
- " <td>1.36</td>\n",
- " <td>0.850574</td>\n",
- " <td>0.063746</td>\n",
- " <td>0.206032</td>\n",
- " <td>2728.820678</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000494</td>\n",
- " <td>1.38</td>\n",
- " <td>0.801766</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>7</th>\n",
- " <td>0.040719</td>\n",
- " <td>0.200956</td>\n",
- " <td>1858.910121</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000772</td>\n",
- " <td>1.36</td>\n",
- " <td>0.884516</td>\n",
- " <td>0.003930</td>\n",
- " <td>0.200956</td>\n",
- " <td>3564.807750</td>\n",
- " <td>...</td>\n",
- " <td>0.000766</td>\n",
- " <td>1.36</td>\n",
- " <td>0.903764</td>\n",
- " <td>0.047257</td>\n",
- " <td>0.200956</td>\n",
- " <td>1429.574407</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000468</td>\n",
- " <td>1.38</td>\n",
- " <td>0.849055</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>8</th>\n",
- " <td>0.028810</td>\n",
- " <td>0.729636</td>\n",
- " <td>1751.818248</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000886</td>\n",
- " <td>1.36</td>\n",
- " <td>0.813391</td>\n",
- " <td>0.007477</td>\n",
- " <td>0.729636</td>\n",
- " <td>1388.286116</td>\n",
- " <td>...</td>\n",
- " <td>0.000813</td>\n",
- " <td>1.36</td>\n",
- " <td>0.914125</td>\n",
- " <td>0.092993</td>\n",
- " <td>0.729636</td>\n",
- " <td>4001.446613</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000504</td>\n",
- " <td>1.38</td>\n",
- " <td>0.844552</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>9</th>\n",
- " <td>0.089758</td>\n",
- " <td>0.665397</td>\n",
- " <td>3768.709188</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000800</td>\n",
- " <td>1.36</td>\n",
- " <td>0.836711</td>\n",
- " <td>0.015648</td>\n",
- " <td>0.665397</td>\n",
- " <td>1298.629577</td>\n",
- " <td>...</td>\n",
- " <td>0.000620</td>\n",
- " <td>1.36</td>\n",
- " <td>0.927904</td>\n",
- " <td>0.048023</td>\n",
- " <td>0.665397</td>\n",
- " <td>3015.289386</td>\n",
- " <td>1.286</td>\n",
- " <td>0.000427</td>\n",
- " <td>1.38</td>\n",
- " <td>0.893833</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "<p>10 rows × 21 columns</p>\n",
- "</div>"
- ],
- "text/plain": [
- " layer0 layer1 \\\n",
- " vhb sao2 a_mie b_mie d n g vhb \n",
- "0 0.003780 0.447583 2425.900882 1.286 0.000907 1.36 0.872626 0.068985 \n",
- "1 0.021198 0.184410 3022.116532 1.286 0.000782 1.36 0.930268 0.063804 \n",
- "2 0.052096 0.307445 1171.322758 1.286 0.000897 1.36 0.924933 0.021053 \n",
- "3 0.076799 0.471304 1599.038671 1.286 0.000878 1.36 0.900637 0.084504 \n",
- "4 0.053123 0.108137 3524.480885 1.286 0.001001 1.36 0.833434 0.095382 \n",
- "5 0.009147 0.866703 372.754799 1.286 0.000943 1.36 0.841274 0.094915 \n",
- "6 0.082903 0.206032 2314.415411 1.286 0.000663 1.36 0.884492 0.038608 \n",
- "7 0.040719 0.200956 1858.910121 1.286 0.000772 1.36 0.884516 0.003930 \n",
- "8 0.028810 0.729636 1751.818248 1.286 0.000886 1.36 0.813391 0.007477 \n",
- "9 0.089758 0.665397 3768.709188 1.286 0.000800 1.36 0.836711 0.015648 \n",
- "\n",
- " ... layer2 \\\n",
- " sao2 a_mie ... d n g vhb \n",
- "0 0.447583 912.591151 ... 0.000503 1.36 0.948700 0.034427 \n",
- "1 0.184410 10.000000 ... 0.000735 1.36 0.830601 0.028247 \n",
- "2 0.307445 1433.788625 ... 0.000738 1.36 0.807348 0.006614 \n",
- "3 0.471304 3228.771326 ... 0.000605 1.36 0.905222 0.043674 \n",
- "4 0.108137 1988.134950 ... 0.000643 1.36 0.920940 0.031201 \n",
- "5 0.866703 1660.695761 ... 0.000505 1.36 0.856969 0.009274 \n",
- "6 0.206032 459.458466 ... 0.000573 1.36 0.850574 0.063746 \n",
- "7 0.200956 3564.807750 ... 0.000766 1.36 0.903764 0.047257 \n",
- "8 0.729636 1388.286116 ... 0.000813 1.36 0.914125 0.092993 \n",
- "9 0.665397 1298.629577 ... 0.000620 1.36 0.927904 0.048023 \n",
- "\n",
- " \n",
- " sao2 a_mie b_mie d n g \n",
- "0 0.447583 3150.494032 1.286 0.000454 1.38 0.804610 \n",
- "1 0.184410 3101.261499 1.286 0.000430 1.38 0.813056 \n",
- "2 0.307445 1002.536901 1.286 0.000485 1.38 0.943837 \n",
- "3 0.471304 1810.114303 1.286 0.000504 1.38 0.868953 \n",
- "4 0.108137 1731.751283 1.286 0.000542 1.38 0.906191 \n",
- "5 0.866703 1991.390563 1.286 0.000439 1.38 0.813544 \n",
- "6 0.206032 2728.820678 1.286 0.000494 1.38 0.801766 \n",
- "7 0.200956 1429.574407 1.286 0.000468 1.38 0.849055 \n",
- "8 0.729636 4001.446613 1.286 0.000504 1.38 0.844552 \n",
- "9 0.665397 3015.289386 1.286 0.000427 1.38 0.893833 \n",
- "\n",
- "[10 rows x 21 columns]"
- ]
- },
- "execution_count": 2,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# 1.2 create spectra - create tissue samples for simulation\n",
- "\n",
- "# setup batch with tissue instances which should be simulated\n",
- "batch = factory.create_batch_to_simulate()\n",
- "# we want to simulate ten tissue instances in this example\n",
- "nr_samples = 10\n",
- "df = batch.create_parameters(10)\n",
- "\n",
- "# lets have a look at the dataframe. Each row corresponds to one tissue instance,\n",
- "# each tissue instance is defined by various layers, which all have certain parameters\n",
- "# like e.g. oxygenation (here sao2)\n",
- "df"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 3,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "text/html": [
- "<div>\n",
- "<table border=\"1\" class=\"dataframe\">\n",
- " <thead>\n",
- " <tr style=\"text-align: right;\">\n",
- " <th></th>\n",
- " <th>4.5e-07</th>\n",
- " <th>4.52e-07</th>\n",
- " <th>4.54e-07</th>\n",
- " <th>4.56e-07</th>\n",
- " <th>4.58e-07</th>\n",
- " <th>4.6e-07</th>\n",
- " <th>4.62e-07</th>\n",
- " <th>4.64e-07</th>\n",
- " <th>4.66e-07</th>\n",
- " <th>4.68e-07</th>\n",
- " <th>...</th>\n",
- " <th>7e-07</th>\n",
- " <th>7.02e-07</th>\n",
- " <th>7.04e-07</th>\n",
- " <th>7.06e-07</th>\n",
- " <th>7.08e-07</th>\n",
- " <th>7.1e-07</th>\n",
- " <th>7.12e-07</th>\n",
- " <th>7.14e-07</th>\n",
- " <th>7.16e-07</th>\n",
- " <th>7.18e-07</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
- " <tr>\n",
- " <th>0</th>\n",
- " <td>0.318616</td>\n",
- " <td>0.346943</td>\n",
- " <td>0.371254</td>\n",
- " <td>0.379878</td>\n",
- " <td>0.385557</td>\n",
- " <td>0.389087</td>\n",
- " <td>0.394877</td>\n",
- " <td>0.397762</td>\n",
- " <td>0.401003</td>\n",
- " <td>0.404130</td>\n",
- " <td>...</td>\n",
- " <td>0.494731</td>\n",
- " <td>0.495162</td>\n",
- " <td>0.495068</td>\n",
- " <td>0.495426</td>\n",
- " <td>0.495447</td>\n",
- " <td>0.495008</td>\n",
- " <td>0.495081</td>\n",
- " <td>0.495093</td>\n",
- " <td>0.494623</td>\n",
- " <td>0.494477</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>1</th>\n",
- " <td>0.140266</td>\n",
- " <td>0.189640</td>\n",
- " <td>0.243554</td>\n",
- " <td>0.259792</td>\n",
- " <td>0.275593</td>\n",
- " <td>0.284833</td>\n",
- " <td>0.296358</td>\n",
- " <td>0.302311</td>\n",
- " <td>0.308877</td>\n",
- " <td>0.314986</td>\n",
- " <td>...</td>\n",
- " <td>0.446426</td>\n",
- " <td>0.447138</td>\n",
- " <td>0.448675</td>\n",
- " <td>0.449469</td>\n",
- " <td>0.450297</td>\n",
- " <td>0.451485</td>\n",
- " <td>0.451886</td>\n",
- " <td>0.451767</td>\n",
- " <td>0.452054</td>\n",
- " <td>0.452514</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>2</th>\n",
- " <td>0.021747</td>\n",
- " <td>0.035154</td>\n",
- " <td>0.056293</td>\n",
- " <td>0.065113</td>\n",
- " <td>0.073610</td>\n",
- " <td>0.080725</td>\n",
- " <td>0.088940</td>\n",
- " <td>0.094565</td>\n",
- " <td>0.100813</td>\n",
- " <td>0.107133</td>\n",
- " <td>...</td>\n",
- " <td>0.378155</td>\n",
- " <td>0.379112</td>\n",
- " <td>0.379953</td>\n",
- " <td>0.381048</td>\n",
- " <td>0.382271</td>\n",
- " <td>0.382699</td>\n",
- " <td>0.384109</td>\n",
- " <td>0.384781</td>\n",
- " <td>0.385816</td>\n",
- " <td>0.386681</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>3</th>\n",
- " <td>0.021931</td>\n",
- " <td>0.031995</td>\n",
- " <td>0.045955</td>\n",
- " <td>0.051771</td>\n",
- " <td>0.056990</td>\n",
- " <td>0.061694</td>\n",
- " <td>0.067690</td>\n",
- " <td>0.071328</td>\n",
- " <td>0.076024</td>\n",
- " <td>0.080335</td>\n",
- " <td>...</td>\n",
- " <td>0.422478</td>\n",
- " <td>0.424793</td>\n",
- " <td>0.425965</td>\n",
- " <td>0.428011</td>\n",
- " <td>0.429414</td>\n",
- " <td>0.430371</td>\n",
- " <td>0.432106</td>\n",
- " <td>0.433527</td>\n",
- " <td>0.433773</td>\n",
- " <td>0.435063</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>4</th>\n",
- " <td>0.069287</td>\n",
- " <td>0.107174</td>\n",
- " <td>0.159794</td>\n",
- " <td>0.177421</td>\n",
- " <td>0.196123</td>\n",
- " <td>0.208005</td>\n",
- " <td>0.221937</td>\n",
- " <td>0.231352</td>\n",
- " <td>0.239231</td>\n",
- " <td>0.247642</td>\n",
- " <td>...</td>\n",
- " <td>0.477140</td>\n",
- " <td>0.478393</td>\n",
- " <td>0.481133</td>\n",
- " <td>0.483172</td>\n",
- " <td>0.485144</td>\n",
- " <td>0.486761</td>\n",
- " <td>0.488254</td>\n",
- " <td>0.490285</td>\n",
- " <td>0.491700</td>\n",
- " <td>0.492445</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>5</th>\n",
- " <td>0.045606</td>\n",
- " <td>0.051312</td>\n",
- " <td>0.058581</td>\n",
- " <td>0.062728</td>\n",
- " <td>0.065359</td>\n",
- " <td>0.068912</td>\n",
- " <td>0.073484</td>\n",
- " <td>0.075951</td>\n",
- " <td>0.080196</td>\n",
- " <td>0.084404</td>\n",
- " <td>...</td>\n",
- " <td>0.382621</td>\n",
- " <td>0.381922</td>\n",
- " <td>0.381471</td>\n",
- " <td>0.381451</td>\n",
- " <td>0.380481</td>\n",
- " <td>0.380568</td>\n",
- " <td>0.379841</td>\n",
- " <td>0.379317</td>\n",
- " <td>0.378714</td>\n",
- " <td>0.378075</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>6</th>\n",
- " <td>0.027393</td>\n",
- " <td>0.044668</td>\n",
- " <td>0.070860</td>\n",
- " <td>0.081027</td>\n",
- " <td>0.091248</td>\n",
- " <td>0.098535</td>\n",
- " <td>0.107426</td>\n",
- " <td>0.112543</td>\n",
- " <td>0.118445</td>\n",
- " <td>0.123929</td>\n",
- " <td>...</td>\n",
- " <td>0.371301</td>\n",
- " <td>0.373190</td>\n",
- " <td>0.375097</td>\n",
- " <td>0.377324</td>\n",
- " <td>0.379127</td>\n",
- " <td>0.380524</td>\n",
- " <td>0.382481</td>\n",
- " <td>0.383658</td>\n",
- " <td>0.385444</td>\n",
- " <td>0.386918</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>7</th>\n",
- " <td>0.048908</td>\n",
- " <td>0.078857</td>\n",
- " <td>0.124928</td>\n",
- " <td>0.142237</td>\n",
- " <td>0.159621</td>\n",
- " <td>0.172280</td>\n",
- " <td>0.186836</td>\n",
- " <td>0.196870</td>\n",
- " <td>0.206029</td>\n",
- " <td>0.216111</td>\n",
- " <td>...</td>\n",
- " <td>0.494583</td>\n",
- " <td>0.496394</td>\n",
- " <td>0.497351</td>\n",
- " <td>0.498217</td>\n",
- " <td>0.499010</td>\n",
- " <td>0.499452</td>\n",
- " <td>0.501481</td>\n",
- " <td>0.501600</td>\n",
- " <td>0.502315</td>\n",
- " <td>0.503171</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>8</th>\n",
- " <td>0.086791</td>\n",
- " <td>0.105141</td>\n",
- " <td>0.125877</td>\n",
- " <td>0.135923</td>\n",
- " <td>0.143073</td>\n",
- " <td>0.151115</td>\n",
- " <td>0.160239</td>\n",
- " <td>0.165631</td>\n",
- " <td>0.173878</td>\n",
- " <td>0.180887</td>\n",
- " <td>...</td>\n",
- " <td>0.516076</td>\n",
- " <td>0.516351</td>\n",
- " <td>0.517303</td>\n",
- " <td>0.517044</td>\n",
- " <td>0.516727</td>\n",
- " <td>0.516664</td>\n",
- " <td>0.515435</td>\n",
- " <td>0.515228</td>\n",
- " <td>0.515323</td>\n",
- " <td>0.514933</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>9</th>\n",
- " <td>0.056338</td>\n",
- " <td>0.071479</td>\n",
- " <td>0.089041</td>\n",
- " <td>0.097041</td>\n",
- " <td>0.103308</td>\n",
- " <td>0.109447</td>\n",
- " <td>0.116874</td>\n",
- " <td>0.120901</td>\n",
- " <td>0.127804</td>\n",
- " <td>0.133711</td>\n",
- " <td>...</td>\n",
- " <td>0.506670</td>\n",
- " <td>0.506889</td>\n",
- " <td>0.507858</td>\n",
- " <td>0.508143</td>\n",
- " <td>0.508351</td>\n",
- " <td>0.508218</td>\n",
- " <td>0.509040</td>\n",
- " <td>0.509576</td>\n",
- " <td>0.508506</td>\n",
- " <td>0.508549</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "<p>10 rows × 135 columns</p>\n",
- "</div>"
- ],
- "text/plain": [
- " 4.500000e-07 4.520000e-07 4.540000e-07 4.560000e-07 4.580000e-07 \\\n",
- "0 0.318616 0.346943 0.371254 0.379878 0.385557 \n",
- "1 0.140266 0.189640 0.243554 0.259792 0.275593 \n",
- "2 0.021747 0.035154 0.056293 0.065113 0.073610 \n",
- "3 0.021931 0.031995 0.045955 0.051771 0.056990 \n",
- "4 0.069287 0.107174 0.159794 0.177421 0.196123 \n",
- "5 0.045606 0.051312 0.058581 0.062728 0.065359 \n",
- "6 0.027393 0.044668 0.070860 0.081027 0.091248 \n",
- "7 0.048908 0.078857 0.124928 0.142237 0.159621 \n",
- "8 0.086791 0.105141 0.125877 0.135923 0.143073 \n",
- "9 0.056338 0.071479 0.089041 0.097041 0.103308 \n",
- "\n",
- " 4.600000e-07 4.620000e-07 4.640000e-07 4.660000e-07 4.680000e-07 \\\n",
- "0 0.389087 0.394877 0.397762 0.401003 0.404130 \n",
- "1 0.284833 0.296358 0.302311 0.308877 0.314986 \n",
- "2 0.080725 0.088940 0.094565 0.100813 0.107133 \n",
- "3 0.061694 0.067690 0.071328 0.076024 0.080335 \n",
- "4 0.208005 0.221937 0.231352 0.239231 0.247642 \n",
- "5 0.068912 0.073484 0.075951 0.080196 0.084404 \n",
- "6 0.098535 0.107426 0.112543 0.118445 0.123929 \n",
- "7 0.172280 0.186836 0.196870 0.206029 0.216111 \n",
- "8 0.151115 0.160239 0.165631 0.173878 0.180887 \n",
- "9 0.109447 0.116874 0.120901 0.127804 0.133711 \n",
- "\n",
- " ... 7.000000e-07 7.020000e-07 7.040000e-07 7.060000e-07 \\\n",
- "0 ... 0.494731 0.495162 0.495068 0.495426 \n",
- "1 ... 0.446426 0.447138 0.448675 0.449469 \n",
- "2 ... 0.378155 0.379112 0.379953 0.381048 \n",
- "3 ... 0.422478 0.424793 0.425965 0.428011 \n",
- "4 ... 0.477140 0.478393 0.481133 0.483172 \n",
- "5 ... 0.382621 0.381922 0.381471 0.381451 \n",
- "6 ... 0.371301 0.373190 0.375097 0.377324 \n",
- "7 ... 0.494583 0.496394 0.497351 0.498217 \n",
- "8 ... 0.516076 0.516351 0.517303 0.517044 \n",
- "9 ... 0.506670 0.506889 0.507858 0.508143 \n",
- "\n",
- " 7.080000e-07 7.100000e-07 7.120000e-07 7.140000e-07 7.160000e-07 \\\n",
- "0 0.495447 0.495008 0.495081 0.495093 0.494623 \n",
- "1 0.450297 0.451485 0.451886 0.451767 0.452054 \n",
- "2 0.382271 0.382699 0.384109 0.384781 0.385816 \n",
- "3 0.429414 0.430371 0.432106 0.433527 0.433773 \n",
- "4 0.485144 0.486761 0.488254 0.490285 0.491700 \n",
- "5 0.380481 0.380568 0.379841 0.379317 0.378714 \n",
- "6 0.379127 0.380524 0.382481 0.383658 0.385444 \n",
- "7 0.499010 0.499452 0.501481 0.501600 0.502315 \n",
- "8 0.516727 0.516664 0.515435 0.515228 0.515323 \n",
- "9 0.508351 0.508218 0.509040 0.509576 0.508506 \n",
- "\n",
- " 7.180000e-07 \n",
- "0 0.494477 \n",
- "1 0.452514 \n",
- "2 0.386681 \n",
- "3 0.435063 \n",
- "4 0.492445 \n",
- "5 0.378075 \n",
- "6 0.386918 \n",
- "7 0.503171 \n",
- "8 0.514933 \n",
- "9 0.508549 \n",
- "\n",
- "[10 rows x 135 columns]"
- ]
- },
- "execution_count": 3,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "# 1.3 create spectra - run simulation\n",
- "\n",
- "# add reflectance column to dataframe\n",
- "for w in WAVELENGTHS:\n",
- " df[\"reflectances\", w] = np.NAN # the reflectances have not been calculated yet, thus set no nan\n",
- "\n",
- "# for each instance in our batch\n",
- "for i in range(df.shape[0]):\n",
- " # set the desired element in the dataframe to be simulated\n",
- " tissue_model.set_dataframe_row(df.loc[i, :])\n",
- " logging.info(\"running simulation \" + str(i) + \" for\\n\" +\n",
- " str(tissue_model))\n",
- " reflectances = create_spectrum(tissue_model, sim_wrapper, WAVELENGTHS)\n",
- " # store in dataframe\n",
- " for r, w in zip(reflectances, WAVELENGTHS):\n",
- " df[\"reflectances\", w][i] = r\n",
- " \n",
- "# clean up temporarily created files\n",
- "os.remove(MCI_FILENAME)\n",
- "created_mco_file = os.path.join(os.path.split(MCML_EXECUTABLE)[0], MCO_FILENAME)\n",
- "if os.path.isfile(created_mco_file):\n",
- " os.remove(created_mco_file)\n",
- "\n",
- "# Hooray, finished,\n",
- "# now our dataframe also contains reflectances for each tissue instance:\n",
- "df[\"reflectances\"]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 4,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
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KK6+QkJBQZSGn567U0dE5i1WszImcw2thr3F1u6vZ+uBWOvh1qNC1IkqAbdqk/Di2b1c2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v3uO8yePRszZ86Em5sbAMBqNSE29na4uYUgPPyT6ot4xsVpFdGnT9fCDCrerxrKyrSaokuXAlu2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\neKBLly7o2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- "text/plain": [
- "<matplotlib.figure.Figure at 0x7f5c563e9090>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "# 2.1 analyse spectra - plot reflectances\n",
- "\n",
- "# the usual settings for plotting in ipython notebooks\n",
- "import matplotlib.pylab as plt\n",
- "%matplotlib inline\n",
- "\n",
- "# let's have a look at our reflectances\n",
- "df[\"reflectances\"].T.plot(kind=\"line\")\n",
- "plt.ylabel(\"reflectance\")\n",
- "plt.xlabel(\"wavelengths [m]\")\n",
- "# put legend outside of plot\n",
- "plt.gca().legend(loc='center left', bbox_to_anchor=(1, 0.5))\n",
- "plt.grid()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 5,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "image/png": 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- "text/plain": [
- "<matplotlib.figure.Figure at 0x7f5c7c155810>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "# 2.1 analyse spectra - show distribution of blood volume fraction (vhb) and sao2\n",
- "\n",
- "# now we need some special pandas functions\n",
- "import pandas as pd\n",
- "\n",
- "# we're interested in the distribution of vhb and sao2 in the first layer (layer0)\n",
- "df_vhb_sao2 = df[\"layer0\"][[\"vhb\", \"sao2\"]]\n",
- "# plot a scatter matrix showing the distribution of vhb and sao2.\n",
- "# of course, with this little data this does not really make sense,\n",
- "# however it is a useful tool for analysis if much data is available\n",
- "pd.tools.plotting.scatter_matrix(df_vhb_sao2, alpha=0.75, figsize=(6, 6))\n",
- "plt.show()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
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ktJktW9Ss4N69SqD16aN++J95Rtmdym3uMpvVBZYvhxUrlHHulltg+HD44gs1n2lHcnJg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\nmtwEbHe+K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- "text/plain": [
- "<matplotlib.figure.Figure at 0x7f5c5609dad0>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "# 3.1 manipulate spectra - apply sliding average\n",
- "# in 3.1 and 3.2 we will adapt the generated spectra to an imaginary imaging system\n",
- "# This system has filters with 20nm bandwith (taken care of in 3.1)\n",
- "# and takes multispectral images in 10nm steps (taken care of in 3.2)\n",
- "\n",
- "# the module mc.dfmanipulations was written to provide some basic,\n",
- "# often needed manipulations of the calculated spectra\n",
- "# all dmfmanipulations are performed inplace, however, the df is also returned.\n",
- "import mc.dfmanipulations as dfmani\n",
- "\n",
- "# first copy to not lose our original data\n",
- "df2 = df.copy()\n",
- "# We apply a sliding average to our data. This is usefull if \n",
- "# we want to see e.g. how the reflectance was recorded by bands with a certain width\n",
- "# a sliding average of 11 will take the five left and five right of the current reflectance\n",
- "# and average. Because we take 2nm steps of reflectance in our simulation this means\n",
- "# a 20nm window.\n",
- "dfmani.fold_by_sliding_average(df2, 11)\n",
- "\n",
- "# lets again plot the reflectances\n",
- "df2[\"reflectances\"].T.plot(kind=\"line\")\n",
- "plt.ylabel(\"reflectance\")\n",
- "plt.xlabel(\"wavelengths [m]\")\n",
- "# put legend outside of plot\n",
- "plt.gca().legend(loc='center left', bbox_to_anchor=(1, 0.5))\n",
- "plt.grid()\n",
- "# we can see that the bump at 560nm is \"smoother\""
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "metadata": {
- "collapsed": false
- },
- "outputs": [
- {
- "data": {
- "image/png": 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k2O6yScqsFLlw5ELFXLsbcI1XIfDompymaQ8Bd4vIM7nbI4CbReT5Asc0BRaJ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\nlZxGo9FoWixayWk0Go2mxfJ/fLzEhddjRjcAAAAASUVORK5CYII=\n",
- "text/plain": [
- "<matplotlib.figure.Figure at 0x7f5c55efd910>"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "# 3.2 manipulate spectra - select certain wavelenghts\n",
- "\n",
- "# our imaginary imaging system takes images in 10nm steps from 470 to 660nm\n",
- "imaging_system_wavelengths = np.arange(470, 670, 10) * 10**-9\n",
- "\n",
- "df3 = df2.copy()\n",
- "dfmani.interpolate_wavelengths(df3, imaging_system_wavelengths)\n",
- "\n",
- "# let's look at the newly created reflectances\n",
- "df3[\"reflectances\"].T.plot(kind=\"line\", marker='o')\n",
- "plt.ylabel(\"reflectance\")\n",
- "plt.xlabel(\"wavelengths [m]\")\n",
- "# put legend outside of plot\n",
- "plt.gca().legend(loc='center left', bbox_to_anchor=(1, 0.5))\n",
- "plt.grid()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 12,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": [
- "# that's it, folks. If you want, you can save the created dataframe easily to csv:\n",
- "df.to_csv(\"results.csv\", index=False)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": false
- },
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "collapsed": true
- },
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 2",
- "language": "python",
- "name": "python2"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 2
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython2",
- "version": "2.7.6"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 0
-}
diff --git a/Modules/Biophotonics/python/iMC/tutorials/README.txt b/Modules/Biophotonics/python/iMC/tutorials/README.txt
deleted file mode 100644
index f6fb2aa8d9..0000000000
--- a/Modules/Biophotonics/python/iMC/tutorials/README.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-The tutorials are not fletched out, since I want to discuss the general direction first.
-I propose IPhython notebooks, as e.g. Google does for the Caffe framework:
-http://nbviewer.jupyter.org/github/BVLC/caffe/blob/master/examples/00-classification.ipynb
-
-I added a tutorial for the monte carlo spectra generation to show how this could look like.
-
diff --git a/Modules/Biophotonics/python/iMC_ipcai_jcars_save/iMC/tox.ini b/Modules/Biophotonics/python/iMC_ipcai_jcars_save/iMC/tox.ini
deleted file mode 100644
index 51e0c9f594..0000000000
--- a/Modules/Biophotonics/python/iMC_ipcai_jcars_save/iMC/tox.ini
+++ /dev/null
@@ -1,9 +0,0 @@
-# content of: tox.ini , put in same dir as setup.py
-[tox]
-envlist = py27
-[testenv]
-deps=discover # install pytest in the venvs
-install_command=pip install -f http://www.simpleitk.org/SimpleITK/resources/software.html --trusted-host www.simpleitk.org {opts} {packages}
-#changedir=tests
-commands=discover
-
diff --git a/Modules/BiophotonicsHardware/CMakeLists.txt b/Modules/BiophotonicsHardware/CMakeLists.txt
deleted file mode 100644
index 29137eaf7c..0000000000
--- a/Modules/BiophotonicsHardware/CMakeLists.txt
+++ /dev/null
@@ -1,26 +0,0 @@
-#MITK_CREATE_MODULE(
-# INCLUDE_DIRS ${MITK_BIN_DIR}
-# INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
-# DEPENDS MitkOpenCVVideoSupport
-# EXPORT_DEFINE MITK_TOFHARDWARE_EXPORT
-# ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
-#)
-
-
-
-#Set Subfolder according to moduls
-set( biophotonicsHardware_module_dir
- SpectroCam
-)
-
-# add_subdirectories for each module
-foreach(biophotonicsHardware_module_dir ${biophotonicsHardware_module_dir})
- add_subdirectory(${biophotonicsHardware_module_dir})
-endforeach()
-
-
-
-
-#IF(BUILD_TESTING)
-# add_subdirectory(Testing)
-#ENDIF(BUILD_TESTING)
diff --git a/Modules/BiophotonicsHardware/SpectroCam/CMakeLists.txt b/Modules/BiophotonicsHardware/SpectroCam/CMakeLists.txt
deleted file mode 100644
index 98b72e720f..0000000000
--- a/Modules/BiophotonicsHardware/SpectroCam/CMakeLists.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-#Begin SpectroCam hardware
-OPTION(MITK_USE_BiophotonicsHardware_SpectroCam "Enable support for SpectroCam camera" OFF)
-
-IF(MITK_USE_BiophotonicsHardware_SpectroCam)
- #Find SpectroCam SDK
- FIND_LIBRARY(MITK_SpectroCam_LIB SpectroCam DOC "SpectroCam access library." HINTS "C:\\Program Files (x86)\\Ocean Thin Films\\SpectroCam SDK\\Stage\\64-Bit")
- FIND_PATH(MITK_SpectroCam_INCLUDE_DIR ISpectroCam.h DOC "Include directory of SpectroCam camera." HINTS "C:\\Program Files (x86)\\Ocean Thin Films\\SpectroCam SDK\\Include")
-
- #Find Jai SDK
- FIND_LIBRARY(MITK_JAI_LIB Jai_Factory DOC "SpectroCam access library." HINTS "C:\\Program Files\\JAI\\SDK\\library\\CPP\\lib\\Win64_x64" "C:\\Programme\\JAI\\SDK\\library\\CPP\\lib\\Win64_x64")
- FIND_PATH(MITK_JAI_INCLUDE_DIR Jai_Factory.h DOC "Include directory of SpectroCam camera." HINTS "C:\\Program Files\\JAI\\SDK\\library\\CPP\\include" "C:\\Programme\\JAI\\SDK\\library\\CPP\\include")
-
- SET(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_SpectroCam_LIB} ${MITK_JAI_LIB})
- SET(INCLUDE_DIRS_INTERNAL ${INCLUDE_DIRS_INTERNAL} ${MITK_SpectroCam_INCLUDE_DIR} ${MITK_JAI_INCLUDE_DIR})
-
-
-MITK_CREATE_MODULE(
- INCLUDE_DIRS ${MITK_BIN_DIR}
- PUBLIC ${INCLUDE_DIRS_INTERNAL}
- ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
- DEPENDS MitkCore MitkOpenCVVideoSupport
- PACKAGE_DEPENDS OpenCV ITK|ITKIOImageBase
-# PUBLIC ${ADDITIONAL_LIBS}
-)
-
-
-Message("SpectroCam Module generated")
-
-ENDIF(MITK_USE_BiophotonicsHardware_SpectroCam)
-#End SpectroCam Hardware
diff --git a/Modules/BiophotonicsHardware/SpectroCam/files.cmake b/Modules/BiophotonicsHardware/SpectroCam/files.cmake
deleted file mode 100644
index 18d1e3c5bb..0000000000
--- a/Modules/BiophotonicsHardware/SpectroCam/files.cmake
+++ /dev/null
@@ -1,8 +0,0 @@
-IF(MITK_USE_BiophotonicsHardware_SpectroCam)
-set(CPP_FILES
-mitkSpectroCamController.cpp
-
-)
-
-
-ENDIF(MITK_USE_BiophotonicsHardware_SpectroCam)
\ No newline at end of file
diff --git a/Modules/BiophotonicsHardware/SpectroCam/mitkSpectroCamController.cpp b/Modules/BiophotonicsHardware/SpectroCam/mitkSpectroCamController.cpp
deleted file mode 100644
index 96360e0b5f..0000000000
--- a/Modules/BiophotonicsHardware/SpectroCam/mitkSpectroCamController.cpp
+++ /dev/null
@@ -1,745 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include "mitkSpectroCamController.h"
-#include "mitkLogMacros.h"
-#include <mitkOpenCVToMitkImageFilter.h>
-#include <mitkImageCast.h>
-
-
-#include <fstream>
-#include <string>
-#include <iostream>
-#include <functional>
-
-//OpenCv includes
-#include <opencv\cv.h>
-#include <opencv\cxcore.h>
-#include <opencv\highgui.h>
-#include <opencv2/contrib/contrib.hpp>
-
-// itk includes
-#include <itkImage.h>
-#include <itkComposeImageFilter.h>
-
-//Spectrocam includes
-#include <ISpectroCam.h>
-#include <Jai_Factory.h>
-
-
-
-using namespace std;
-using namespace cv;
-
-
-namespace mitk {
-
-
- typedef itk::VectorImage<unsigned short, 2> CompositeCameraImageType;
-
- /**
- Here basically all of the implementation for the Spectrocam Controller is located.
- This pimpl implementation is necessary because of the additional JAI and SpectroCam libraries, which should be totally hidden
- to external modules/plugins.
- + due to the c - nature of the Spectrocam callback mechanism we need some global variable sharing which is not nice and should
- be hidden from users.
- */
- class SpectroCamController_pimpl
- {
- public:
- SpectroCamController_pimpl();
- ~SpectroCamController_pimpl();
-
- bool Ini();
- int OpenCameraConnection();
- int CloseCameraConnection();
- bool isCameraRunning();
-
-
- void SetCurrentImageAsWhiteBalance();
-
- mitk::Image::Pointer GetCurrentImage();
-
- CompositeCameraImageType::Pointer m_CompositeItkImage_1;
- CompositeCameraImageType::Pointer m_CompositeItkImage_2;
- mitk::Image::Pointer m_CompositeMitkImage;
-
- cv::Mat m_CurrentStackSmall;
- cv::Mat m_CurrentTransformedStack;
- cv::Mat m_FlatfieldSmall;
- cv::Mat m_LLSQSolutionSmall;
-
- const int m_FullWidth;
- const int m_FullHeight;
-
- const int m_SmallWidth;
- const int m_SmallHeight;
-
- bool m_ShowOxygenation;
-
- // for image double buffer swap
- bool m_Image1Selected;
-
- std::string mode;
- std::string model;
-
- private:
-
- void InitializeItkImage(mitk::CompositeCameraImageType::Pointer& compositeImage);
-
- bool m_IsCameraRunning;
-
- unsigned m_NumRecordedImages;
-
- ISpectroCam* spectroCam; //SpectroCam var
-
- STREAM_HANDLE m_hDS; // Handle to the data stream
-
- uint32_t m_iValidBuffers; // Number of buffers allocated to image acquisition
- BUF_HANDLE m_pAquBufferID; // Handles for all the image buffers
- HANDLE m_hEventKill; // Event used for speeding up the termination of image capture
-
-
- //Vars for Ini from file
- FastModeSettings fastSettings;
- SequenceModeSettings seqSettings;
- IndexModeSettings indexSettings;
-
- void SaveCameraStreamToDisk();
- };
-
-}
-
-
-// Implementation
-
-static mitk::SpectroCamController_pimpl* my_SpectroCamController;
-
-mitk::Image::Pointer mitk::SpectroCamController_pimpl::GetCurrentImage()
-{
- mitk::CompositeCameraImageType::Pointer selectedImage;
-
- // TODO SW: semaphore here so it cannot interfere with callback readout of m_Image1Selected
- if (this->m_Image1Selected)
- {
- this->m_Image1Selected = !this->m_Image1Selected;
- selectedImage = this->m_CompositeItkImage_1;
- }
- else
- {
- this->m_Image1Selected = !this->m_Image1Selected;
- selectedImage = this->m_CompositeItkImage_2;
- }
-
- this->m_CompositeMitkImage = mitk::Image::New();
- MITK_INFO << "Image created";
- this->m_CompositeMitkImage->InitializeByItk<mitk::CompositeCameraImageType>(selectedImage);
- MITK_INFO << "Initialized image by ITK";
- this->m_CompositeMitkImage->SetVolume(selectedImage->GetBufferPointer());
- MITK_INFO << "Copied data";
-
-
- return m_CompositeMitkImage;
-}
-
-static cv::Mat createLLSQSolutionFromHMatrix()
-{
- //Create the H-Matrix
- // Ox DOx //Lookup values at http://omlc.org/spectra/hemoglobin/summary.html
- float H[8][4]= {{50104 , 37020. , 405, 1.}, //Filter0 = 580nm +- 10
- {33209.2 , 16156.4 , 785., 1.}, //Filter1 = 470nm +- 10
- {319.6 , 3226.56 , 280., 1.}, //Filter2 = 660nm +- 10
- {32613.2 , 53788 , 495., 1.}, //Filter3 = 560nm +- 10
- {26629.2 , 14550 , 760., 1.}, //Filter4 = 480nm +- 12,5
- {20035.2 , 25773.6 , 665., 1.}, //Filter5 = 511nm +- 10 ->took 510nm
- {3200 , 14677.2 , 380., 1.}, //Filter6 = 600nm +- 10
- {290 , 1794.28 , 220., 1.}}; //Filter7 = 700nm
-
- //Create the hMatrix
- cv::Mat hMatrix = cv::Mat(8, 4, CV_32F, &H ); //cv::Mat(rows, cols, type, fill with)
-
- cv::Mat transH;
- transpose(hMatrix,transH);
- cv::Mat mulImage = transH * hMatrix;
- cv::Mat invImage = mulImage.inv();
- cv::Mat HCompononentsForLLSQ = invImage * transH;
-
- return HCompononentsForLLSQ;
-}
-
-mitk::SpectroCamController_pimpl::SpectroCamController_pimpl()
- :m_hDS(nullptr),
- m_NumRecordedImages(1),
- m_IsCameraRunning(false),
- m_SmallWidth(614),
- m_SmallHeight(514),
- m_FullWidth(2456),
- m_FullHeight(2058),
- m_Image1Selected(true),
- m_ShowOxygenation(false)
-{
- my_SpectroCamController = this;
- m_CurrentStackSmall = cv::Mat(8, m_SmallWidth * m_SmallHeight, CV_32F, cv::Scalar(0));
- m_FlatfieldSmall = cv::Mat(8, m_SmallWidth * m_SmallHeight, CV_32F, cv::Scalar(1));
- m_CurrentTransformedStack = cv::Mat(8, m_SmallWidth * m_SmallHeight, CV_32F, cv::Scalar(1));
-
-
- m_LLSQSolutionSmall = createLLSQSolutionFromHMatrix();
-
-
-}
-
-void mitk::SpectroCamController_pimpl::SetCurrentImageAsWhiteBalance()
-{
- // deep copy of current image stack
- m_FlatfieldSmall = m_CurrentStackSmall.clone();
-
- cv::namedWindow("Oxygenation Estimate", WINDOW_AUTOSIZE);
- m_ShowOxygenation = true;
-}
-
-
-
-mitk::SpectroCamController_pimpl::~SpectroCamController_pimpl()
-{
-}
-
-
-
-
-
-void mitk::SpectroCamController_pimpl::SaveCameraStreamToDisk()
-{
- /*
- //=================================Save Images to HDD=================================
- imagesRecoreded=0;
-
- //If Rec is pressed -> Save Images to Harddrive
- if (rec == true) //On pressing the Rec-Button we wan to save x Stacks with 8 images each
- {
- //Save Image
- saveImage(in); //std::cout<< "save no."<< imagesRecoreded<< std::endl;
- //Icrement counter
- imagesRecoreded++;
-
- if (imagesRecoreded >= (NumberOfStacksToBeRecorded*8) ) //If number of images is bigger or equal to the the Image Stack we want to tecord, untoggle the rec button and reset the counter!
- {
- imagesRecoreded=0;
- rec=false;
- ReCButtonControl_Pointer->EnableWindow(TRUE);
- }
- }
- */
-}
-
-
-
-//Initialize Camera Controller
-bool mitk::SpectroCamController_pimpl::Ini()
-{
- //===============Get Ini from File===============
- //Get model from file std::string CChildWindowSampleDlg::getModelNameFromIni()
- std::ifstream fin("C:\\ModeSettings.txt"); //Set File to read
- std::ofstream fout("C:\\ModeSettingsCheck.txt"); //Set output
- const int bufferSize = 1000;
- char buffer[bufferSize];
-
- if (fin.fail())
- {
- MITK_INFO << "Failed opening file ModeSettings.txt!" << endl ;
- }
-
- fin.getline(buffer, bufferSize);
- fin.getline(buffer, bufferSize);
- model = buffer;
-
-
- //Get mode from file
- //Skipping model, getting mode
- for (int i = 0; i < 3; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
-
- mode = buffer;
-
- // [FastModeExposure]
- for (int i = 0; i < 2; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
-
- fin >> fastSettings.exposure;
- fout << fastSettings.exposure << endl;;
-
- // [FastModeGain]
- for (int i = 0; i < 3; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
-
- fin >> fastSettings.gain;
- fout << fastSettings.gain << endl;
-
- // [SequenceModeExposures]
- for (int i = 0; i < 3; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
-
- for (int i = 0; i < NUMBER_FILTERS; ++i)
- {
- fin >> seqSettings.exposures[i];
- fout << seqSettings.exposures[i] << endl;
- }
-
- // [SequenceModeGains]
- for (int i = 0; i < 3; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
-
- for (int i = 0; i < NUMBER_FILTERS; ++i)
- {
- fin >> seqSettings.gains[i];
- fout << seqSettings.gains[i] << endl;
- }
-
- // [IndexModeExposures]
- for (int i = 0; i < 3; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
-
- for (int i = 0; i < NUMBER_FILTERS; ++i)
- {
- fin >> indexSettings.exposures[i];
- fout << indexSettings.exposures[i] << endl;
- }
-
- // [IndexModeGains]
- for (int i = 0; i < 3; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
- for (int i = 0; i < NUMBER_FILTERS; ++i)
- {
- fin >> indexSettings.gains[i];
- fout << indexSettings.gains[i] << endl;
- }
-
- // [IndexModeNumberFilterIterations]
- for (int i = 0; i < 3; ++i)
- {
- fin.getline(buffer, bufferSize);
- fout << buffer << endl;
- }
-
- for (int i = 0; i < NUMBER_FILTERS; ++i)
- {
- fin >> indexSettings.numFilterIterations[i];
- fout << indexSettings.numFilterIterations[i] << endl;
- }
-
- //After reading files -> close stream
- fin.close();
- fout.close();
-
- return 0;
-
-}
-
-void mitk::SpectroCamController_pimpl::InitializeItkImage(mitk::CompositeCameraImageType::Pointer& compositeImage)
-{
- if (compositeImage.IsNull())
- {
-
- MITK_INFO << "initializing itk::Composite Image";
- mitk::CompositeCameraImageType::RegionType region;
- mitk::CompositeCameraImageType::RegionType::SizeType size;
- mitk::CompositeCameraImageType::RegionType::IndexType index;
- mitk::CompositeCameraImageType::SpacingType spacing;
- size.Fill( 1 );
- size[0] = this->m_FullWidth;
- size[1] = this->m_FullHeight;
- index.Fill(0);
- spacing.Fill(1);
- region.SetSize(size);
- region.SetIndex(index);
-
- compositeImage = mitk::CompositeCameraImageType::New();
- compositeImage->SetRegions(region);
- compositeImage->SetSpacing(spacing);
- compositeImage->SetNumberOfComponentsPerPixel(NUMBER_FILTERS);
- compositeImage->Allocate();
- }
-}
-
-/**
-* this c callback function is where the magic happens.
-* it is called every time a new image has arrived from the SpectroCam.
-*/
-static void DisplayCameraStream(SpectroCamImage image)
-{
-
- MITK_INFO << "image callback call";
- try
- {
- if (image.m_FilterNum < 0 || image.m_FilterNum >= NUMBER_FILTERS)
- {
- std::cout << "Filter number out of range.\n"<< std::endl;
- }
- else
- {
- // Allocate the buffer to hold converted the image. (We only want to do this once for performance reasons)
- if (image.m_pAcqImage->pImageBuffer == nullptr)
- {
- if (J_Image_Malloc(image.m_pAcqImage, image.m_pAcqImage) != J_ST_SUCCESS)
- {
- return;
- }
- }
-
-
- //============= Get data from spectrocam to opencv
-
- // TODO SW: probably we can get around this memcopy by simply setting data pointer? Not sure.
- cv::Mat data = cv::Mat( image.m_pAcqImage->iSizeY, image.m_pAcqImage->iSizeX, CV_16U);
- memcpy( data.datastart , image.m_pAcqImage->pImageBuffer , image.m_pAcqImage->iImageSize); //Copy Image from JAI-Format to OCV´s IplImage
-
-
- //============= From opencv to mitk::Image (VectorImage)
-
- mitk::CompositeCameraImageType::Pointer selectedImage;
-
- if (my_SpectroCamController->m_Image1Selected)
- {
- selectedImage = my_SpectroCamController->m_CompositeItkImage_1;
- }
- else
- {
- selectedImage = my_SpectroCamController->m_CompositeItkImage_2;
- }
-
- itk::ImageRegionIterator<mitk::CompositeCameraImageType> imageIterator(selectedImage, selectedImage->GetLargestPossibleRegion());
-
- MatConstIterator_<unsigned short> it, end;
- it = data.begin<unsigned short>();
- end = data.end<unsigned short>();
-
-
- while(!imageIterator.IsAtEnd())
- {
- mitk::CompositeCameraImageType::PixelType compositePixel = imageIterator.Get();
-
- compositePixel[image.m_FilterNum] = *it;
-
- ++it;
- ++imageIterator;
- }
-
- //both matrix and itk image shall reach end at the same time.
- assert(it == end);
-
-
- //============= Display image as opencv window ==
-
- cv::Mat display;
- cv::resize(data, display, cvSize(my_SpectroCamController->m_SmallWidth, my_SpectroCamController->m_SmallHeight) ); //do some resizeing for faster display
-
- display *= 16; // image is only 12 bit large, but datatype is 16 bit. Expand to full range for displaying by multiplying by 2^4.
-
-
-
- //Display Image
- cv::imshow("Display window", display); //Display image
- //MITK_INFO << "pixel 100,100" << display.at<unsigned short>(0,100);
-
-
- //============= TODO: live oxygenation estimation
-
- if (my_SpectroCamController->m_ShowOxygenation)
- {
- cv::Range slice[2];
- slice[0] = cv::Range( image.m_FilterNum, image.m_FilterNum+1 );
- slice[1] = cv::Range::all();
-
- cv::Mat currentSlice = my_SpectroCamController->m_CurrentStackSmall(slice);
-
- cv::Mat currentImageF32;
- display.convertTo(currentImageF32, CV_32F);
-
- currentImageF32 = currentImageF32.reshape(0, 1);
- currentImageF32.copyTo(currentSlice);
-
- cv::Mat currentWorkingSlice = currentSlice.clone();
-
- cv::Mat currentFlatfieldSlice = my_SpectroCamController->m_FlatfieldSmall(slice);
- MITK_INFO << "flat current: " << currentFlatfieldSlice.at<float>(0,100);
-
-
- MITK_INFO << "raw measured pixel value: " << currentWorkingSlice.at<float>(0,100);
-
- cv::divide(currentWorkingSlice, currentFlatfieldSlice, currentWorkingSlice);
- MITK_INFO << "corrected by flatfield pixel: " << currentWorkingSlice.at<float>(0,100);
-
- cv::log(currentWorkingSlice, currentWorkingSlice);
- currentWorkingSlice = -0.43429 * currentWorkingSlice;
- MITK_INFO << "to absorption: " << currentWorkingSlice.at<float>(0,100);
-
- currentWorkingSlice.copyTo(my_SpectroCamController->m_CurrentTransformedStack(slice) );
-
- //MITK_INFO << "slice 0: " << my_SpectroCamController->m_CurrentTransformedStack.at<float>(0,100);;
-
- cv::Mat currentEstimate = my_SpectroCamController->m_LLSQSolutionSmall * my_SpectroCamController->m_CurrentTransformedStack;
- cv::Range oxyHemo[2];
- oxyHemo[0] = cv::Range(0,1);
- oxyHemo[1] = cv::Range::all();
-
- cv::Range deOxyHemo[2];
- deOxyHemo[0] = cv::Range(1,2);
- deOxyHemo[1] = cv::Range::all();
-
- cv::Mat saO2 = currentEstimate(oxyHemo) / (currentEstimate(oxyHemo) + currentEstimate(deOxyHemo));
-
- cv::Mat saO2Image = saO2.reshape(0, my_SpectroCamController->m_SmallHeight);
- MITK_INFO << "saO2, 200 200: " << saO2Image.at<float>(200,200);
-
- cv::threshold(saO2Image, saO2Image, 1., 1., cv::THRESH_TRUNC);
- cv::threshold(saO2Image, saO2Image, 0., 0., cv::THRESH_TOZERO);
-
- saO2Image = saO2Image * 637.;// 255.;
-
- cv::Mat SaO2IntImage;
- saO2Image.convertTo(SaO2IntImage, CV_8U);
- // MITK_INFO << saO2Image.at<float>(0,100);
-
- cv::Mat colorImage;
- cv::applyColorMap(SaO2IntImage, colorImage, COLORMAP_JET);
- cv::imshow("Oxygenation Estimate", colorImage); //Display image
- }
-
-
- cv::waitKey(1);
- }
-
- }//try
-
- catch (std::exception &e) {
- MITK_INFO << e.what();
- }
-}
-
-
-
-int mitk::SpectroCamController_pimpl::OpenCameraConnection()
-{
- //=====================OpenFactoryAndCamera=====================
- //Create Factory and cam based on //BOOL OpenFactoryAndCamera(); // Open factory and search for cameras. Open first camera
- spectroCam = CreateSpectroCam(&DisplayCameraStream, nullptr, 0);
- MITK_INFO << "Camera " << model << " is running in: " << mode << "-mode" << endl;
-
-
-
- //=====================Open Streams=====================
- J_STATUS_TYPE status = spectroCam->initialize(model.c_str(), (std::string("C:\\") + model + "\\").c_str());
-
- if (status != J_ST_SUCCESS)
- {
- MITK_INFO << "Could not initialize camera!" << endl;
- }
-
- // initialize VectorImage
- this->InitializeItkImage(this->m_CompositeItkImage_1);
- this->InitializeItkImage(this->m_CompositeItkImage_2);
-
-
-
- //=====================Open Streams=====================
- if (mode == "Fast")
- {
- status = status | spectroCam->start(fastSettings);
- }
-
- else if (mode == "Sequence")
- {
- status = status | spectroCam->start(seqSettings);
- }
-
- else if (mode == "IndexFast")
- {
- indexSettings.filterModeSpeed = IndexModeSettings::INDEX_FAST;
- status = status | spectroCam->start(indexSettings);
- }
-
- else if (mode == "IndexSlow")
- {
- indexSettings.filterModeSpeed = IndexModeSettings::INDEX_SLOW;
- status = status | spectroCam->start(indexSettings);
- }
-
- else if (mode == "IndexTriggered")
- {
- indexSettings.filterModeSpeed = IndexModeSettings::INDEX_TRIGGERED;
- status = status | spectroCam->start(indexSettings);
- }
-
- else
- {
- status = status | spectroCam->start(fastSettings);
- }
-
- MITK_INFO << "status flag: " << status;
-
- if (status == J_ST_SUCCESS)
- {
- m_IsCameraRunning = true;
- }
-
-
- cv::namedWindow( "Display window", WINDOW_AUTOSIZE );// Create a window for display.
-
- return status;
-}
-
-bool mitk::SpectroCamController_pimpl::isCameraRunning()
-{
- return m_IsCameraRunning;
-}
-
-
-
-//Method to close down connections
-int mitk::SpectroCamController_pimpl::CloseCameraConnection()
-{
-
- // On click -> Stop acquisition
- J_STATUS_TYPE retval = 0;
- CAM_HANDLE hCam = spectroCam->GetCameraHandle();
-
- // Stop Acquision
- if (hCam)
- {
- retval = retval | J_Camera_ExecuteCommand(hCam, (int8_t*) NODE_NAME_ACQSTOP);
- }
-
-
- MITK_INFO << "execute acqstop command";
-
-
- // Close stream (this frees all allocated buffers)
- // Stop the image acquisition engine
- J_DataStream_StopAcquisition(m_hDS, ACQ_STOP_FLAG_KILL);
-
-
- MITK_INFO << "execute stop aqui";
-
- // UnPrepare Buffers (this removed the buffers from the acquisition engine and frees buffers)
- {
- void *pPrivate;
- void *pBuffer;
-
- // Flush Queues
- J_DataStream_FlushQueue(m_hDS, ACQ_QUEUE_INPUT_TO_OUTPUT);
- J_DataStream_FlushQueue(m_hDS, ACQ_QUEUE_OUTPUT_DISCARD);
-
- // Remove the frame buffer from the Acquisition engine.
- J_DataStream_RevokeBuffer(m_hDS, m_pAquBufferID, &pBuffer , &pPrivate);
-
- m_pAquBufferID = 0;
-
- m_iValidBuffers = 0;
- }
-
- MITK_INFO << "unprepared buffers";
-
-
- // Close Stream
- if(m_hDS)
- {
- J_DataStream_Close(m_hDS);
- m_hDS = nullptr;
- }
-
-
- MITK_INFO << "closed stream";
-
- //===================Close Factory and destroy Cam=====================
- //void CloseFactoryAndCamera(); // Close camera and factory to clean up
- retval = retval | spectroCam->stop();
-
-
- MITK_INFO << "stopped camera";
-
- //BOOL TerminateStreamThread(void); // Terminate the image acquisition thread
- if (spectroCam)
- {
- //DestroySpectroCam(spectroCam); //Destroy SpectroCam-Objekt
- }
-
- MITK_INFO << "destroyed spectrocam";
-
- if (J_ST_SUCCESS == retval)
- {
- m_IsCameraRunning = false;
- }
-
- return retval;
-}
-
-
-mitk::SpectroCamController::SpectroCamController()
-{
- m_SpectroCamController_pimpl = new SpectroCamController_pimpl();
-}
-
-mitk::SpectroCamController::~SpectroCamController()
-{
- delete m_SpectroCamController_pimpl;
-}
-
-int mitk::SpectroCamController::OpenCameraConnection()
-{
- return m_SpectroCamController_pimpl->OpenCameraConnection();
-}
-
-int mitk::SpectroCamController::CloseCameraConnection()
-{
- return m_SpectroCamController_pimpl->CloseCameraConnection();
-}
-
-bool mitk::SpectroCamController::Ini()
-{
- return m_SpectroCamController_pimpl->Ini();
-}
-
-bool mitk::SpectroCamController::isCameraRunning()
-{
- return m_SpectroCamController_pimpl->isCameraRunning();
-}
-
-
-mitk::Image::Pointer mitk::SpectroCamController::GetCurrentImage()
-{
- return m_SpectroCamController_pimpl->GetCurrentImage();
-}
-
-void mitk::SpectroCamController::SetCurrentImageAsWhiteBalance()
-{
- m_SpectroCamController_pimpl->SetCurrentImageAsWhiteBalance();
-}
diff --git a/Modules/BiophotonicsHardware/SpectroCam/mitkSpectroCamController.h b/Modules/BiophotonicsHardware/SpectroCam/mitkSpectroCamController.h
deleted file mode 100644
index 3a755e08d4..0000000000
--- a/Modules/BiophotonicsHardware/SpectroCam/mitkSpectroCamController.h
+++ /dev/null
@@ -1,55 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#ifndef mitkSpectroCamController_h
-#define mitkSpectroCamController_h
-
-#include <string>
-
-
-#include <MitkSpectroCamExports.h>
-#include <mitkImage.h>
-
-namespace mitk
-{
- // forward declaration of the implementation for the SpectroCam
- class SpectroCamController_pimpl;
-
- /**
- * @brief Controller for Pixelteq SpectroCam
- *
- *
- * @ingroup BiophotonicsHardware
- */
- class MITKSPECTROCAM_EXPORT SpectroCamController
- {
- public:
- SpectroCamController();
- ~SpectroCamController();
-
- bool Ini();
- int OpenCameraConnection();
- int CloseCameraConnection();
- bool isCameraRunning();
-
- /**
- Returns the current image stack. Is of VectorType, unsigned short
- */
- mitk::Image::Pointer GetCurrentImage();
-
- void SetCurrentImageAsWhiteBalance();
-
- private:
- SpectroCamController_pimpl* m_SpectroCamController_pimpl;
- };
-
-}
-#endif
diff --git a/Modules/CEST/CMakeLists.txt b/Modules/CEST/CMakeLists.txt
index 0b43dac056..a35980ee61 100644
--- a/Modules/CEST/CMakeLists.txt
+++ b/Modules/CEST/CMakeLists.txt
@@ -1,9 +1,9 @@
MITK_CREATE_MODULE(
DEPENDS MitkCore
PRIVATE MitkDICOM
PACKAGE_DEPENDS
- PRIVATE ITK|ITKIOImageBase+ITKIOGDCM Poco
+ PRIVATE Poco
)
add_subdirectory(autoload/IO)
add_subdirectory(test)
diff --git a/Modules/CEST/autoload/IO/CMakeLists.txt b/Modules/CEST/autoload/IO/CMakeLists.txt
index bd424d386a..9b6aa610fa 100644
--- a/Modules/CEST/autoload/IO/CMakeLists.txt
+++ b/Modules/CEST/autoload/IO/CMakeLists.txt
@@ -1,6 +1,4 @@
MITK_CREATE_MODULE( CESTIO
DEPENDS MitkCEST MitkDICOM
- PACKAGE_DEPENDS
- PRIVATE ITK|ITKIOGDCM
AUTOLOAD_WITH MitkDICOM
)
diff --git a/Modules/CEST/autoload/IO/resource/cest_DKFZ.xml b/Modules/CEST/autoload/IO/resource/cest_DKFZ.xml
index b87f554740..6a35902e76 100644
--- a/Modules/CEST/autoload/IO/resource/cest_DKFZ.xml
+++ b/Modules/CEST/autoload/IO/resource/cest_DKFZ.xml
@@ -1,11 +1,11 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="DKFZ internal CEST image configuration"
description="Based on ClassicDICOMSeriesReader for 3D+t images"
class="ClassicDICOMSeriesReader"
version="2"
group3DnT="true"
fixTiltByShearing="true"
onlyCondenseSameSeries="false"
>
-</DICOMFileReader>
\ No newline at end of file
+</DICOMFileReader>
diff --git a/Modules/CameraCalibration/mitkCameraIntrinsics.cpp b/Modules/CameraCalibration/mitkCameraIntrinsics.cpp
index cb81b0f60b..fbb1ce2894 100644
--- a/Modules/CameraCalibration/mitkCameraIntrinsics.cpp
+++ b/Modules/CameraCalibration/mitkCameraIntrinsics.cpp
@@ -1,507 +1,508 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkCameraIntrinsics.h"
#include <itkMutexLockHolder.h>
#include <mitkEndoMacros.h>
#include <mitkEndoDebug.h>
+#include <tinyxml2.h>
mitk::CameraIntrinsics::CameraIntrinsics()
: m_Valid(false), m_Mutex(itk::FastMutexLock::New())
{
m_CameraMatrix = cv::Mat::zeros(3, 3, cv::DataType<double>::type);
m_CameraMatrix.at<double>(2,2) = 1.0;
m_DistorsionCoeffs = cv::Mat::zeros(1, 5, cv::DataType<double>::type);
}
mitk::CameraIntrinsics::CameraIntrinsics(const CameraIntrinsics& other)
: itk::Object()
, mitk::XMLSerializable()
, m_Valid(false)
, m_Mutex(itk::FastMutexLock::New())
{
this->Copy(&other);
}
mitk::CameraIntrinsics::~CameraIntrinsics()
{
}
bool mitk::CameraIntrinsics::Equals( const CameraIntrinsics* other ) const
{
return other->GetDistorsionCoeffsAsPoint4D()==
this->GetDistorsionCoeffsAsPoint4D() &&
other->GetFocalPoint()==
this->GetFocalPoint() &&
other->GetPrincipalPoint()
== this->GetPrincipalPoint();
}
void mitk::CameraIntrinsics::Copy(const CameraIntrinsics* other)
{
this->SetIntrinsics( other->GetCameraMatrix().clone()
, other->GetDistorsionCoeffs().clone() );
this->SetValid(other->m_Valid);
}
bool mitk::CameraIntrinsics::IsValid() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
return m_Valid;
}
vnl_matrix_fixed<mitk::ScalarType, 3, 3>
mitk::CameraIntrinsics::GetVnlCameraMatrix() const
{
vnl_matrix_fixed<mitk::ScalarType, 3, 3> mat;
mat.set_identity();
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
mat(0,0) = m_CameraMatrix.at<double>(0,0);
mat(1,1) = m_CameraMatrix.at<double>(1,1);
mat(0,2) = m_CameraMatrix.at<double>(0,2);
mat(1,2) = m_CameraMatrix.at<double>(1,2);
}
return mat;
}
void mitk::CameraIntrinsics::SetCameraMatrix(
const vnl_matrix_fixed<mitk::ScalarType, 3, 3>& _CameraMatrix )
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_CameraMatrix.at<double>(0,0) = _CameraMatrix(0,0);
m_CameraMatrix.at<double>(1,1) = _CameraMatrix(1,1);
m_CameraMatrix.at<double>(0,2) = _CameraMatrix(0,2);
m_CameraMatrix.at<double>(1,2) = _CameraMatrix(1,2);
}
vnl_matrix_fixed<mitk::ScalarType, 3, 4>
mitk::CameraIntrinsics::GetVnlCameraMatrix3x4() const
{
vnl_matrix_fixed<mitk::ScalarType, 3, 4> mat;
mat.fill(0);
mat.update( this->GetVnlCameraMatrix().as_matrix() );
return mat;
}
void mitk::CameraIntrinsics::SetIntrinsics( const cv::Mat& _CameraMatrix
, const cv::Mat& _DistorsionCoeffs)
{
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
if( _CameraMatrix.cols != 3 || _CameraMatrix.rows != 3)
throw std::invalid_argument("Wrong format of camera matrix. Should be 3x3"
" double.");
endoAssertMsg( (_DistorsionCoeffs.cols == 5) &&
_DistorsionCoeffs.rows == 1, "Wrong format of distorsion coefficients"
" vector. Should be 5x1 double.");
m_CameraMatrix = _CameraMatrix.clone();
m_DistorsionCoeffs = _DistorsionCoeffs.clone();
m_Valid = true;
}
this->Modified();
}
void mitk::CameraIntrinsics::SetIntrinsics( const mitk::Point3D& focalPoint,
const mitk::Point3D& principalPoint,
const mitk::Point4D& distortionCoefficients)
{
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_CameraMatrix.at<double>(0,0) = focalPoint[0];
m_CameraMatrix.at<double>(1,1) = focalPoint[1];
m_CameraMatrix.at<double>(0,2) = principalPoint[0];
m_CameraMatrix.at<double>(1,2) = principalPoint[1];
m_DistorsionCoeffs.at<double>(0,0) = distortionCoefficients[0];
m_DistorsionCoeffs.at<double>(0,1) = distortionCoefficients[1];
m_DistorsionCoeffs.at<double>(0,2) = distortionCoefficients[2];
m_DistorsionCoeffs.at<double>(0,3) = distortionCoefficients[3];
}
this->Modified();
}
void mitk::CameraIntrinsics::SetFocalLength( double x, double y )
{
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_CameraMatrix.at<double>(0,0) = x;
m_CameraMatrix.at<double>(1,1) = y;
}
this->Modified();
}
void mitk::CameraIntrinsics::SetPrincipalPoint( double x, double y )
{
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_CameraMatrix.at<double>(0,2) = x;
m_CameraMatrix.at<double>(1,2) = y;
}
this->Modified();
}
void mitk::CameraIntrinsics::SetDistorsionCoeffs( double k1, double k2,
double p1, double p2 )
{
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_DistorsionCoeffs.at<double>(0,0) = k1;
m_DistorsionCoeffs.at<double>(0,1) = k2;
m_DistorsionCoeffs.at<double>(0,2) = p1;
m_DistorsionCoeffs.at<double>(0,3) = p2;
}
this->Modified();
}
cv::Mat mitk::CameraIntrinsics::GetCameraMatrix() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
return m_CameraMatrix.clone(); // return a copy of this small matrix
}
cv::Mat mitk::CameraIntrinsics::GetDistorsionCoeffs() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
return m_DistorsionCoeffs.clone(); // return a copy of this small matrix
}
cv::Mat mitk::CameraIntrinsics::GetDistorsionCoeffs()
{
const CameraIntrinsics* intrinsics = this;
return intrinsics->GetDistorsionCoeffs();
}
std::string mitk::CameraIntrinsics::ToString() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
std::ostringstream s; s.precision(12);
const cv::Mat& CameraMatrix = m_CameraMatrix;
const cv::Mat& DistorsionCoeffs = m_DistorsionCoeffs;
s.str(""); s << this->GetNameOfClass() << ": ";
s << "fx = " << CameraMatrix.at<double>(0,0);
s << ", fy = " << CameraMatrix.at<double>(1,1);
s << ", cx = " << CameraMatrix.at<double>(0,2);
s << ", cy = " << CameraMatrix.at<double>(1,2);
s << ", k1 = " << DistorsionCoeffs.at<double>(0,0);
s << ", k2 = " << DistorsionCoeffs.at<double>(0,1);
s << ", p1 = " << DistorsionCoeffs.at<double>(0,2);
s << ", p2 = " << DistorsionCoeffs.at<double>(0,3);
//s << ", k3 = " << DistorsionCoeffs.at<double>(0,4);
return s.str();
}
-void mitk::CameraIntrinsics::ToXML(TiXmlElement* elem) const
+void mitk::CameraIntrinsics::ToXML(tinyxml2::XMLElement* elem) const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
elem->SetValue(this->GetNameOfClass());
std::ostringstream s; s.precision(12);
const cv::Mat& CameraMatrix = m_CameraMatrix;
s.str(""); s << CameraMatrix.at<double>(0,0);
- elem->SetAttribute( "fx", s.str() );
+ elem->SetAttribute( "fx", s.str().c_str() );
s.str(""); s << CameraMatrix.at<double>(1,1);
- elem->SetAttribute( "fy", s.str() );
+ elem->SetAttribute( "fy", s.str().c_str());
s.str(""); s << CameraMatrix.at<double>(0,2);
- elem->SetAttribute( "cx", s.str() );
+ elem->SetAttribute( "cx", s.str().c_str());
s.str(""); s << CameraMatrix.at<double>(1,2);
- elem->SetAttribute( "cy", s.str() );
+ elem->SetAttribute( "cy", s.str().c_str());
const cv::Mat& DistorsionCoeffs = m_DistorsionCoeffs;
s.str(""); s << DistorsionCoeffs.at<double>(0,0);
- elem->SetAttribute( "k1", s.str() );
+ elem->SetAttribute( "k1", s.str().c_str());
s.str(""); s << DistorsionCoeffs.at<double>(0,1);
- elem->SetAttribute( "k2", s.str() );
+ elem->SetAttribute( "k2", s.str().c_str());
s.str(""); s << DistorsionCoeffs.at<double>(0,2);
- elem->SetAttribute( "p1", s.str() );
+ elem->SetAttribute( "p1", s.str().c_str());
s.str(""); s << DistorsionCoeffs.at<double>(0,3);
- elem->SetAttribute( "p2", s.str() );
- elem->SetAttribute("Valid", m_Valid);
+ elem->SetAttribute( "p2", s.str().c_str());
+ elem->SetAttribute("Valid", static_cast<int>(m_Valid));
//s.str(""); s << DistorsionCoeffs.at<double>(4,0);
- //elem->SetAttribute( "k3", s.str() );
+ //elem->SetAttribute( "k3", s.str().c_str() );
}
-void mitk::CameraIntrinsics::FromGMLCalibrationXML(TiXmlElement* elem)
+void mitk::CameraIntrinsics::FromGMLCalibrationXML(const tinyxml2::XMLElement* elem)
{
assert( elem );
- assert( elem->ValueStr() == "results" );
+ assert( std::string(elem->Value()) == "results" );
cv::Mat CameraMatrix = cv::Mat::zeros(3, 3, cv::DataType<double>::type);
CameraMatrix.at<double>(2,2) = 1.0;
cv::Mat DistorsionCoeffs = cv::Mat::zeros(1, 5, cv::DataType<double>::type);
- TiXmlElement* focus_lenXElem = elem->FirstChildElement("focus_lenX");
+ const auto* focus_lenXElem = elem->FirstChildElement("focus_lenX");
endoAssert( focus_lenXElem != nullptr );
CameraMatrix.at<double>(0,0) = atof( focus_lenXElem->GetText() );
- TiXmlElement* focus_lenYElem = elem->FirstChildElement("focus_lenY");
+ const auto* focus_lenYElem = elem->FirstChildElement("focus_lenY");
endoAssert( focus_lenYElem != nullptr );
CameraMatrix.at<double>(1,1) = atof( focus_lenYElem->GetText() );
- TiXmlElement* PrincipalXElem = elem->FirstChildElement("PrincipalX");
+ const auto* PrincipalXElem = elem->FirstChildElement("PrincipalX");
endoAssert( PrincipalXElem != nullptr );
CameraMatrix.at<double>(0,2) = atof( PrincipalXElem->GetText() );
- TiXmlElement* PrincipalYElem = elem->FirstChildElement("PrincipalY");
+ const auto* PrincipalYElem = elem->FirstChildElement("PrincipalY");
endoAssert( PrincipalYElem != nullptr );
CameraMatrix.at<double>(1,2) = atof( PrincipalYElem->GetText() );
// DISTORSION COEFFS
- TiXmlElement* Dist1Elem = elem->FirstChildElement("Dist1");
+ const auto* Dist1Elem = elem->FirstChildElement("Dist1");
endoAssert( Dist1Elem != nullptr );
DistorsionCoeffs.at<double>(0,0) = atof( Dist1Elem->GetText() );
- TiXmlElement* Dist2Elem = elem->FirstChildElement("Dist2");
+ const auto* Dist2Elem = elem->FirstChildElement("Dist2");
endoAssert( Dist2Elem != nullptr );
DistorsionCoeffs.at<double>(0,1) = atof( Dist2Elem->GetText() );
- TiXmlElement* Dist3Elem = elem->FirstChildElement("Dist3");
+ const auto* Dist3Elem = elem->FirstChildElement("Dist3");
endoAssert( Dist3Elem != nullptr );
DistorsionCoeffs.at<double>(0,2) = atof( Dist3Elem->GetText() );
- TiXmlElement* Dist4Elem = elem->FirstChildElement("Dist4");
+ const auto* Dist4Elem = elem->FirstChildElement("Dist4");
endoAssert( Dist4Elem != nullptr );
DistorsionCoeffs.at<double>(0,3) = atof( Dist4Elem->GetText() );
int valid = 0;
elem->QueryIntAttribute("Valid", &valid);
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_Valid = static_cast<bool>(valid);
m_CameraMatrix = CameraMatrix;
m_DistorsionCoeffs = DistorsionCoeffs;
}
this->Modified();
}
-void mitk::CameraIntrinsics::FromXML(TiXmlElement* elem)
+void mitk::CameraIntrinsics::FromXML(const tinyxml2::XMLElement* elem)
{
endoAssert ( elem );
MITK_DEBUG << elem->Value();
- std::string filename;
- if(elem->QueryStringAttribute("file", &filename) == TIXML_SUCCESS)
+ const char* filename = elem->Attribute("file");
+ if(nullptr != filename)
{
this->FromXMLFile(filename);
return;
}
else if(strcmp(elem->Value(), "CalibrationProject") == 0)
{
this->FromGMLCalibrationXML(elem->FirstChildElement("results"));
return;
}
assert ( elem );
if(strcmp(elem->Value(), this->GetNameOfClass()) != 0)
elem = elem->FirstChildElement(this->GetNameOfClass());
std::ostringstream err;
// CAMERA MATRIX
cv::Mat CameraMatrix = cv::Mat::zeros(3, 3, cv::DataType<double>::type);
CameraMatrix.at<double>(2,2) = 1.0;
double val = 0.0;
- if(elem->QueryDoubleAttribute("fx", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("fx", &val) == tinyxml2::XML_SUCCESS)
CameraMatrix.at<double>(0,0) = val;
else
err << "fx, ";
- if(elem->QueryDoubleAttribute("fy", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("fy", &val) == tinyxml2::XML_SUCCESS)
CameraMatrix.at<double>(1,1) = val;
else
err << "fy, ";
- if(elem->QueryDoubleAttribute("cx", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("cx", &val) == tinyxml2::XML_SUCCESS)
CameraMatrix.at<double>(0,2) = val;
else
err << "cx, ";
- if(elem->QueryDoubleAttribute("cy", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("cy", &val) == tinyxml2::XML_SUCCESS)
CameraMatrix.at<double>(1,2) = val;
else
err << "cy, ";
// DISTORSION COEFFS
endodebug( "creating DistorsionCoeffs from XML file")
cv::Mat DistorsionCoeffs = cv::Mat::zeros(1, 5, cv::DataType<double>::type);
- if(elem->QueryDoubleAttribute("k1", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("k1", &val) == tinyxml2::XML_SUCCESS)
DistorsionCoeffs.at<double>(0,0) = val;
else
err << "k1, ";
- if(elem->QueryDoubleAttribute("k2", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("k2", &val) == tinyxml2::XML_SUCCESS)
DistorsionCoeffs.at<double>(0,1) = val;
else
err << "k2, ";
- if(elem->QueryDoubleAttribute("p1", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("p1", &val) == tinyxml2::XML_SUCCESS)
DistorsionCoeffs.at<double>(0,2) = val;
else
err << "p1, ";
- if(elem->QueryDoubleAttribute("p2", &val) == TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("p2", &val) == tinyxml2::XML_SUCCESS)
DistorsionCoeffs.at<double>(0,3) = val;
else
err << "p2, ";
DistorsionCoeffs.at<double>(0,4) = 0.0;
- /*if(elem->QueryDoubleAttribute("k3", &val) == TIXML_SUCCESS)
+ /*if(elem->QueryDoubleAttribute("k3", &val) == tinyxml2::XML_SUCCESS)
DistorsionCoeffs.at<double>(4,0) = val;
else
err << "k3, ";*/
std::string errorStr = err.str();
int errLength = errorStr.length();
if(errLength > 0)
{
errorStr = errorStr.substr(0, errLength-2);
errorStr.append(" not found");
throw std::invalid_argument(err.str());
}
int valid = 0;
elem->QueryIntAttribute("Valid", &valid);
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_Valid = static_cast<bool>(valid);
m_CameraMatrix = CameraMatrix;
m_DistorsionCoeffs = DistorsionCoeffs;
}
this->Modified();
}
double mitk::CameraIntrinsics::GetFocalLengthX() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
double FocalLengthX = m_CameraMatrix.at<double>(0,0);
return FocalLengthX;
}
double mitk::CameraIntrinsics::GetFocalLengthY() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
double FocalLengthY = m_CameraMatrix.at<double>(1,1);;
return FocalLengthY;
}
double mitk::CameraIntrinsics::GetPrincipalPointX() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
double PrincipalPointX = m_CameraMatrix.at<double>(0,2);
return PrincipalPointX;
}
double mitk::CameraIntrinsics::GetPrincipalPointY() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
double PrincipalPointY = m_CameraMatrix.at<double>(1,2);
return PrincipalPointY;
}
mitk::Point4D mitk::CameraIntrinsics::GetDistorsionCoeffsAsPoint4D() const
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
mitk::Point4D coeffs;
coeffs[0] = m_DistorsionCoeffs.at<double>(0,0);
coeffs[1] = m_DistorsionCoeffs.at<double>(0,1);
coeffs[2] = m_DistorsionCoeffs.at<double>(0,2);
coeffs[3] = m_DistorsionCoeffs.at<double>(0,3);
return coeffs;
}
mitk::Point3D mitk::CameraIntrinsics::GetFocalPoint() const
{
mitk::Point3D p;
p[0] = this->GetFocalLengthX();
p[1] = this->GetFocalLengthY();
p[2] = 0;
return p;
}
mitk::Point3D mitk::CameraIntrinsics::GetPrincipalPoint() const
{
mitk::Point3D p;
p[0] = this->GetPrincipalPointX();
p[1] = this->GetPrincipalPointY();
p[2] = 0;
return p;
}
vnl_vector_fixed<mitk::ScalarType, 2>
mitk::CameraIntrinsics::GetFocalPointAsVnlVector() const
{
vnl_vector_fixed<mitk::ScalarType, 2> vec;
vec[0] = this->GetFocalLengthX();
vec[1] = this->GetFocalLengthY();
return vec;
}
vnl_vector_fixed<mitk::ScalarType, 2>
mitk::CameraIntrinsics::GetPrincipalPointAsVnlVector() const
{
vnl_vector_fixed<mitk::ScalarType, 2> vec;
vec[0] = this->GetPrincipalPointX();
vec[1] = this->GetPrincipalPointY();
return vec;
}
std::ostream& operator<< (std::ostream& os, mitk::CameraIntrinsics::Pointer p)
{
os << p->ToString();
return os;
}
std::string mitk::CameraIntrinsics::GetString()
{
return this->ToString();
}
std::string mitk::CameraIntrinsics::ToOctaveString(
const std::string& varName)
{
std::ostringstream s;
s << varName << " = [" << this->GetFocalLengthX() << " 0 "
<< this->GetPrincipalPointX() << "; 0 " <<
this->GetFocalLengthY() << " " << this->GetPrincipalPointY() << ";"
<< " 0 0 1 ];";
return s.str();
}
void mitk::CameraIntrinsics::SetValid( bool valid )
{
itk::MutexLockHolder<itk::FastMutexLock> lock(*m_Mutex);
m_Valid = valid;
}
itk::LightObject::Pointer mitk::CameraIntrinsics::InternalClone() const
{
itk::LightObject::Pointer result(new Self(*this));
result->UnRegister();
return result;
}
diff --git a/Modules/CameraCalibration/mitkCameraIntrinsics.h b/Modules/CameraCalibration/mitkCameraIntrinsics.h
index a6004b8960..a36cbf0a7f 100644
--- a/Modules/CameraCalibration/mitkCameraIntrinsics.h
+++ b/Modules/CameraCalibration/mitkCameraIntrinsics.h
@@ -1,141 +1,141 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkCameraIntrinsics_h
#define mitkCameraIntrinsics_h
#include <mitkCommon.h>
#include <mitkNumericTypes.h>
#include <itkDataObject.h>
#include <itkFastMutexLock.h>
#include <vnl/vnl_matrix_fixed.h>
#include "mitkXMLSerializable.h"
#include <MitkCameraCalibrationExports.h>
#include "opencv2/core.hpp"
int mitkCameraIntrinsicsTest(int, char* []);
namespace mitk
{
///
/// \brief class representing camera intrinsics and related functions
///
class MITKCAMERACALIBRATION_EXPORT CameraIntrinsics: virtual public itk::Object,
virtual public mitk::XMLSerializable
{
public:
///
/// for testing purposes
///
friend int mitkCameraIntrinsicsTest(int argc, char* argv[]);
///
/// smartpointer typedefs
///
mitkClassMacroItkParent(CameraIntrinsics, itk::Object);
///
/// the static new function
///
itkFactorylessNewMacro(Self);
///
/// make a clone of this intrinsics
///
itkCloneMacro(Self);
///
/// copy information from other to this
///
void Copy(const CameraIntrinsics* other);
///
/// checks two intrinsics for equality
///
bool Equals( const CameraIntrinsics* other ) const;
///
/// \return the intrinsic parameter matrix as a 3x3 vnl matrix
///
vnl_matrix_fixed<mitk::ScalarType, 3, 3> GetVnlCameraMatrix() const;
///
/// \return the intrinsic parameter matrix as a 3x4 vnl matrix
/// (the last column only containing zeros)
///
vnl_matrix_fixed<mitk::ScalarType, 3, 4> GetVnlCameraMatrix3x4() const;
///
/// \return true if the intrinsics are set (some plausibility checks
/// may be done here)
///
bool IsValid() const;
void SetValid(bool valid);
cv::Mat GetCameraMatrix() const;
cv::Mat GetDistorsionCoeffs();
cv::Mat GetDistorsionCoeffs() const;
- void ToXML(TiXmlElement* elem) const override;
+ void ToXML(tinyxml2::XMLElement* elem) const override;
std::string ToString() const;
std::string GetString();
double GetFocalLengthX() const;
double GetFocalLengthY() const;
double GetPrincipalPointX() const;
double GetPrincipalPointY() const;
mitk::Point4D GetDistorsionCoeffsAsPoint4D() const;
mitk::Point3D GetFocalPoint() const;
mitk::Point3D GetPrincipalPoint() const;
vnl_vector_fixed<mitk::ScalarType, 2> GetFocalPointAsVnlVector() const;
vnl_vector_fixed<mitk::ScalarType, 2> GetPrincipalPointAsVnlVector() const;
///
/// set a new camera matrix utilizing a vnl matrix
///
void SetCameraMatrix( const vnl_matrix_fixed<mitk::ScalarType, 3, 3>&
_CameraMatrix );
void SetIntrinsics( const cv::Mat& _CameraMatrix
, const cv::Mat& _DistorsionCoeffs);
void SetFocalLength( double x, double y );
void SetPrincipalPoint( double x, double y );
void SetDistorsionCoeffs( double k1, double k2, double p1, double p2 );
void SetIntrinsics( const mitk::Point3D& focalPoint,
const mitk::Point3D& principalPoint,
const mitk::Point4D& distortionCoefficients);
- void FromXML(TiXmlElement* elem) override;
- void FromGMLCalibrationXML(TiXmlElement* elem);
+ void FromXML(const tinyxml2::XMLElement* elem) override;
+ void FromGMLCalibrationXML(const tinyxml2::XMLElement* elem);
std::string ToOctaveString(const std::string& varName="CameraIntrinsics");
~CameraIntrinsics() override;
protected:
CameraIntrinsics();
CameraIntrinsics(const CameraIntrinsics& other);
cv::Mat m_CameraMatrix;
cv::Mat m_DistorsionCoeffs;
bool m_Valid;
itk::FastMutexLock::Pointer m_Mutex;
private:
itk::LightObject::Pointer InternalClone() const override;
};
} // namespace mitk
MITKCAMERACALIBRATION_EXPORT std::ostream& operator<<
(std::ostream& os, mitk::CameraIntrinsics::Pointer p);
#endif // mitkCameraIntrinsics_h
diff --git a/Modules/CameraCalibration/mitkEndoDebugFromXmlFile.cpp b/Modules/CameraCalibration/mitkEndoDebugFromXmlFile.cpp
index a88a588b80..e9b827e034 100644
--- a/Modules/CameraCalibration/mitkEndoDebugFromXmlFile.cpp
+++ b/Modules/CameraCalibration/mitkEndoDebugFromXmlFile.cpp
@@ -1,159 +1,169 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkEndoDebugFromXmlFile.h"
#include <itksys/SystemTools.hxx>
-#include <tinyxml.h>
+#include <tinyxml2.h>
#include <set>
using namespace std;
namespace mitk
{
struct EndoDebugFromXmlFileData
{
const std::string* m_FileName;
// private
EndoDebug* m_EndoDebug;
long int m_FileModifiedTime;
};
EndoDebugFromXmlFile::EndoDebugFromXmlFile(
const std::string* _FileName, EndoDebug* _EndoDebug )
: d( new EndoDebugFromXmlFileData )
{
d->m_FileName = _FileName;
d->m_EndoDebug = _EndoDebug;
d->m_FileModifiedTime = 0;
}
EndoDebugFromXmlFile::~EndoDebugFromXmlFile()
{
delete d;
}
void StringExplode(string str, string separator, set<string>* results){
std::size_t found;
found = str.find_first_of(separator);
while(found != string::npos){
if(found != 0){
results->insert(str.substr(0,found));
}
str = str.substr(found+1);
found = str.find_first_of(separator);
}
if(!str.empty()){
results->insert(str);
}
}
#ifdef _MSC_VER
# pragma warning(push)
# pragma warning(disable:4390)
#endif
void EndoDebugFromXmlFile::Update()
{
endodebug( __FUNCTION__ )
std::string _FileName = *d->m_FileName;
if( !itksys::SystemTools::FileExists( _FileName.c_str() ) )
{
endodebug(_FileName << " does not exist");
return;
}
long int _FileModifiedTime
= itksys::SystemTools::ModifiedTime( _FileName.c_str() );
// file has changed: we know an older version...
if( d->m_FileModifiedTime >= _FileModifiedTime )
{
endodebug("File not changed. No Update necessary.");
return;
}
// reread
- endodebugvar( _FileName )
- TiXmlDocument doc( _FileName );
- doc.LoadFile();
- TiXmlHandle docHandle( &doc );
- TiXmlElement* elem = docHandle.FirstChildElement().FirstChildElement( "EndoDebug" ).ToElement();
+ endodebugvar(_FileName)
+ tinyxml2::XMLDocument doc;
+ doc.LoadFile(_FileName.c_str());
+ tinyxml2::XMLHandle docHandle(&doc);
+ auto* elem = docHandle.FirstChildElement().FirstChildElement( "EndoDebug" ).ToElement();
if(elem == nullptr)
{
endodebug("EndoDebug element not found");
return;
}
int _DebugEnabled = d->m_EndoDebug->GetDebugEnabled();
- if( elem->QueryIntAttribute("DebugEnabled",&_DebugEnabled) != TIXML_SUCCESS )
+ if( elem->QueryIntAttribute("DebugEnabled",&_DebugEnabled) != tinyxml2::XML_SUCCESS )
{
endodebug("DebugEnabled attribute not found");
}
int _ShowImagesInDebug = d->m_EndoDebug->GetShowImagesInDebug();
- if( elem->QueryIntAttribute("ShowImagesInDebug",&_ShowImagesInDebug) != TIXML_SUCCESS )
+ if( elem->QueryIntAttribute("ShowImagesInDebug",&_ShowImagesInDebug) != tinyxml2::XML_SUCCESS)
{
endodebug("ShowImagesInDebug attribute not found");
}
int _ShowImagesTimeOut = static_cast<int>(d->m_EndoDebug->GetShowImagesTimeOut());
- if( elem->QueryIntAttribute("ShowImagesTimeOut",&_ShowImagesTimeOut) != TIXML_SUCCESS )
+ if( elem->QueryIntAttribute("ShowImagesTimeOut",&_ShowImagesTimeOut) != tinyxml2::XML_SUCCESS)
{
endodebug("ShowImagesTimeOut attribute not found");
}
- std::string _DebugImagesOutputDirectory = d->m_EndoDebug->GetDebugImagesOutputDirectory();
- if( elem->QueryStringAttribute("DebugImagesOutputDirectory",&_DebugImagesOutputDirectory) != TIXML_SUCCESS )
+ std::string _DebugImagesOutputDirectory;
+ const char* _DebugImagesOutputDirectoryC = elem->Attribute("DebugImagesOutputDirectory");
+ if(nullptr == _DebugImagesOutputDirectoryC)
{
+ _DebugImagesOutputDirectory = d->m_EndoDebug->GetDebugImagesOutputDirectory();
endodebug("DebugImagesOutputDirectory attribute not found");
}
+ else
+ {
+ _DebugImagesOutputDirectory = _DebugImagesOutputDirectoryC;
+ }
std::set<std::string> _FilesToDebug;
std::string _FilesToDebugString;
- if( elem->QueryStringAttribute("FilesToDebug",&_FilesToDebugString) != TIXML_SUCCESS )
+ const char* _FilesToDebugStringC = elem->Attribute("FilesToDebug");
+ if(nullptr == _FilesToDebugStringC)
{
endodebug("FilesToDebug attribute not found");
}
else
{
- StringExplode( _FilesToDebugString, ";", &_FilesToDebug );
+ _FilesToDebugString = _FilesToDebugStringC;
+ StringExplode( _FilesToDebugString, ";", &_FilesToDebug );
}
std::set<std::string> _SymbolsToDebug;
std::string _SymbolsToDebugString;
- if( elem->QueryStringAttribute("SymbolsToDebug",&_SymbolsToDebugString) != TIXML_SUCCESS )
+ const char* _SymbolsToDebugStringC = elem->Attribute("SymbolsToDebug");
+ if( nullptr == _SymbolsToDebugStringC )
{
endodebug("SymbolsToDebug attribute not found");
}
else
{
- StringExplode( _SymbolsToDebugString, ";", &_SymbolsToDebug );
+ _SymbolsToDebugString = _SymbolsToDebugStringC;
+ StringExplode( _SymbolsToDebugString, ";", &_SymbolsToDebug );
}
// save
mitk::EndoDebug::GetInstance().SetDebugEnabled( _DebugEnabled == 1? true: false );
mitk::EndoDebug::GetInstance().SetShowImagesInDebug( _ShowImagesInDebug == 1? true: false );
mitk::EndoDebug::GetInstance().SetShowImagesTimeOut( _ShowImagesTimeOut );
mitk::EndoDebug::GetInstance().SetDebugImagesOutputDirectory( _DebugImagesOutputDirectory );
mitk::EndoDebug::GetInstance().SetFilesToDebug(_FilesToDebug);
mitk::EndoDebug::GetInstance().SetSymbolsToDebug(_SymbolsToDebug);
// save that modified time
d->m_FileModifiedTime = _FileModifiedTime;
}
#ifdef _MSC_VER
# pragma warning(pop)
#endif
}
diff --git a/Modules/CameraCalibration/mitkEndoDebugToXmlFile.cpp b/Modules/CameraCalibration/mitkEndoDebugToXmlFile.cpp
index 8e0a52463c..82a0e184c1 100644
--- a/Modules/CameraCalibration/mitkEndoDebugToXmlFile.cpp
+++ b/Modules/CameraCalibration/mitkEndoDebugToXmlFile.cpp
@@ -1,121 +1,122 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkEndoDebugToXmlFile.h"
-#include <tinyxml.h>
+#include <tinyxml2.h>
namespace mitk
{
struct EndoDebugToXmlFileData
{
EndoDebug* m_EndoDebug;
const std::string* m_FileName;
};
EndoDebugToXmlFile::EndoDebugToXmlFile(EndoDebug *_EndoDebug,
const std::string* _FileName)
: d( new EndoDebugToXmlFileData )
{
d->m_EndoDebug = _EndoDebug;
d->m_FileName = _FileName;
}
EndoDebugToXmlFile::~EndoDebugToXmlFile()
{
delete d;
}
void EndoDebugToXmlFile::Update()
{
std::string _FileName = *d->m_FileName;
- TiXmlDocument doc( _FileName.c_str() );
- TiXmlElement* root = nullptr;
- TiXmlElement* elem = nullptr;
+ tinyxml2::XMLDocument doc;
+ tinyxml2::XMLElement* root = nullptr;
+ tinyxml2::XMLElement* elem = nullptr;
// check if element is already available
- if(doc.LoadFile())
+ if(tinyxml2::XML_SUCCESS == doc.LoadFile(_FileName.c_str()))
{
root = doc.FirstChildElement("data");
- if(root)
+ if(nullptr != root)
{
elem = root->FirstChildElement( "EndoDebug" );
- if(elem)
- root->RemoveChild(elem);
- elem = nullptr;
+ if (nullptr != elem)
+ {
+ root->DeleteChild(elem);
+ elem = nullptr;
+ }
}
}
else
{
// document did not exist, create new one with declration
- auto decl = new TiXmlDeclaration( "1.0", "", "" );
- doc.LinkEndChild( decl );
+ doc.InsertEndChild( doc.NewDeclaration() );
// create root
- root = new TiXmlElement( "data" );
- doc.LinkEndChild( root );
+ root = doc.NewElement( "data" );
+ doc.InsertEndChild( root );
}
// create elem if not existent
- elem = new TiXmlElement( "EndoDebug" );
+ elem = doc.NewElement( "EndoDebug" );
elem->SetAttribute( "DebugEnabled",
(d->m_EndoDebug->GetDebugEnabled()? 1:0) );
elem->SetAttribute( "ShowImagesInDebug",
(d->m_EndoDebug->GetShowImagesInDebug()? 1:0) );
elem->SetAttribute( "ShowImagesTimeOut",
(static_cast<int>(d->m_EndoDebug->GetShowImagesTimeOut())) );
elem->SetAttribute( "DebugImagesOutputDirectory",
- d->m_EndoDebug->GetDebugImagesOutputDirectory() );
+ d->m_EndoDebug->GetDebugImagesOutputDirectory().c_str() );
std::set<std::string> _FilesToDebug = d->m_EndoDebug->GetFilesToDebug();
std::string _FilesToDebugString;
auto it = _FilesToDebug.begin();
while( it != _FilesToDebug.end() )
{
if( it != _FilesToDebug.begin() )
_FilesToDebugString.append( ";" );
_FilesToDebugString.append( *it );
++it;
}
- elem->SetAttribute( "FilesToDebug", _FilesToDebugString );
+ elem->SetAttribute( "FilesToDebug", _FilesToDebugString.c_str() );
std::set<std::string> _SymbolsToDebug = d->m_EndoDebug->GetSymbolsToDebug();
std::string _SymbolsToDebugString;
it = _SymbolsToDebug.begin();
while( it != _SymbolsToDebug.end() )
{
if( it != _SymbolsToDebug.begin() )
_SymbolsToDebugString.append( ";" );
_SymbolsToDebugString.append( *it );
++it;
}
- elem->SetAttribute( "SymbolsToDebug", _SymbolsToDebugString );
+ elem->SetAttribute( "SymbolsToDebug", _SymbolsToDebugString.c_str() );
endodebug("adding the EndoDebug as child element of the data node")
- root->LinkEndChild(elem);
+ root->InsertEndChild(elem);
endodebug("saving file " << _FileName)
- if( !doc.SaveFile( _FileName ) )
+ if( tinyxml2::XML_SUCCESS != doc.SaveFile( _FileName.c_str() ) )
{
endodebug("File " << _FileName << " could not be written. Please check permissions.");
}
}
void EndoDebugToXmlFile::SetEndoDebug(EndoDebug *_EndoDebug)
{
d->m_EndoDebug = _EndoDebug;
}
void EndoDebugToXmlFile::SetFileName(const std::string *_FileName)
{
d->m_FileName = _FileName;
}
}
diff --git a/Modules/CameraCalibration/mitkTransform.cpp b/Modules/CameraCalibration/mitkTransform.cpp
index d77d2d87fe..0a65753afb 100644
--- a/Modules/CameraCalibration/mitkTransform.cpp
+++ b/Modules/CameraCalibration/mitkTransform.cpp
@@ -1,745 +1,750 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkTransform.h"
#include <fstream>
#include <vnl/vnl_inverse.h>
#include <mitkVnlVectorFixedCaster.h>
#include <mitkVnlVectorFromCvMat.h>
#include <mitkVnlMatrixFromCvMat.h>
#include <mitkCvMatFromVnlVector.h>
+#include <tinyxml2.h>
+
namespace mitk
{
// DO NOT CHANGE THE VALUES OF THESE CONSTANTS!!
const std::string Transform::UNKNOWN_TYPE = "Unknown type";
const std::string Transform::ENDOSCOPE_SCOPE_TOOL = "Endoscope scope tool";
const std::string Transform::ENDOSCOPE_CAM_TOOL = "Endoscope camera tool";
const std::string Transform::CHESSBOARD_TOOL = "Chessboard tool";
const std::string Transform::POINTER_TOOL = "Pointer tool";
const std::string Transform::POINTER_TO_CHESSBOARD_ORIGIN = "Pointer to chessboard origin";
const std::string Transform::POINTER_TO_CHESSBOARD_X_SUPPORT_POINT = "Pointer to chessboard X support origin";
const std::string Transform::POINTER_TO_CHESSBOARD_Y_SUPPORT_POINT = "Pointer to chessboard Y support origin";
const std::string Transform::BOARD_TO_BOARD_TOOL = "Board to board tool";
const std::string Transform::REFERENCE_CAMERA_TRANSFORM = "Reference camera transform";
const std::string Transform::REFERENCE_SCOPE_TRANSFORM = "Reference scope transform";
const std::string Transform::EYE_TO_HAND_TRANSFORM = "Eye to hand transform";
const std::string Transform::CAMERA_EXTRINSICS = "Camera extrinsics";
Transform::Transform()
: m_NavData(mitk::NavigationData::New()), m_Type( UNKNOWN_TYPE )
{
vnl_matrix_fixed<mitk::ScalarType, 3, 3> rot;
rot.set_identity();
this->SetRotation( rot );
}
Transform::Transform(const mitk::NavigationData* nd)
: m_NavData(mitk::NavigationData::New()), m_Type( UNKNOWN_TYPE )
{
m_NavData->Graft(nd);
}
Transform::Transform(const std::string& s)
: m_NavData(mitk::NavigationData::New()), m_Type( s )
{
vnl_matrix_fixed<mitk::ScalarType, 3, 3> rot;
rot.set_identity();
this->SetRotation( rot );
}
void Transform::Copy(const mitk::NavigationData* nd)
{
(const_cast<mitk::NavigationData*>(m_NavData.GetPointer()))->Graft(nd);
}
void Transform::Concatenate( mitk::Transform* transform )
{
vnl_matrix_fixed<mitk::ScalarType, 4, 4> mat = transform->GetMatrix();
mat = mat * this->GetMatrix(); //
this->SetMatrix( mat );
}
void Transform::Concatenate( const vnl_matrix_fixed<mitk::ScalarType, 4, 4>&
transform )
{
Transform::Pointer t = Transform::New();
t->SetMatrix( transform );
this->Concatenate( t );
}
void Transform::Concatenate( const vtkMatrix4x4* transform )
{
Transform::Pointer t = Transform::New();
t->SetMatrix( transform );
this->Concatenate( t );
}
void Transform::Reset()
{
mitk::NavigationData::Pointer nd
= NavigationData::New();
this->Copy( nd );
}
void Transform::SetOrientation(
const vnl_quaternion<mitk::ScalarType>& orientation)
{
m_NavData->SetOrientation(orientation);
this->Modified();
}
void Transform::SetTranslation( const vnl_vector_fixed<mitk::ScalarType, 3>&
transl)
{
mitk::Point3D p;
for(unsigned int i=0; i<3; ++i)
p[i] = transl[i];
m_NavData->SetPosition(p);
this->Modified();
}
void Transform::SetTranslation( float* array )
{
vnl_vector_fixed<mitk::ScalarType, 3> vec;
for(unsigned int i=0; i<vec.size(); i++)
vec(i) = array[i];
this->SetTranslation( vec );
}
void Transform::SetRotation( float* array )
{
vnl_matrix_fixed<mitk::ScalarType, 3, 3> mat;
unsigned int row = 0;
unsigned int col = 0;
for(unsigned int i=0; i<mat.rows()*mat.cols(); i++)
{
if( i > 0 && i % 3 == 0 )
{
++row;
col = 0;
}
mat(row,col) = array[i];
++col;
}
this->SetRotation( mat );
}
void Transform::SetOrientation( const vnl_quaternion<float>& orientation)
{
vnl_vector_fixed<mitk::ScalarType, 4> qvec;
VnlVectorFixedCaster<float, mitk::ScalarType, 4> caster( &orientation, &qvec );
caster.Update();
mitk::Quaternion p( qvec );
this->SetOrientation( p );
}
vnl_vector_fixed<double, 3> Transform::GetVnlDoubleTranslation() const
{
vnl_vector_fixed<mitk::ScalarType, 3> vecFloat = this->GetVnlTranslation();
vnl_vector_fixed<double, 3> vecDouble;
VnlVectorFixedCaster<mitk::ScalarType, double, 3> caster( &vecFloat, &vecDouble );
caster.Update();
return vecDouble;
}
void Transform::SetTranslation( const vnl_vector<double>& transl)
{
vnl_vector_fixed<double, 3> dTransl(transl);
vnl_vector_fixed<mitk::ScalarType, 3> fTransl;
VnlVectorFixedCaster<double, mitk::ScalarType, 3> caster( &dTransl, &fTransl );
caster.Update();
this->SetTranslation( fTransl );
}
vnl_quaternion<double> Transform::GetVnlDoubleQuaternion() const
{
mitk::Quaternion fOrientation = this->GetOrientation();
vnl_quaternion<double> dOrientation;
VnlVectorFixedCaster<mitk::ScalarType, double, 4> caster( &fOrientation, &dOrientation );
caster.Update();
return dOrientation;
}
void Transform::FromCSVFile(const std::string& file)
{
std::ifstream csvFile (file.c_str());
endoAssert ( csvFile.fail() == false );
mitk::Transform::Pointer transform = mitk::Transform::New();
vnl_matrix_fixed<mitk::ScalarType, 4, 4> mat;
std::string line;
mitk::ScalarType d = 0.0f;
int row=0,column = 0;
while (std::getline (csvFile, line))
{
std::istringstream linestream(line);
std::string item;
column = 0;
while (std::getline (linestream, item, ','))
{
std::istringstream number;
number.str(item);
number >> d;
mat(row, column) = d;
++column;
}
++row;
}
endoAssert( row == 4 && column == 4 );
transform->SetMatrix( mat );
this->SetNavigationData( transform->GetNavigationData() );
// modified is called in SetNavigationData
}
std::string Transform::ToCSVString() const
{
std::ostringstream s; s.precision(12);
vnl_matrix_fixed<mitk::ScalarType, 4, 4> mat
= this->GetMatrix();
for( unsigned int j=0; j<mat.rows(); ++j )
{
for( unsigned int k=0; k<mat.cols(); ++k )
{
s << mat(j,k);
if(k+1<mat.cols())
s << ",";
}
if(j+1<mat.rows())
s << std::endl;
}
return s.str();
}
std::string Transform::ToMatlabString(const std::string& varname
, bool printLastRow) const
{
std::ostringstream s; s.precision(12);
vnl_matrix_fixed<mitk::ScalarType, 4, 4> mat
= this->GetMatrix();
s << varname << " = [";
for( unsigned int j=0; j<mat.rows(); ++j )
{
if( !printLastRow && j+1 == mat.rows() )
break;
for( unsigned int k=0; k<mat.cols(); ++k )
{
s << mat(j,k) << " ";
}
s << ";";
}
s << "];" << std::endl;
return s.str();
}
void Transform::Copy( const mitk::Transform* transform )
{
m_NavData->Graft(transform->GetNavigationData());
m_Type = transform->GetType();
}
mitk::Transform::Pointer Transform::Clone() const
{
Transform::Pointer copy = Transform::New();
copy->Copy( this );
return copy;
}
void Transform::SetMatrix( const vtkMatrix4x4* mat)
{
vnl_matrix_fixed<mitk::ScalarType, 4, 4> vnlMat;
for(unsigned int i=0; i<4; ++i)
for(unsigned int j=0; j<4; ++j)
vnlMat(i,j) = mat->GetElement(i, j);
this->SetMatrix( vnlMat );
}
void Transform::ToCSVFile(const std::string& file) const
{
std::ofstream csvFile;
csvFile.open(file.c_str());
endoAssert ( csvFile.fail() == false );
csvFile << this->ToCSVString();
csvFile.close();
}
void Transform::ToMatlabFile(const std::string& file
, const std::string& varname) const
{
std::ofstream csvFile;
csvFile.open(file.c_str());
endoAssert ( csvFile.fail() == false );
csvFile << this->ToMatlabString(varname);
csvFile.close();
}
void Transform::SetNavigationData( const mitk::NavigationData* naviData )
{
endoAssert( naviData != nullptr );
m_NavData->Graft( naviData );
this->Modified();
}
void Transform::SetRotation( vnl_matrix_fixed<mitk::ScalarType, 3, 3>& mat)
{
this->m_NavData->SetOrientation( mitk::Quaternion(mat) );
this->Modified();
}
void Transform::SetRotation( vnl_matrix<mitk::ScalarType>& mat)
{
vnl_matrix_fixed<mitk::ScalarType, 3, 3> tmp(mat);
this->SetRotation( tmp );
}
void Transform::SetPosition( const mitk::Point3D& transl)
{
this->SetTranslation( transl.GetVnlVector() );
}
void Transform::SetTranslation( double array[3] )
{
mitk::Point3D p;
for(unsigned int i = 0; i < 3; ++i)
p.SetElement(i, array[i]);
this->SetTranslation( p.GetVnlVector() );
}
void Transform::SetRotation( double array[3][3] )
{
vnl_matrix_fixed<mitk::ScalarType, 3, 3> mat;
for(unsigned int i = 0; i < 3; ++i)
for(unsigned int j = 0; j < 3; ++j)
mat(i, j) = array[i][j];
this->SetRotation( mat );
}
void Transform::Invert()
{
vnl_matrix_fixed<mitk::ScalarType, 4, 4> tmp(this->GetMatrix());
this->SetMatrix( vnl_inverse( tmp ) );
}
void Transform::SetMatrix(
const vnl_matrix_fixed<mitk::ScalarType, 4, 4>& mat)
{
// set translation first
vnl_vector<mitk::ScalarType> transl = mat.get_column(3);
mitk::Point3D p;
for(unsigned int i=0; i<3; ++i)
p[i] = transl[i];
m_NavData->SetPosition(p);
// set rotation
vnl_matrix_fixed<mitk::ScalarType, 3, 3> rotMatFixed(
mat.extract(3,3));
this->SetRotation(rotMatFixed);
}
bool Transform::IsValid() const
{
return m_NavData->IsDataValid();
}
void Transform::SetTranslation( const cv::Mat& transl)
{
vnl_vector<mitk::ScalarType> vec(3);
VnlVectorFromCvMat<mitk::ScalarType> _VnlVectorFromCvMat( &transl, &vec );
_VnlVectorFromCvMat.Update();
this->SetTranslation( vnl_vector_fixed<mitk::ScalarType, 3>( vec ) );
}
void Transform::SetRotation( const cv::Mat& mat )
{
vnl_matrix<mitk::ScalarType> vnlMat(3, 3);
VnlMatrixFromCvMat<mitk::ScalarType> _VnlMatrixFromCvMat( &mat, &vnlMat );
_VnlMatrixFromCvMat.Update();
vnl_matrix_fixed<mitk::ScalarType, 3, 3> vnlMatFixed(vnlMat);
this->SetRotation(vnlMatFixed);
}
void Transform::SetRotationVector( const cv::Mat& rotVec )
{
cv::Mat rotMat;
cv::Rodrigues( rotVec, rotMat );
vnl_matrix<mitk::ScalarType> vnlMat(3, 3);
VnlMatrixFromCvMat<mitk::ScalarType> _VnlMatrixFromCvMat( &rotMat, &vnlMat );
_VnlMatrixFromCvMat.Update();
vnl_matrix_fixed<mitk::ScalarType, 3, 3> vnlMatFixed(vnlMat);
this->SetRotation( vnlMatFixed );
}
//# getter
mitk::NavigationData::Pointer Transform::GetNavigationData() const
{
return m_NavData;
}
mitk::Point3D Transform::GetTranslation() const
{
return m_NavData->GetPosition();
}
mitk::Point3D Transform::GetPosition() const
{
return m_NavData->GetPosition();
}
mitk::Quaternion Transform::GetOrientation() const
{
return m_NavData->GetOrientation();
}
void Transform::GetMatrix(vtkMatrix4x4* matrix) const
{
vnl_matrix_fixed<mitk::ScalarType, 4, 4> vnlMat = this->GetMatrix();
for(unsigned int i=0; i<vnlMat.rows(); ++i)
for(unsigned int j=0; j<vnlMat.cols(); ++j)
matrix->SetElement(i,j, vnlMat(i,j));
}
void Transform::GetVtkOpenGlMatrix(vtkMatrix4x4* matrix) const
{
vnl_matrix<mitk::ScalarType> vnlRotation
= this->GetVnlRotationMatrix().as_matrix();
// normalize rows of rotation matrix
vnlRotation.normalize_rows();
vnl_matrix<mitk::ScalarType> vnlInverseRotation(3,3);
// invert rotation
vnlInverseRotation = vnl_matrix_inverse<mitk::ScalarType>(vnlRotation);
vnl_vector<mitk::ScalarType> vnlTranslation
= this->GetPosition().GetVnlVector();
// rotate translation vector by inverse rotation P = P'
vnlTranslation = vnlInverseRotation * vnlTranslation;
vnlTranslation *= -1; // save -P'
// set position
mitk::Transform::Pointer tmp = mitk::Transform::New();
tmp->SetTranslation( vnlTranslation );
tmp->SetRotation( vnlRotation );
tmp->GetMatrix(matrix);
}
mitk::Point3D Transform::TransformPoint(mitk::Point3D point) const
{
itk::Matrix<mitk::ScalarType,3,3> R(GetVnlRotationMatrix());
itk::Point<mitk::ScalarType,3> pointR = (R * point);
mitk::Point3D retPoint = pointR;
retPoint[0] = pointR[0] + GetPosition()[0];
retPoint[1] = pointR[1] + GetPosition()[1];
retPoint[2] = pointR[2] + GetPosition()[2];
return retPoint;
}
//# cv getter
cv::Mat Transform::GetCvTranslation() const
{
cv::Mat mat;
vnl_vector<mitk::ScalarType> vec = this->GetVnlTranslation().as_vector();
endodebugvar( vec )
CvMatFromVnlVector<mitk::ScalarType> _CvMatFromVnlVector(&vec, &mat);
_CvMatFromVnlVector.Update();
return mat;
}
cv::Mat Transform::GetCvRotationMatrix() const
{
cv::Mat mat;
vnl_matrix<mitk::ScalarType> vec = this->GetVnlRotationMatrix().as_matrix();
endodebugvar( vec )
CvMatFromVnlMatrix<mitk::ScalarType> _CvMatFromVnlMatrix(&vec, &mat);
_CvMatFromVnlMatrix.Update();
return mat;
}
cv::Mat Transform::GetCvMatrix() const
{
cv::Mat mat;
vnl_matrix<mitk::ScalarType> vec = this->GetMatrix().as_matrix();
CvMatFromVnlMatrix<mitk::ScalarType> _CvMatFromVnlMatrix(&vec, &mat);
_CvMatFromVnlMatrix.Update();
return mat;
}
cv::Mat Transform::GetCvRotationVector() const
{
cv::Mat rotVec(3,1,cv::DataType<mitk::ScalarType>::type);
cv::Rodrigues( this->GetCvRotationMatrix(), rotVec );
return rotVec;
}
//# vnl getter
vnl_vector_fixed<mitk::ScalarType, 3> Transform::GetVnlTranslation() const
{
vnl_vector_fixed<mitk::ScalarType, 3> vec(m_NavData->GetPosition()
.GetVnlVector());
return vec;
}
vnl_matrix_fixed<mitk::ScalarType, 3, 3> Transform::GetVnlRotationMatrix() const
{
return m_NavData->GetOrientation().rotation_matrix_transpose();
}
vnl_matrix_fixed<double, 4, 4> Transform::GetVnlDoubleMatrix() const
{
vnl_matrix_fixed<mitk::ScalarType, 4, 4> mat = this->GetMatrix();
vnl_matrix_fixed<double, 4, 4> doubleMat;
for(unsigned int i=0; i<mat.rows(); ++i)
for(unsigned int j=0; j<mat.cols(); ++j)
doubleMat(i,j) = static_cast<double>( mat(i,j) );
return doubleMat;
}
vnl_matrix_fixed<mitk::ScalarType, 4, 4> Transform::GetMatrix()
const
{
vnl_vector_fixed<mitk::ScalarType, 3> transl = this->GetVnlTranslation();
vnl_matrix_fixed<mitk::ScalarType, 3, 3> rot = this->GetVnlRotationMatrix();
vnl_matrix_fixed<mitk::ScalarType, 4, 4> homMat;
homMat.set_identity();
//std::cout << homMat << std::endl;
for(unsigned int i=0; i<rot.rows(); ++i)
for(unsigned int j=0; j<rot.cols(); ++j)
homMat(i,j) = rot(i,j);
for(unsigned int i=0; i<transl.size(); ++i)
homMat(i,3) = transl[i];
return homMat;
}
void Transform::TransposeRotation()
{
vnl_matrix_fixed<mitk::ScalarType, 3, 3> rotMat = this->GetVnlRotationMatrix().transpose();
this->SetRotation( rotMat );
}
void Transform::SetValid( bool valid )
{
if( m_NavData->IsDataValid() == valid )
return;
m_NavData->SetDataValid( valid );
this->Modified();
}
std::string mitk::Transform::ToString() const
{
std::ostringstream s; s.precision(12);
mitk::NavigationData::PositionType position;
position.Fill(0.0);
position = m_NavData->GetPosition();
mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0);
orientation = m_NavData->GetOrientation();
s << "Translation: [" << position[0] << ", " << position[1] << ", "
<< position[2] << "]";
s << ", orientation: [" << orientation[0] << ", " << orientation[1] << ", "
<< orientation[2] << ", " << orientation[3] << "]";
s << ", valid: [" << (this->IsValid()? "true": "false") << "]";
return s.str();
}
- void mitk::Transform::ToXML(TiXmlElement* elem) const
+ void mitk::Transform::ToXML(tinyxml2::XMLElement* elem) const
{
- std::string value = elem->ValueStr();
+ std::string value = elem->Value() != nullptr ? elem->Value() : "";
if(value.empty())
elem->SetValue(this->GetNameOfClass());
mitk::NavigationData::PositionType position;
position.Fill(0.0);
position = m_NavData->GetPosition();
mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0);
orientation = m_NavData->GetOrientation();
mitk::NavigationData::CovarianceMatrixType matrix;
matrix.SetIdentity();
matrix = m_NavData->GetCovErrorMatrix();
bool hasPosition = true;
hasPosition = m_NavData->GetHasPosition();
bool hasOrientation = true;
hasOrientation = m_NavData->GetHasOrientation();
bool dataValid = false;
dataValid = m_NavData->IsDataValid();
mitk::NavigationData::TimeStampType timestamp=0.0;
- elem->SetAttribute("Type", m_Type);
- elem->SetDoubleAttribute("Time", timestamp);
- elem->SetDoubleAttribute("X", position[0]);
- elem->SetDoubleAttribute("Y", position[1]);
- elem->SetDoubleAttribute("Z", position[2]);
-
- elem->SetDoubleAttribute("QX", orientation[0]);
- elem->SetDoubleAttribute("QY", orientation[1]);
- elem->SetDoubleAttribute("QZ", orientation[2]);
- elem->SetDoubleAttribute("QR", orientation[3]);
-
- elem->SetDoubleAttribute("C00", matrix[0][0]);
- elem->SetDoubleAttribute("C01", matrix[0][1]);
- elem->SetDoubleAttribute("C02", matrix[0][2]);
- elem->SetDoubleAttribute("C03", matrix[0][3]);
- elem->SetDoubleAttribute("C04", matrix[0][4]);
- elem->SetDoubleAttribute("C05", matrix[0][5]);
- elem->SetDoubleAttribute("C10", matrix[1][0]);
- elem->SetDoubleAttribute("C11", matrix[1][1]);
- elem->SetDoubleAttribute("C12", matrix[1][2]);
- elem->SetDoubleAttribute("C13", matrix[1][3]);
- elem->SetDoubleAttribute("C14", matrix[1][4]);
- elem->SetDoubleAttribute("C15", matrix[1][5]);
+ elem->SetAttribute("Type", m_Type.c_str());
+ elem->SetAttribute("Time", timestamp);
+ elem->SetAttribute("X", position[0]);
+ elem->SetAttribute("Y", position[1]);
+ elem->SetAttribute("Z", position[2]);
+
+ elem->SetAttribute("QX", orientation[0]);
+ elem->SetAttribute("QY", orientation[1]);
+ elem->SetAttribute("QZ", orientation[2]);
+ elem->SetAttribute("QR", orientation[3]);
+
+ elem->SetAttribute("C00", matrix[0][0]);
+ elem->SetAttribute("C01", matrix[0][1]);
+ elem->SetAttribute("C02", matrix[0][2]);
+ elem->SetAttribute("C03", matrix[0][3]);
+ elem->SetAttribute("C04", matrix[0][4]);
+ elem->SetAttribute("C05", matrix[0][5]);
+ elem->SetAttribute("C10", matrix[1][0]);
+ elem->SetAttribute("C11", matrix[1][1]);
+ elem->SetAttribute("C12", matrix[1][2]);
+ elem->SetAttribute("C13", matrix[1][3]);
+ elem->SetAttribute("C14", matrix[1][4]);
+ elem->SetAttribute("C15", matrix[1][5]);
if (dataValid)
elem->SetAttribute("Valid",1);
else
elem->SetAttribute("Valid",0);
if (hasOrientation)
elem->SetAttribute("hO",1);
else
elem->SetAttribute("hO",0);
if (hasPosition)
elem->SetAttribute("hP",1);
else
elem->SetAttribute("hP",0);
}
- void mitk::Transform::FromXML(TiXmlElement* elem)
+ void mitk::Transform::FromXML(const tinyxml2::XMLElement* elem)
{
assert(elem);
mitk::NavigationData::Pointer nd = mitk::NavigationData::New();
mitk::NavigationData::PositionType position;
mitk::NavigationData::OrientationType orientation(0.0,0.0,0.0,0.0);
mitk::NavigationData::TimeStampType timestamp = -1;
mitk::NavigationData::CovarianceMatrixType matrix;
bool hasPosition = true;
bool hasOrientation = true;
bool dataValid = false;
position.Fill(0.0);
matrix.SetIdentity();
- std::string type = Transform::UNKNOWN_TYPE;
- elem->QueryStringAttribute("Type", &type);
+ const char* typeC = elem->Attribute("Type");
+ std::string type = nullptr == typeC
+ ? Transform::UNKNOWN_TYPE
+ : typeC;
+
elem->QueryDoubleAttribute("Time",×tamp);
// position and orientation is mandatory!
- if(elem->QueryDoubleAttribute("X", &position[0]) != TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("X", &position[0]) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("No X position found in xml");
- if(elem->QueryDoubleAttribute("Y", &position[1]) != TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("Y", &position[1]) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("No Y position found in xml");
- if(elem->QueryDoubleAttribute("Z", &position[2]) != TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("Z", &position[2]) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("No Z position found in xml");
- if(elem->QueryDoubleAttribute("QX", &orientation[0]) != TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("QX", &orientation[0]) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("No QX orientation found in xml");
- if(elem->QueryDoubleAttribute("QY", &orientation[1]) != TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("QY", &orientation[1]) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("No QY orientation found in xml");
- if(elem->QueryDoubleAttribute("QZ", &orientation[2]) != TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("QZ", &orientation[2]) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("No QZ orientation found in xml");
- if(elem->QueryDoubleAttribute("QR", &orientation[3]) != TIXML_SUCCESS)
+ if(elem->QueryDoubleAttribute("QR", &orientation[3]) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("No QR orientation found in xml");
elem->QueryDoubleAttribute("C00", &matrix[0][0]);
elem->QueryDoubleAttribute("C01", &matrix[0][1]);
elem->QueryDoubleAttribute("C02", &matrix[0][2]);
elem->QueryDoubleAttribute("C03", &matrix[0][3]);
elem->QueryDoubleAttribute("C04", &matrix[0][4]);
elem->QueryDoubleAttribute("C05", &matrix[0][5]);
elem->QueryDoubleAttribute("C10", &matrix[1][0]);
elem->QueryDoubleAttribute("C11", &matrix[1][1]);
elem->QueryDoubleAttribute("C12", &matrix[1][2]);
elem->QueryDoubleAttribute("C13", &matrix[1][3]);
elem->QueryDoubleAttribute("C14", &matrix[1][4]);
elem->QueryDoubleAttribute("C15", &matrix[1][5]);
int tmpval = 0;
elem->QueryIntAttribute("Valid", &tmpval);
if (tmpval == 0)
dataValid = false;
else
dataValid = true;
tmpval = 0;
elem->QueryIntAttribute("hO", &tmpval);
if (tmpval == 0)
hasOrientation = false;
else
hasOrientation = true;
tmpval = 0;
elem->QueryIntAttribute("hP", &tmpval);
if (tmpval == 0)
hasPosition = false;
else
hasPosition = true;
nd->SetIGTTimeStamp(timestamp);
nd->SetPosition(position);
nd->SetOrientation(orientation);
nd->SetCovErrorMatrix(matrix);
nd->SetDataValid(dataValid);
nd->SetHasOrientation(hasOrientation);
nd->SetHasPosition(hasPosition);
m_NavData = nd;
m_Type = type;
this->Modified();
}
} // namespace mitk
std::ostream& operator<< (std::ostream& os, mitk::Transform::Pointer p)
{
os << p->ToString();
return os;
}
diff --git a/Modules/CameraCalibration/mitkTransform.h b/Modules/CameraCalibration/mitkTransform.h
index 233abbc5b2..7aeabdd4b5 100644
--- a/Modules/CameraCalibration/mitkTransform.h
+++ b/Modules/CameraCalibration/mitkTransform.h
@@ -1,301 +1,300 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKTRANSFORM_H
#define MITKTRANSFORM_H
#include <itkObject.h>
#include <opencv2/calib3d.hpp>
#include <mitkCommon.h>
#include <mitkNumericTypes.h>
#include <mitkNavigationData.h>
-#include <tinyxml.h>
#include <sstream>
#include <vtkMatrix4x4.h>
#include <mitkXMLSerializable.h>
#include <MitkCameraCalibrationExports.h>
namespace mitk {
///
/// \brief class representing a transfrom in 3D
///
/// internally it stores a mitk navigation data. this is more
/// or less a wrapper for navigation data for easy casting
/// between opencv/vnl/mitk/xml representations of transform
/// data
///
class MITKCAMERACALIBRATION_EXPORT Transform: public itk::Object,
public XMLSerializable
{
public:
mitkClassMacroItkParent(Transform, itk::Object);
itkFactorylessNewMacro(Transform);
mitkNewMacro1Param(Transform, const mitk::NavigationData*);
mitkNewMacro1Param(Transform, const std::string&);
///
/// constants describing the type of transform
/// represented here
///
static const std::string UNKNOWN_TYPE;
static const std::string ENDOSCOPE_SCOPE_TOOL;
static const std::string ENDOSCOPE_CAM_TOOL;
static const std::string CHESSBOARD_TOOL;
static const std::string POINTER_TOOL;
static const std::string POINTER_TO_CHESSBOARD_ORIGIN;
static const std::string POINTER_TO_CHESSBOARD_X_SUPPORT_POINT;
static const std::string POINTER_TO_CHESSBOARD_Y_SUPPORT_POINT;
static const std::string BOARD_TO_BOARD_TOOL;
static const std::string REFERENCE_CAMERA_TRANSFORM;
static const std::string REFERENCE_SCOPE_TRANSFORM;
static const std::string EYE_TO_HAND_TRANSFORM;
static const std::string CAMERA_EXTRINSICS;
itkGetConstMacro(Type, std::string);
itkSetMacro(Type, std::string&);
///
/// Copies the content of transform to this
/// instance
///
void Copy( const mitk::Transform* transform );
///
/// Copies the content of transform to this
/// instance
///
void Copy( const mitk::NavigationData* transform );
///
/// Inverts the rotation of this transform
/// (Polaris navigation Data have inverted rotation
/// so you may want to call this function when using
/// polaris data)
///
void TransposeRotation();
///
/// get a copy of this transform
///
mitk::Transform::Pointer Clone() const;
///
/// concatenate this transform with the given one,
/// i.e. this transform is done first, then transform
/// ( if x is this transform, y is transform, then this will be y*x)
/// post multiply semantics!
/// \see vtkTransform
///
void Concatenate( mitk::Transform* transform );
///
/// same as above with vnl mat argument
///
void Concatenate( const vnl_matrix_fixed<mitk::ScalarType, 4, 4>& transform );
///
/// same as above with vtk mat argument
///
void Concatenate( const vtkMatrix4x4* transform );
///
/// invert this transform
///
void Invert();
///
/// resets the internal variables except type
///
void Reset();
///
/// read from xml
///
- void FromXML(TiXmlElement* elem) override;
+ void FromXML(const tinyxml2::XMLElement* elem) override;
///
/// read csv file
///
void FromCSVFile(const std::string& file);
///
/// grafts the data from naviData to this transform
///
void SetNavigationData( const mitk::NavigationData* naviData );
///
/// method to set orientation quat
///
void SetOrientation( const vnl_quaternion<mitk::ScalarType>& orientation);
///
/// method to set float valued orientation quat
///
void SetOrientation( const vnl_quaternion<float>& orientation);
///
/// method to set translation
///
void SetTranslation( const vnl_vector_fixed<mitk::ScalarType, 3>& transl);
///
/// method to set a vector of doubles as translation
///
void SetTranslation( const vnl_vector<double>& transl);
///
/// method to set a mitk::Point3D as position
///
void SetPosition( const mitk::Point3D& transl);
///
/// sets rotation with a rotation matrix
///
void SetRotation( vnl_matrix_fixed<mitk::ScalarType, 3, 3>& mat);
///
/// sets rotation with a non fixed rotation matrix
///
void SetRotation( vnl_matrix<mitk::ScalarType>& mat);
///
/// sets rotation and translation with a transformation matrix
///
void SetMatrix( const vnl_matrix_fixed<mitk::ScalarType, 4, 4>& mat);
///
/// sets rotation and translation with a vtk transformation matrix
///
void SetMatrix( const vtkMatrix4x4* mat);
///
/// sets translation from a POD vector
///
void SetTranslation( float* array );
///
/// sets translation from a POD vector. this must be a
/// 3x3=9 sized vector in row major format (first row = first
/// three elements)
///
void SetRotation( float* array );
///
/// sets translation from a POD vector
///
void SetTranslation( double array[3] );
///
/// sets translation from a POD vector
///
void SetRotation( double array[3][3] );
///
/// method to set translation by cv vector
///
void SetTranslation( const cv::Mat& transl);
///
/// sets rotation with a rotation matrix
///
void SetRotation( const cv::Mat& mat );
///
/// sets rotation with a rodrigues rotation vector
///
void SetRotationVector( const cv::Mat& rotVec);
///
/// \return the navigation data that stores all information
///
mitk::NavigationData::Pointer GetNavigationData() const;
///
/// calls navigationdata::GetPosition()
///
mitk::Point3D GetPosition() const;
///
/// same as GetPosition
///
mitk::Point3D GetTranslation() const;
///
/// calls navigationdata::IsValid()
///
bool IsValid() const;
///
/// calls navigationdata::SetValid()
///
void SetValid(bool valid);
///
/// calls navigationdata::GetOrientation()
///
mitk::Quaternion GetOrientation() const;
///
/// \return the homogeneous matrix representing this transform
///
vnl_matrix_fixed<mitk::ScalarType, 4, 4> GetMatrix() const;
///
/// \return the homogeneous vtk matrix representing this transform
///
void GetMatrix(vtkMatrix4x4* matrix) const;
///
/// \return the homogeneous vtk matrix representing this transform
/// in !OpenGL! left handed coordinate system
///
void GetVtkOpenGlMatrix(vtkMatrix4x4* matrix) const;
mitk::Point3D TransformPoint(mitk::Point3D point) const;
///
/// create xml representation
///
- void ToXML(TiXmlElement* elem) const override;
+ void ToXML(tinyxml2::XMLElement* elem) const override;
///
/// create string representation
///
std::string ToString() const;
///
/// create string csv representation (only the transformation values!!!!)
///
std::string ToCSVString() const;
///
/// create matlab representation
///
std::string ToMatlabString(const std::string& varname="transform",
bool printLastRow=true) const;
///
/// write csv representation to file (only the transformation values!!!!)
///
void ToCSVFile(const std::string& file) const;
///
/// write matlab representation to file
///
void ToMatlabFile(const std::string& file
, const std::string& varname="transform") const;
///
/// conversion to cv types
///
cv::Mat GetCvTranslation() const;
cv::Mat GetCvRotationVector() const;
cv::Mat GetCvRotationMatrix() const;
cv::Mat GetCvMatrix() const;
///
/// conversion to vnl types
///
vnl_vector_fixed<mitk::ScalarType, 3> GetVnlTranslation() const;
vnl_vector_fixed<double, 3> GetVnlDoubleTranslation() const;
vnl_quaternion<double> GetVnlDoubleQuaternion() const;
vnl_matrix_fixed<mitk::ScalarType, 3, 3> GetVnlRotationMatrix() const;
vnl_matrix_fixed<double, 4, 4> GetVnlDoubleMatrix() const;
protected:
Transform();
Transform(const mitk::NavigationData* nd);
Transform(const std::string& s);
// everything is stored here
mitk::NavigationData::Pointer m_NavData;
///
/// saves the type of the transform (Default is UNKNOWN_TYPE)
///
std::string m_Type;
};
} // namespace mitk
MITKCAMERACALIBRATION_EXPORT std::ostream& operator<<
(std::ostream& os, mitk::Transform::Pointer p);
#endif // MITKTRANSFORM_H
diff --git a/Modules/CameraCalibration/mitkXMLSerializable.cpp b/Modules/CameraCalibration/mitkXMLSerializable.cpp
index 525f8456de..0479a46ab1 100644
--- a/Modules/CameraCalibration/mitkXMLSerializable.cpp
+++ b/Modules/CameraCalibration/mitkXMLSerializable.cpp
@@ -1,137 +1,137 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <mitkXMLSerializable.h>
#include "mitkEndoDebug.h"
#include "mitkEndoMacros.h"
#include <itksys/SystemTools.hxx>
+#include <tinyxml2.h>
namespace mitk
{
const std::string XMLSerializable::FILE_REFERENCE_ATTRIBUTE_NAME = "fileRef";
const std::string XMLSerializable::ROOT_NAME = "data";
void mitk::XMLSerializable::ToXMLFile(const std::string& file
, const std::string& elemName)
{
- TiXmlElement * rootElem=nullptr;
- TiXmlElement * element=nullptr;
+ tinyxml2::XMLElement * rootElem=nullptr;
+ tinyxml2::XMLElement* element=nullptr;
// determine element to write to
std::string elementName = elemName;
if(elementName.empty())
elementName = this->GetNameOfClass();
- TiXmlDocument doc( file.c_str() );
- bool loadOkay = doc.LoadFile();
+ tinyxml2::XMLDocument doc;
// if the document already exists ...
- if(loadOkay)
+ if(tinyxml2::XML_SUCCESS == doc.LoadFile(file.c_str()))
{
// try to identify the XML element of this class as the root
// or as the child of the root
rootElem = doc.RootElement();
endoAssertMsg( rootElem, "No root element found in " << file );
// if root element represents this element remove the root
- if( rootElem->ValueStr() == elementName )
+ if( std::string(rootElem->Value() != nullptr ? rootElem->Value() : "") == elementName )
{
- doc.RemoveChild(rootElem);
+ doc.DeleteChild(rootElem);
rootElem = nullptr;
}
else
{
// if it is a child of the root remove it too
- element = rootElem->FirstChildElement(elementName);
+ element = rootElem->FirstChildElement(elementName.c_str());
if(element)
- rootElem->RemoveChild(element);
+ rootElem->DeleteChild(element);
}
}
else
{
// document did not exist, create new one with declration
- auto decl = new TiXmlDeclaration( "1.0", "", "" );
- doc.LinkEndChild( decl );
+ doc.InsertEndChild( doc.NewDeclaration() );
}
m_XMLFileName = file;
// create element (if the document already exists this element was removed)
- element = new TiXmlElement( elementName );
+ element = doc.NewElement( elementName.c_str() );
this->ToXML( element );
// if we do not have a root element create a new one
if(!rootElem)
- rootElem = new TiXmlElement( ROOT_NAME );
+ rootElem = doc.NewElement( ROOT_NAME.c_str() );
// add the element node as child
- rootElem->LinkEndChild(element);
+ rootElem->InsertEndChild(element);
// if no root element exists, add it now
if(doc.RootElement() == nullptr)
- doc.LinkEndChild( rootElem );
+ doc.InsertEndChild( rootElem );
- if(!doc.SaveFile( file ))
+ if(tinyxml2::XML_SUCCESS != doc.SaveFile( file.c_str() ))
{
std::ostringstream s; s << "File " << file
<< " could not be written. Please check permissions.";
throw std::logic_error(s.str());
}
}
std::string mitk::XMLSerializable::GetXMLFileName() const
{
return m_XMLFileName;
}
void mitk::XMLSerializable::FromXMLFile(const std::string& file
, const std::string& elemName)
{
endodebug( "Trying to read from " << file )
- TiXmlDocument doc( file.c_str() );
- bool loadOkay = doc.LoadFile();
- if(!loadOkay)
+ tinyxml2::XMLDocument doc;
+ if(tinyxml2::XML_SUCCESS != doc.LoadFile(file.c_str()))
{
std::ostringstream s; s << "File " << file
<< " could not be loaded!";
throw std::logic_error(s.str().c_str());
}
m_XMLFileName = file;
- TiXmlElement* elem = doc.FirstChildElement();
+ auto* elem = doc.FirstChildElement();
endoAssertMsg( elem, "No root element found" );
// determine element to read from
std::string elementName = elemName;
if(elementName.empty())
elementName = this->GetNameOfClass();
// try again with the first element
if(strcmp(elem->Value(), elementName.c_str()) != 0)
elem = elem->FirstChildElement(elementName.c_str());
endoAssertMsg( elem, "No child element \"" << elementName <<
"\" found in " << file );
// if theres an attribute as file reference try to load the class
// from that file
- std::string filename;
- if(elem->QueryStringAttribute(FILE_REFERENCE_ATTRIBUTE_NAME.c_str(), &filename)
- == TIXML_SUCCESS)
+ const char* filenameC = elem->Attribute(FILE_REFERENCE_ATTRIBUTE_NAME.c_str());
+ std::string filename = nullptr != filenameC
+ ? filenameC
+ : "";
+ if(!filename.empty())
{
if( !itksys::SystemTools::FileIsFullPath(filename.c_str()) )
filename = itksys::SystemTools::GetFilenamePath(file) + "/" + filename;
this->FromXMLFile(filename);
return; // exit!
}
this->FromXML( elem );
}
}
diff --git a/Modules/CameraCalibration/mitkXMLSerializable.h b/Modules/CameraCalibration/mitkXMLSerializable.h
index 31dc61d346..8c0d78ecb9 100644
--- a/Modules/CameraCalibration/mitkXMLSerializable.h
+++ b/Modules/CameraCalibration/mitkXMLSerializable.h
@@ -1,88 +1,92 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKXMLSerializable_H
#define MITKXMLSerializable_H
#include <string>
-#include <tinyxml.h>
#include <itkObject.h>
#include <itkMacro.h>
#include <MitkCameraCalibrationExports.h>
+namespace tinyxml2
+{
+ class XMLElement;
+}
+
namespace mitk
{
///
/// \brief interface for all classes able to write themselves to XML files
///
class MITKCAMERACALIBRATION_EXPORT XMLSerializable
{
public:
///
/// value of the special tag for file references
/// if this is attribute is found the class
/// will be loaded from the file in the attributes value
///
static const std::string FILE_REFERENCE_ATTRIBUTE_NAME;
///
/// the name of the root node that is created when the element is saved
///
static const std::string ROOT_NAME;
///
/// the tag value will be equals to the class name (function
/// implemented by the itkTypeMacro)
///
virtual const char* GetNameOfClass() const = 0;
///
/// write your values here to elem
///
- virtual void ToXML(TiXmlElement* elem) const = 0;
+ virtual void ToXML(tinyxml2::XMLElement* elem) const = 0;
///
/// read your values here from elem
///
- virtual void FromXML(TiXmlElement* elem) = 0;
+ virtual void FromXML(const tinyxml2::XMLElement* elem) = 0;
///
/// tries to write the xml data obtained in ToXML() to file
///
virtual void ToXMLFile(const std::string& file
, const std::string& elemName="");
///
/// loads the XML file and calls FromXML()
/// takes the first child of the document
/// if this root node value is not equal to GetNameOfClass()
/// the method will try to find the first children of the root
/// node with the value of GetNameOfClass()
/// if elemName is not empty then this value will be used instead
/// of GetNameOfClass()
/// if this node is found it will check if an attribute named
/// FILE_REFERENCE_ATTRIBUTE_NAME is found: in this case
/// the method calls itself with this attributes value as parameter
///
virtual void FromXMLFile(const std::string& file
, const std::string& elemName="");
///
/// \see m_XMLFileName
///
std::string GetXMLFileName() const;
private:
///
/// saves the xmlfile name set for this serializable ( in FromXMLFile() )
///
std::string m_XMLFileName;
};
}
#endif
diff --git a/Modules/Classification/CLLibSVM/test/CMakeLists.txt b/Modules/Classification/CLLibSVM/test/CMakeLists.txt
index b4f2e87ef6..5a6a2c1bf5 100644
--- a/Modules/Classification/CLLibSVM/test/CMakeLists.txt
+++ b/Modules/Classification/CLLibSVM/test/CMakeLists.txt
@@ -1,5 +1,5 @@
MITK_CREATE_MODULE_TESTS()
if(TARGET ${TESTDRIVER})
- mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK)
+ mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK|IOCSV)
endif()
diff --git a/Modules/Classification/CLMRUtilities/test/CMakeLists.txt b/Modules/Classification/CLMRUtilities/test/CMakeLists.txt
index b4f2e87ef6..153cd81e2e 100644
--- a/Modules/Classification/CLMRUtilities/test/CMakeLists.txt
+++ b/Modules/Classification/CLMRUtilities/test/CMakeLists.txt
@@ -1,5 +1 @@
MITK_CREATE_MODULE_TESTS()
-
-if(TARGET ${TESTDRIVER})
- mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK)
-endif()
diff --git a/Modules/Classification/CLMiniApps/CMakeLists.txt b/Modules/Classification/CLMiniApps/CMakeLists.txt
index 6e45122c9a..fb5bb3b6c8 100644
--- a/Modules/Classification/CLMiniApps/CMakeLists.txt
+++ b/Modules/Classification/CLMiniApps/CMakeLists.txt
@@ -1,117 +1,117 @@
option(BUILD_ClassificationMiniApps "Build commandline tools for classification" OFF)
if(BUILD_ClassificationMiniApps OR MITK_BUILD_ALL_APPS)
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
# list of miniapps
# if an app requires additional dependencies
# they are added after a "^^" and separated by "_"
set( classificationminiapps
RandomForestTraining^^MitkCLVigraRandomForest
NativeHeadCTSegmentation^^MitkCLVigraRandomForest
ManualSegmentationEvaluation^^MitkCLVigraRandomForest
CLScreenshot^^MitkCore_MitkQtWidgetsExt_MitkCLUtilities
CLDicom2Nrrd^^MitkCore
CLResampleImageToReference^^MitkCore
CLGlobalImageFeatures^^MitkCLUtilities_MitkQtWidgetsExt
CLMRNormalization^^MitkCLUtilities_MitkCLMRUtilities
CLStaple^^MitkCLUtilities
CLVoxelFeatures^^MitkCLUtilities
CLPolyToNrrd^^
CLPlanarFigureToNrrd^^MitkCore_MitkSegmentation_MitkMultilabel
CLSimpleVoxelClassification^^MitkDataCollection_MitkCLVigraRandomForest
CLVoxelClassification^^MitkDataCollection_MitkCLImportanceWeighting_MitkCLVigraRandomForest
CLBrainMask^^MitkCLUtilities
XRaxSimulationFromCT^^MitkCLUtilities
CLRandomSampling^^MitkCore_MitkCLUtilities
CLRemoveEmptyVoxels^^MitkCore
CLN4^^MitkCore
CLSkullMask^^MitkCore
CLPointSetToSegmentation^^
CLMultiForestPrediction^^MitkDataCollection_MitkCLVigraRandomForest
CLNrrdToPoly^^MitkCore
CL2Dto3DImage^^MitkCore
CLWeighting^^MitkCore_MitkCLImportanceWeighting_MitkCLUtilities
CLOverlayRoiCenterOfMass^^MitkCore_MitkCLUtilities_MitkQtWidgetsExt
CLLungSegmentation^^MitkCore_MitkSegmentation_MitkMultilabel
)
foreach(classificationminiapps ${classificationminiapps})
# extract mini app name and dependencies
string(REPLACE "^^" "\\;" miniapp_info ${classificationminiapps})
set(miniapp_info_list ${miniapp_info})
list(GET miniapp_info_list 0 appname)
list(GET miniapp_info_list 1 raw_dependencies)
string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
set(dependencies_list ${dependencies})
mitk_create_executable(${appname}
DEPENDS MitkCore MitkCLCore MitkCommandLine ${dependencies_list}
- PACKAGE_DEPENDS ITK Qt5|Core Vigra VTK|IOImage
+ PACKAGE_DEPENDS Qt5|Core Vigra VTK|IOImage
CPP_FILES ${appname}.cpp
)
if(EXECUTABLE_IS_ENABLED)
# On Linux, create a shell script to start a relocatable application
if(UNIX AND NOT APPLE)
install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${EXECUTABLE_TARGET}.sh)
endif()
get_target_property(_is_bundle ${EXECUTABLE_TARGET} MACOSX_BUNDLE)
if(APPLE)
if(_is_bundle)
set(_target_locations ${EXECUTABLE_TARGET}.app)
set(${_target_locations}_qt_plugins_install_dir ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_bundle_dest_dir ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_qt_plugins_for_current_bundle ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_qt_conf_install_dirs ${EXECUTABLE_TARGET}.app/Contents/Resources)
install(TARGETS ${EXECUTABLE_TARGET} BUNDLE DESTINATION . )
else()
if(NOT MACOSX_BUNDLE_NAMES)
set(_qt_conf_install_dirs bin)
set(_target_locations bin/${EXECUTABLE_TARGET})
set(${_target_locations}_qt_plugins_install_dir bin)
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
else()
foreach(bundle_name ${MACOSX_BUNDLE_NAMES})
list(APPEND _qt_conf_install_dirs ${bundle_name}.app/Contents/Resources)
set(_current_target_location ${bundle_name}.app/Contents/MacOS/${EXECUTABLE_TARGET})
list(APPEND _target_locations ${_current_target_location})
set(${_current_target_location}_qt_plugins_install_dir ${bundle_name}.app/Contents/MacOS)
message( " set(${_current_target_location}_qt_plugins_install_dir ${bundle_name}.app/Contents/MacOS) ")
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION ${bundle_name}.app/Contents/MacOS/)
endforeach()
endif()
endif()
else()
set(_target_locations bin/${EXECUTABLE_TARGET}${CMAKE_EXECUTABLE_SUFFIX})
set(${_target_locations}_qt_plugins_install_dir bin)
set(_qt_conf_install_dirs bin)
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
endif()
endif()
endforeach()
mitk_create_executable(CLMatchPointReg
DEPENDS MitkCore MitkCLUtilities MitkMatchPointRegistration MitkCommandLine MitkMatchPointRegistrationUI
- PACKAGE_DEPENDS ITK Qt5|Core Vigra MatchPoint
+ PACKAGE_DEPENDS Qt5|Core Vigra MatchPoint
CPP_FILES CLMatchPointReg.cpp
)
# On Linux, create a shell script to start a relocatable application
if(UNIX AND NOT APPLE)
install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${EXECUTABLE_TARGET}.sh)
endif()
if(EXECUTABLE_IS_ENABLED)
MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET})
endif()
endif()
diff --git a/Modules/Classification/CLUtilities/CMakeLists.txt b/Modules/Classification/CLUtilities/CMakeLists.txt
index 3c7f86a35d..0f05dd8069 100644
--- a/Modules/Classification/CLUtilities/CMakeLists.txt
+++ b/Modules/Classification/CLUtilities/CMakeLists.txt
@@ -1,14 +1,10 @@
mitk_create_module(
DEPENDS MitkCore MitkCLCore MitkCommandLine MitkDICOM
- PACKAGE_DEPENDS PUBLIC Eigen PRIVATE tinyxml VTK|FiltersStatistics
+ PACKAGE_DEPENDS PUBLIC Eigen OpenMP PRIVATE tinyxml2 VTK|FiltersStatistics
)
if(TARGET ${MODULE_TARGET})
- if(MITK_USE_OpenMP)
- target_link_libraries(${MODULE_TARGET} PUBLIC OpenMP::OpenMP_CXX)
- endif()
-
if(BUILD_TESTING)
add_subdirectory(test)
endif()
endif()
diff --git a/Modules/Classification/CLUtilities/src/mitkCLResultXMLWriter.cpp b/Modules/Classification/CLUtilities/src/mitkCLResultXMLWriter.cpp
index 0d3bf0c5ef..c884a41381 100644
--- a/Modules/Classification/CLUtilities/src/mitkCLResultXMLWriter.cpp
+++ b/Modules/Classification/CLUtilities/src/mitkCLResultXMLWriter.cpp
@@ -1,318 +1,321 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <mitkCLResultXMLWriter.h>
#include <iostream>
#include <locale>
#include <iomanip>
#include <ctime>
#include <sstream>
#include <mitkDICOMTagPath.h>
#include <mitkDICOMProperty.h>
#include <mitkLocaleSwitch.h>
#include <mitkIOMetaInformationPropertyConstants.h>
#include <mitkDICOMIOMetaInformationPropertyConstants.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
template <class charT>
class punct_facet : public std::numpunct<charT> {
public:
punct_facet(charT sep) :
m_Sep(sep)
{
}
protected:
charT do_decimal_point() const override { return m_Sep; }
private:
charT m_Sep;
};
-void AddPropertyAsNode(const mitk::Image* image, const std::string& key, const std::string& tag, TiXmlElement* rootNode)
+void AddPropertyAsNode(const mitk::Image* image, const std::string& key, const std::string& tag, tinyxml2::XMLElement* rootNode)
{
auto prop = image->GetProperty(key.c_str());
if (prop.IsNotNull())
{
- auto propNode = new TiXmlElement(tag);
- TiXmlText* valueText = new TiXmlText(prop->GetValueAsString());
- propNode->LinkEndChild(valueText);
+ auto* doc = rootNode->GetDocument();
+ auto propNode = doc->NewElement(tag.c_str());
+ auto* valueText = doc->NewText(prop->GetValueAsString().c_str());
+ propNode->InsertEndChild(valueText);
- rootNode->LinkEndChild(propNode);
+ rootNode->InsertEndChild(propNode);
}
}
-void AddSeriesInstanceUID(const mitk::Image* image, TiXmlElement* xmlNode)
+void AddSeriesInstanceUID(const mitk::Image* image, tinyxml2::XMLElement* xmlNode)
{
AddPropertyAsNode(image, mitk::DICOMTagPathToPropertyName(mitk::DICOMTagPath(0x0020, 0x000e)), "mp:seriesInstanceUID", xmlNode);
}
-void AddFilePath(const mitk::Image* image, TiXmlElement* xmlNode)
+void AddFilePath(const mitk::Image* image, tinyxml2::XMLElement* xmlNode)
{
AddPropertyAsNode(image, mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_INPUTLOCATION()), "mp:filePath", xmlNode);
}
-void AddSOPInstanceUIDs(const mitk::Image* image, TiXmlElement* xmlNode)
+void AddSOPInstanceUIDs(const mitk::Image* image, tinyxml2::XMLElement* xmlNode)
{
auto prop = image->GetProperty(mitk::DICOMTagPathToPropertyName(mitk::DICOMTagPath(0x0008, 0x0018)).c_str());
auto dicomProp = dynamic_cast<const mitk::DICOMProperty*>(prop.GetPointer());
+ auto* doc = xmlNode->GetDocument();
if (dicomProp != nullptr)
{
- auto instanceUIDsNode = new TiXmlElement("mp:sopInstanceUIDs");
- xmlNode->LinkEndChild(instanceUIDsNode);
+ auto* instanceUIDsNode = doc->NewElement("mp:sopInstanceUIDs");
+ xmlNode->InsertEndChild(instanceUIDsNode);
if (dicomProp->IsUniform())
{
- auto instanceUIDNode = new TiXmlElement("mp:sopInstanceUID");
- TiXmlText* valueText = new TiXmlText(dicomProp->GetValueAsString());
- instanceUIDNode->LinkEndChild(valueText);
- instanceUIDsNode->LinkEndChild(instanceUIDNode);
+ auto* instanceUIDNode = doc->NewElement("mp:sopInstanceUID");
+ auto* valueText = doc->NewText(dicomProp->GetValueAsString().c_str());
+ instanceUIDNode->InsertEndChild(valueText);
+ instanceUIDsNode->InsertEndChild(instanceUIDNode);
}
else
{
const auto timeSteps = dicomProp->GetAvailableTimeSteps();
for (auto timeStep : timeSteps)
{
const auto slices = dicomProp->GetAvailableSlices(timeStep);
for (auto slice : slices)
{
- auto instanceUIDNode = new TiXmlElement("mp:sopInstanceUID");
- instanceUIDNode->SetAttribute("z", slice);
- instanceUIDNode->SetAttribute("t", timeStep);
- TiXmlText* valueText = new TiXmlText(dicomProp->GetValue(timeStep, slice));
- instanceUIDNode->LinkEndChild(valueText);
- instanceUIDsNode->LinkEndChild(instanceUIDNode);
+ auto instanceUIDNode = doc->NewElement("mp:sopInstanceUID");
+ instanceUIDNode->SetAttribute("z", static_cast<int>(slice));
+ instanceUIDNode->SetAttribute("t", static_cast<int>(timeStep));
+ auto* valueText = doc->NewText(dicomProp->GetValue(timeStep, slice).c_str());
+ instanceUIDNode->InsertEndChild(valueText);
+ instanceUIDsNode->InsertEndChild(instanceUIDNode);
}
}
}
}
}
-void AddDateAndTime(TiXmlElement* rootNode)
+void AddDateAndTime(tinyxml2::XMLElement* rootNode)
{
- auto dateNode = new TiXmlElement("mp:generationDate");
+ auto* doc = rootNode->GetDocument();
+ auto* dateNode = doc->NewElement("mp:generationDate");
auto time = std::time(nullptr);
std::ostringstream sstream;
sstream << std::put_time(std::localtime(&time), "%Y%m%d");
- TiXmlText* valueText = new TiXmlText(sstream.str());
- dateNode->LinkEndChild(valueText);
+ auto* valueText = doc->NewText(sstream.str().c_str());
+ dateNode->InsertEndChild(valueText);
- rootNode->LinkEndChild(dateNode);
+ rootNode->InsertEndChild(dateNode);
- auto timeNode = new TiXmlElement("mp:generationTime");
+ auto* timeNode = doc->NewElement("mp:generationTime");
std::ostringstream timestream;
timestream << std::put_time(std::localtime(&time), "%H%M%S");
- valueText = new TiXmlText(timestream.str());
- timeNode->LinkEndChild(valueText);
+ valueText = doc->NewText(timestream.str().c_str());
+ timeNode->InsertEndChild(valueText);
- rootNode->LinkEndChild(timeNode);
+ rootNode->InsertEndChild(timeNode);
}
-void AddParameters(const std::map<std::string, us::Any>& parameters, TiXmlElement* paramsNode)
+void AddParameters(const std::map<std::string, us::Any>& parameters, tinyxml2::XMLElement* paramsNode)
{
+ auto* doc = paramsNode->GetDocument();
for (const auto& param : parameters)
{
mitk::LocaleSwitch lswitch("C");
- auto paramNode = new TiXmlElement("mp:parameter");
- paramNode->SetAttribute("name", param.first);
- TiXmlText* valueText = new TiXmlText(param.second.ToString());
- paramNode->LinkEndChild(valueText);
- paramsNode->LinkEndChild(paramNode);
+ auto paramNode = doc->NewElement("mp:parameter");
+ paramNode->SetAttribute("name", param.first.c_str());
+ auto* valueText = doc->NewText(param.second.ToString().c_str());
+ paramNode->InsertEndChild(valueText);
+ paramsNode->InsertEndChild(paramNode);
}
}
-void AddFeatures(const mitk::AbstractGlobalImageFeature::FeatureListType& features, TiXmlElement* featsNode)
+void AddFeatures(const mitk::AbstractGlobalImageFeature::FeatureListType& features, tinyxml2::XMLElement* featsNode)
{
+ auto* doc = featsNode->GetDocument();
for (const auto& feat : features)
{
- auto featNode = new TiXmlElement("mp:feature");
- featNode->SetAttribute("name", feat.first.name);
- featNode->SetAttribute("version", feat.first.version);
- featNode->SetAttribute("class", feat.first.featureClass);
- featNode->SetAttribute("setting", feat.first.settingID);
+ auto featNode = doc->NewElement("mp:feature");
+ featNode->SetAttribute("name", feat.first.name.c_str());
+ featNode->SetAttribute("version", feat.first.version.c_str());
+ featNode->SetAttribute("class", feat.first.featureClass.c_str());
+ featNode->SetAttribute("setting", feat.first.settingID.c_str());
std::ostringstream sstream;
sstream.imbue(std::locale("C"));
sstream << feat.second;
- TiXmlText* valueText = new TiXmlText(sstream.str());
- featNode->LinkEndChild(valueText);
- featsNode->LinkEndChild(featNode);
+ auto* valueText = doc->NewText(sstream.str().c_str());
+ featNode->InsertEndChild(valueText);
+ featsNode->InsertEndChild(featNode);
}
}
-void AddFeatureSettings(const mitk::AbstractGlobalImageFeature::FeatureListType& features, TiXmlElement* featSettingsNode)
+void AddFeatureSettings(const mitk::AbstractGlobalImageFeature::FeatureListType& features, tinyxml2::XMLElement* featSettingsNode)
{
+ auto* doc = featSettingsNode->GetDocument();
std::list<std::string> coveredSettings;
for (const auto& feat : features)
{
auto finding = std::find(coveredSettings.begin(), coveredSettings.end(), feat.first.settingID);
if (finding == coveredSettings.end())
{
- auto featSettingNode = new TiXmlElement("mp:featureSetting");
- featSettingsNode->LinkEndChild(featSettingNode);
- featSettingNode->SetAttribute("name", feat.first.settingID);
+ auto featSettingNode = doc->NewElement("mp:featureSetting");
+ featSettingsNode->InsertEndChild(featSettingNode);
+ featSettingNode->SetAttribute("name", feat.first.settingID.c_str());
AddParameters(feat.first.parameters, featSettingNode);
coveredSettings.push_back(feat.first.settingID);
}
}
}
-void AddReaderInfo(const mitk::Image* image, TiXmlElement* imageNode)
+void AddReaderInfo(const mitk::Image* image, tinyxml2::XMLElement* imageNode)
{
- auto ioNode = new TiXmlElement("mp:IOReader");
- imageNode->LinkEndChild(ioNode);
+ auto* doc = imageNode->GetDocument();
+ auto ioNode = doc->NewElement("mp:IOReader");
+ imageNode->InsertEndChild(ioNode);
AddPropertyAsNode(image, mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_DESCRIPTION()), "mp:description", ioNode);
AddPropertyAsNode(image, mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_VERSION()), "mp:version", ioNode);
AddPropertyAsNode(image, mitk::PropertyKeyPathToPropertyName(mitk::DICOMIOMetaInformationPropertyConstants::READER_CONFIGURATION()), "mp:configuration", ioNode);
AddPropertyAsNode(image, mitk::PropertyKeyPathToPropertyName(mitk::DICOMIOMetaInformationPropertyConstants::READER_GDCM()), "mp:gdcmVersion", ioNode);
AddPropertyAsNode(image, mitk::PropertyKeyPathToPropertyName(mitk::DICOMIOMetaInformationPropertyConstants::READER_DCMTK()), "mp:dcmtkVersion", ioNode);
}
void WriteDocument(std::ostream& stream, const mitk::Image* image, const mitk::Image* mask,
const mitk::AbstractGlobalImageFeature::FeatureListType& features, const std::string& methodName,
const std::string& organisation, const std::string& version, const std::string& pipelineUID,
const std::map<std::string, us::Any>& cliArgs)
{
- TiXmlDocument doc;
- doc.SetCondenseWhiteSpace(false);
+ tinyxml2::XMLDocument doc;
+ doc.InsertEndChild(doc.NewDeclaration());
- auto decl = new TiXmlDeclaration(
- "1.0", "UTF-8", "");
- doc.LinkEndChild(decl);
-
- auto rootNode = new TiXmlElement("mp:measurement");
+ auto* rootNode = doc.NewElement("mp:measurement");
rootNode->SetAttribute("xmlns:mp", "http://www.mitk.org/Phenotyping");
- doc.LinkEndChild(rootNode);
+ doc.InsertEndChild(rootNode);
- auto methodNode = new TiXmlElement("mp:measurementMethod");
- rootNode->LinkEndChild(methodNode);
+ auto* methodNode = doc.NewElement("mp:measurementMethod");
+ rootNode->InsertEndChild(methodNode);
- auto methodNameNode = new TiXmlElement("mp:name");
- TiXmlText* valueText = new TiXmlText(methodName);
- methodNameNode->LinkEndChild(valueText);
- methodNode->LinkEndChild(methodNameNode);
+ auto* methodNameNode = doc.NewElement("mp:name");
+ auto* valueText = doc.NewText(methodName.c_str());
+ methodNameNode->InsertEndChild(valueText);
+ methodNode->InsertEndChild(methodNameNode);
- auto organisationNode = new TiXmlElement("mp:organisation");
- valueText = new TiXmlText(organisation);
- organisationNode->LinkEndChild(valueText);
- methodNode->LinkEndChild(organisationNode);
+ auto* organisationNode = doc.NewElement("mp:organisation");
+ valueText = doc.NewText(organisation.c_str());
+ organisationNode->InsertEndChild(valueText);
+ methodNode->InsertEndChild(organisationNode);
- auto versionNode = new TiXmlElement("mp:version");
- valueText = new TiXmlText(version);
- versionNode->LinkEndChild(valueText);
- methodNode->LinkEndChild(versionNode);
+ auto* versionNode = doc.NewElement("mp:version");
+ valueText = doc.NewText(version.c_str());
+ versionNode->InsertEndChild(valueText);
+ methodNode->InsertEndChild(versionNode);
- auto imageNode = new TiXmlElement("mp:image");
- rootNode->LinkEndChild(imageNode);
+ auto* imageNode = doc.NewElement("mp:image");
+ rootNode->InsertEndChild(imageNode);
AddSeriesInstanceUID(image, imageNode);
AddFilePath(image, imageNode);
AddSOPInstanceUIDs(image, imageNode);
AddReaderInfo(image,imageNode);
- auto maskNode = new TiXmlElement("mp:mask");
- rootNode->LinkEndChild(maskNode);
+ auto* maskNode = doc.NewElement("mp:mask");
+ rootNode->InsertEndChild(maskNode);
AddSeriesInstanceUID(mask, maskNode);
AddFilePath(mask, maskNode);
AddSOPInstanceUIDs(mask, maskNode);
AddReaderInfo(mask, maskNode);
//todo mask reader meta info
AddDateAndTime(rootNode);
- auto pipelineNode = new TiXmlElement("mp:pipelineUID");
- valueText = new TiXmlText(pipelineUID);
- pipelineNode->LinkEndChild(valueText);
- rootNode->LinkEndChild(pipelineNode);
+ auto* pipelineNode = doc.NewElement("mp:pipelineUID");
+ valueText = doc.NewText(pipelineUID.c_str());
+ pipelineNode->InsertEndChild(valueText);
+ rootNode->InsertEndChild(pipelineNode);
- auto paramsNode = new TiXmlElement("mp:parameters");
- rootNode->LinkEndChild(paramsNode);
+ auto* paramsNode = doc.NewElement("mp:parameters");
+ rootNode->InsertEndChild(paramsNode);
AddParameters(cliArgs, paramsNode);
- auto featsNode = new TiXmlElement("mp:features");
- rootNode->LinkEndChild(featsNode);
+ auto* featsNode = doc.NewElement("mp:features");
+ rootNode->InsertEndChild(featsNode);
AddFeatures(features, featsNode);
- auto featSettingsNode = new TiXmlElement("mp:featureSettings");
- rootNode->LinkEndChild(featSettingsNode);
+ auto* featSettingsNode = doc.NewElement("mp:featureSettings");
+ rootNode->InsertEndChild(featSettingsNode);
AddFeatureSettings(features, featSettingsNode);
- TiXmlPrinter printer;
+ tinyxml2::XMLPrinter printer;
+ doc.Print(&printer);
- doc.Accept(&printer);
- stream << printer.Str();
+ stream << printer.CStr();
}
void mitk::cl::CLResultXMLWriter::SetImage(const Image* image)
{
m_Image = image;
}
void mitk::cl::CLResultXMLWriter::SetMask(const Image* mask)
{
m_Mask = mask;
}
void mitk::cl::CLResultXMLWriter::SetFeatures(const mitk::AbstractGlobalImageFeature::FeatureListType& features)
{
m_Features = features;
}
void mitk::cl::CLResultXMLWriter::SetMethodName(const std::string& name)
{
m_MethodName = name;
}
void mitk::cl::CLResultXMLWriter::SetMethodVersion(const std::string& version)
{
m_MethodVersion = version;
}
void mitk::cl::CLResultXMLWriter::SetOrganisation(const std::string& orga)
{
m_Organisation = orga;
}
void mitk::cl::CLResultXMLWriter::SetPipelineUID(const std::string& pipelineUID)
{
m_PipelineUID = pipelineUID;
}
void mitk::cl::CLResultXMLWriter::SetCLIArgs(const std::map<std::string, us::Any>& args)
{
m_CLIArgs = args;
}
void mitk::cl::CLResultXMLWriter::write(const std::string& filePath) const
{
std::ofstream resultFile;
resultFile.open(filePath.c_str());
if (resultFile.is_open())
{
this->write(resultFile);
resultFile.close();
}
else
{
MITK_ERROR << "Cannot write xml results. Unable to open file: \""<<filePath<<"\"";
}
}
void mitk::cl::CLResultXMLWriter::write(std::ostream& stream) const
{
WriteDocument(stream, m_Image, m_Mask, m_Features, m_MethodName, m_Organisation, m_MethodVersion, m_PipelineUID, m_CLIArgs);
}
diff --git a/Modules/Classification/CLUtilities/test/CMakeLists.txt b/Modules/Classification/CLUtilities/test/CMakeLists.txt
index b4f2e87ef6..153cd81e2e 100644
--- a/Modules/Classification/CLUtilities/test/CMakeLists.txt
+++ b/Modules/Classification/CLUtilities/test/CMakeLists.txt
@@ -1,5 +1 @@
MITK_CREATE_MODULE_TESTS()
-
-if(TARGET ${TESTDRIVER})
- mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK)
-endif()
diff --git a/Modules/Classification/CLVigraRandomForest/CMakeLists.txt b/Modules/Classification/CLVigraRandomForest/CMakeLists.txt
index 7fd5788e78..e16e415d6a 100644
--- a/Modules/Classification/CLVigraRandomForest/CMakeLists.txt
+++ b/Modules/Classification/CLVigraRandomForest/CMakeLists.txt
@@ -1,8 +1,8 @@
MITK_CREATE_MODULE(
DEPENDS MitkCLCore MitkCLUtilities MitkSceneSerializationBase
#AUTOLOAD_WITH MitkCore
PACKAGE_DEPENDS
- PRIVATE Vigra ITK|ITKIONRRD
+ PRIVATE ITK|IONRRD Vigra
)
add_subdirectory(test)
diff --git a/Modules/Classification/CLVigraRandomForest/test/CMakeLists.txt b/Modules/Classification/CLVigraRandomForest/test/CMakeLists.txt
index b4f2e87ef6..5a6a2c1bf5 100644
--- a/Modules/Classification/CLVigraRandomForest/test/CMakeLists.txt
+++ b/Modules/Classification/CLVigraRandomForest/test/CMakeLists.txt
@@ -1,5 +1,5 @@
MITK_CREATE_MODULE_TESTS()
if(TARGET ${TESTDRIVER})
- mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK)
+ mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK|IOCSV)
endif()
diff --git a/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp b/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp
index a27d5607b4..c2eff3c43f 100755
--- a/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp
+++ b/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp
@@ -1,216 +1,228 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <mitkContourModelUtils.h>
#include <mitkContourModelToSurfaceFilter.h>
#include <mitkLabelSetImage.h>
#include <mitkSurface.h>
#include <vtkImageStencil.h>
#include <vtkPointData.h>
#include <vtkPolyData.h>
#include <vtkPolyDataToImageStencil.h>
mitk::ContourModelUtils::ContourModelUtils()
{
}
mitk::ContourModelUtils::~ContourModelUtils()
{
}
mitk::ContourModel::Pointer mitk::ContourModelUtils::ProjectContourTo2DSlice(
Image *slice, ContourModel *contourIn3D, bool, bool)
{
if (nullptr == slice || nullptr == contourIn3D)
return nullptr;
auto projectedContour = ContourModel::New();
projectedContour->Initialize(*contourIn3D);
auto sliceGeometry = slice->GetGeometry();
auto numberOfTimesteps = static_cast<int>(contourIn3D->GetTimeSteps());
for (decltype(numberOfTimesteps) t = 0; t < numberOfTimesteps; ++t)
{
auto iter = contourIn3D->Begin(t);
auto end = contourIn3D->End(t);
while (iter != end)
{
const auto ¤tPointIn3D = (*iter)->Coordinates;
Point3D projectedPointIn2D;
projectedPointIn2D.Fill(0.0);
sliceGeometry->WorldToIndex(currentPointIn3D, projectedPointIn2D);
projectedContour->AddVertex(projectedPointIn2D, t);
++iter;
}
}
return projectedContour;
}
mitk::ContourModel::Pointer mitk::ContourModelUtils::BackProjectContourFrom2DSlice(
const BaseGeometry *sliceGeometry, ContourModel *contourIn2D, bool)
{
if (nullptr == sliceGeometry || nullptr == contourIn2D)
return nullptr;
auto worldContour = ContourModel::New();
worldContour->Initialize(*contourIn2D);
auto numberOfTimesteps = static_cast<int>(contourIn2D->GetTimeSteps());
for (decltype(numberOfTimesteps) t = 0; t < numberOfTimesteps; ++t)
{
auto iter = contourIn2D->Begin(t);
auto end = contourIn2D->End(t);
while (iter != end)
{
const auto ¤tPointIn2D = (*iter)->Coordinates;
Point3D worldPointIn3D;
worldPointIn3D.Fill(0.0);
sliceGeometry->IndexToWorld(currentPointIn2D, worldPointIn3D);
worldContour->AddVertex(worldPointIn3D, t);
++iter;
}
}
return worldContour;
}
void mitk::ContourModelUtils::FillContourInSlice(
ContourModel *projectedContour, Image *sliceImage, Image::Pointer workingImage, int paintingPixelValue)
{
FillContourInSlice(projectedContour, 0, sliceImage, workingImage, paintingPixelValue);
}
void mitk::ContourModelUtils::FillContourInSlice(
ContourModel *projectedContour, unsigned int t, Image *sliceImage, Image::Pointer workingImage, int paintingPixelValue)
{
auto contourModelFilter = mitk::ContourModelToSurfaceFilter::New();
contourModelFilter->SetInput(projectedContour);
contourModelFilter->Update();
auto surface = mitk::Surface::New();
surface = contourModelFilter->GetOutput();
if (nullptr == surface->GetVtkPolyData(t))
{
MITK_WARN << "Could not create surface from contour model.";
return;
}
auto surface2D = vtkSmartPointer<vtkPolyData>::New();
surface2D->SetPoints(surface->GetVtkPolyData(t)->GetPoints());
surface2D->SetLines(surface->GetVtkPolyData(t)->GetLines());
auto image = vtkSmartPointer<vtkImageData>::New();
image->DeepCopy(sliceImage->GetVtkImageData());
const double FOREGROUND_VALUE = 255.0;
const double BACKGROUND_VALUE = 0.0;
vtkIdType count = image->GetNumberOfPoints();
for (decltype(count) i = 0; i < count; ++i)
image->GetPointData()->GetScalars()->SetTuple1(i, FOREGROUND_VALUE);
auto polyDataToImageStencil = vtkSmartPointer<vtkPolyDataToImageStencil>::New();
// Set a minimal tolerance, so that clipped pixels will be added to contour as well.
polyDataToImageStencil->SetTolerance(mitk::eps);
polyDataToImageStencil->SetInputData(surface2D);
polyDataToImageStencil->Update();
auto imageStencil = vtkSmartPointer<vtkImageStencil>::New();
imageStencil->SetInputData(image);
imageStencil->SetStencilConnection(polyDataToImageStencil->GetOutputPort());
imageStencil->ReverseStencilOff();
imageStencil->SetBackgroundValue(BACKGROUND_VALUE);
imageStencil->Update();
vtkSmartPointer<vtkImageData> filledImage = imageStencil->GetOutput();
vtkSmartPointer<vtkImageData> resultImage = sliceImage->GetVtkImageData();
FillSliceInSlice(filledImage, resultImage, workingImage, paintingPixelValue);
sliceImage->SetVolume(resultImage->GetScalarPointer());
}
void mitk::ContourModelUtils::FillSliceInSlice(
vtkSmartPointer<vtkImageData> filledImage, vtkSmartPointer<vtkImageData> resultImage, mitk::Image::Pointer image, int paintingPixelValue)
{
auto labelImage = dynamic_cast<LabelSetImage *>(image.GetPointer());
auto numberOfPoints = filledImage->GetNumberOfPoints();
if (nullptr == labelImage)
{
for (decltype(numberOfPoints) i = 0; i < numberOfPoints; ++i)
{
if (1 < filledImage->GetPointData()->GetScalars()->GetTuple1(i))
resultImage->GetPointData()->GetScalars()->SetTuple1(i, paintingPixelValue);
}
}
else
{
auto backgroundValue = labelImage->GetExteriorLabel()->GetValue();
if (paintingPixelValue != backgroundValue)
{
for (decltype(numberOfPoints) i = 0; i < numberOfPoints; ++i)
{
if (1 < filledImage->GetPointData()->GetScalars()->GetTuple1(i))
{
auto existingValue = resultImage->GetPointData()->GetScalars()->GetTuple1(i);
if (!labelImage->GetLabel(existingValue, labelImage->GetActiveLayer())->GetLocked())
resultImage->GetPointData()->GetScalars()->SetTuple1(i, paintingPixelValue);
}
}
}
else
{
auto activePixelValue = labelImage->GetActiveLabel(labelImage->GetActiveLayer())->GetValue();
for (decltype(numberOfPoints) i = 0; i < numberOfPoints; ++i)
{
if (1 < filledImage->GetPointData()->GetScalars()->GetTuple1(i))
{
if (resultImage->GetPointData()->GetScalars()->GetTuple1(i) == activePixelValue)
resultImage->GetPointData()->GetScalars()->SetTuple1(i, paintingPixelValue);
}
}
}
}
}
mitk::ContourModel::Pointer mitk::ContourModelUtils::MoveZerothContourTimeStep(const ContourModel *contour, unsigned int t)
{
if (nullptr == contour)
return nullptr;
auto resultContour = ContourModel::New();
resultContour->Expand(t + 1);
std::for_each(contour->Begin(), contour->End(), [&resultContour, t](ContourElement::VertexType *vertex) {
resultContour->AddVertex(vertex, t);
});
return resultContour;
}
+
+int mitk::ContourModelUtils::GetActivePixelValue(mitk::Image* workingImage)
+{
+ auto* labelSetImage = dynamic_cast<LabelSetImage*>(workingImage);
+ int activePixelValue = 1;
+ if (nullptr != labelSetImage)
+ {
+ activePixelValue = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer())->GetValue();
+ }
+
+ return activePixelValue;
+}
diff --git a/Modules/ContourModel/Algorithms/mitkContourModelUtils.h b/Modules/ContourModel/Algorithms/mitkContourModelUtils.h
index 42c91c021e..61a33c0c87 100644
--- a/Modules/ContourModel/Algorithms/mitkContourModelUtils.h
+++ b/Modules/ContourModel/Algorithms/mitkContourModelUtils.h
@@ -1,96 +1,106 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkContourModelUtils_h
#define mitkContourModelUtils_h
#include <mitkContourModel.h>
#include <mitkImage.h>
#include <vtkSmartPointer.h>
#include <MitkContourModelExports.h>
namespace mitk
{
/**
* \brief Helpful methods for working with contours and images
*
*
*/
class MITKCONTOURMODEL_EXPORT ContourModelUtils : public itk::Object
{
public:
mitkClassMacroItkParent(ContourModelUtils, itk::Object);
/**
\brief Projects a contour onto an image point by point. Converts from world to index coordinates.
\param slice
\param contourIn3D
\param correctionForIpSegmentation adds 0.5 to x and y index coordinates (difference between ipSegmentation and
MITK contours)
\param constrainToInside
*/
static ContourModel::Pointer ProjectContourTo2DSlice(Image *slice,
ContourModel *contourIn3D,
bool correctionForIpSegmentation,
bool constrainToInside);
/**
\brief Projects a slice index coordinates of a contour back into world coordinates.
\param sliceGeometry
\param contourIn2D
\param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between ipSegmentation
and MITK contours)
*/
static ContourModel::Pointer BackProjectContourFrom2DSlice(const BaseGeometry *sliceGeometry,
ContourModel *contourIn2D,
bool correctionForIpSegmentation = false);
/**
\brief Fill a contour in a 2D slice with a specified pixel value at time step 0.
*/
static void FillContourInSlice(ContourModel *projectedContour,
Image *sliceImage,
mitk::Image::Pointer workingImage,
int paintingPixelValue = 1);
/**
\brief Fill a contour in a 2D slice with a specified pixel value at a given time step.
*/
static void FillContourInSlice(ContourModel *projectedContour,
unsigned int timeStep,
Image *sliceImage,
mitk::Image::Pointer workingImage,
int paintingPixelValue = 1);
/**
\brief Fills a image (filledImage) into another image (resultImage) by incorporating the rules of LabelSet-Images
*/
static void FillSliceInSlice(vtkSmartPointer<vtkImageData> filledImage,
vtkSmartPointer<vtkImageData> resultImage,
mitk::Image::Pointer image,
int paintingPixelValue);
/**
\brief Move the contour in time step 0 to to a new contour model at the given time step.
*/
static ContourModel::Pointer MoveZerothContourTimeStep(const ContourModel *contour, unsigned int timeStep);
+ /**
+ \brief Retrieves the active pixel value of a (labelset) image.
+ If the image is basic image, the pixel value 1 (one) will be returned.
+ If the image is actually a labelset image, the pixel value of the active label of the active layer will be
+ returned.
+
+ \param workingImage The (labelset) image to retrieve the active pixel value of.
+ */
+ static int GetActivePixelValue(mitk::Image* workingImage);
+
protected:
ContourModelUtils();
~ContourModelUtils() override;
};
}
#endif
diff --git a/Modules/ContourModel/CMakeLists.txt b/Modules/ContourModel/CMakeLists.txt
index 98b2e63246..d07e6a5245 100644
--- a/Modules/ContourModel/CMakeLists.txt
+++ b/Modules/ContourModel/CMakeLists.txt
@@ -1,8 +1,8 @@
-MITK_CREATE_MODULE(
+mitk_create_module(
INCLUDE_DIRS Algorithms DataManagement IO Rendering
DEPENDS MitkCore MitkSceneSerializationBase MitkLegacyGL MitkAnnotation MitkMultilabel
- PACKAGE_DEPENDS PRIVATE ITK|ITKReview VTK|RenderingContext2D+RenderingContextOpenGL2
+ PACKAGE_DEPENDS PRIVATE VTK|RenderingContext2D+RenderingContextOpenGL2
# AUTOLOAD_WITH MitkCore TODO: Create IO Submodule and autoload that one instead.
)
add_subdirectory(Testing)
diff --git a/Modules/ContourModel/IO/mitkContourModelReader.cpp b/Modules/ContourModel/IO/mitkContourModelReader.cpp
index fa0ead2c5f..1b25342e91 100644
--- a/Modules/ContourModel/IO/mitkContourModelReader.cpp
+++ b/Modules/ContourModel/IO/mitkContourModelReader.cpp
@@ -1,157 +1,173 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkContourModelReader.h"
#include <fstream>
#include <iostream>
+#include <regex>
#include <mitkCustomMimeType.h>
#include <mitkLocaleSwitch.h>
+#include <tinyxml2.h>
+
+namespace
+{
+ // Previous versions of the ContourModelSetWriter produced flawed
+ // XML files with multiple XML declarations.
+ std::string RemoveErroneousXMLDeclarations(const std::string& filename)
+ {
+ std::ifstream file(filename);
+ file.seekg(0, std::ios_base::end);
+ auto size = file.tellg();
+ std::string string(size, '\0');
+ file.seekg(0);
+ file.read(&string[0], size);
+ file.close();
+ std::regex regex("><\\?xml.+\\?>");
+ return std::regex_replace(string, regex, ">");
+ }
+}
mitk::ContourModelReader::ContourModelReader(const mitk::ContourModelReader &other) : mitk::AbstractFileReader(other)
{
}
mitk::ContourModelReader::ContourModelReader() : AbstractFileReader()
{
std::string category = "Contour File";
mitk::CustomMimeType customMimeType;
customMimeType.SetCategory(category);
customMimeType.AddExtension("cnt");
this->SetDescription(category);
this->SetMimeType(customMimeType);
m_ServiceReg = this->RegisterService();
}
mitk::ContourModelReader::~ContourModelReader()
{
}
std::vector<itk::SmartPointer<mitk::BaseData>> mitk::ContourModelReader::DoRead()
{
std::vector<itk::SmartPointer<mitk::BaseData>> result;
std::string location = GetInputLocation();
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
try
{
- TiXmlDocument doc(location.c_str());
- bool loadOkay = doc.LoadFile();
- if (loadOkay)
+ auto string = RemoveErroneousXMLDeclarations(location);
+
+ tinyxml2::XMLDocument doc;
+ if (tinyxml2::XML_SUCCESS == doc.Parse(string.c_str()))
{
- TiXmlHandle docHandle(&doc);
+ tinyxml2::XMLHandle docHandle(&doc);
/*++++ handle n contourModels within data tags ++++*/
- for (TiXmlElement *currentContourElement = docHandle.FirstChildElement("contourModel").ToElement();
+ for (auto *currentContourElement = docHandle.FirstChildElement("contourModel").ToElement();
currentContourElement != nullptr;
currentContourElement = currentContourElement->NextSiblingElement())
{
mitk::ContourModel::Pointer newContourModel = mitk::ContourModel::New();
if (currentContourElement->FirstChildElement("data")->FirstChildElement("timestep") != nullptr)
{
- // handle geometry information
- // TiXmlElement* currentGeometryInfo =
- // currentContourElement->FirstChildElement("head")->FirstChildElement("geometryInformation")->ToElement();
- ///////////// NOT SUPPORTED YET ////////////////
-
/*++++ handle n timesteps within timestep tags ++++*/
- for (TiXmlElement *currentTimeSeries =
+ for (auto *currentTimeSeries =
currentContourElement->FirstChildElement("data")->FirstChildElement("timestep")->ToElement();
currentTimeSeries != nullptr;
currentTimeSeries = currentTimeSeries->NextSiblingElement())
{
unsigned int currentTimeStep(0);
currentTimeStep = atoi(currentTimeSeries->Attribute("n"));
this->ReadPoints(newContourModel, currentTimeSeries, currentTimeStep);
int isClosed;
currentTimeSeries->QueryIntAttribute("isClosed", &isClosed);
if (isClosed)
{
newContourModel->Close(currentTimeStep);
}
}
/*++++ END handle n timesteps within timestep tags ++++*/
}
else
{
// this should not happen
MITK_WARN << "wrong file format!";
// newContourModel = this->ReadPoint(newContourModel, currentContourElement, 0);
}
newContourModel->UpdateOutputInformation();
result.push_back(dynamic_cast<mitk::BaseData *>(newContourModel.GetPointer()));
}
/*++++ END handle n contourModels within data tags ++++*/
}
else
{
MITK_WARN << "XML parser error!";
}
}
catch (...)
{
MITK_ERROR << "Cannot read contourModel.";
}
return result;
}
mitk::ContourModelReader *mitk::ContourModelReader::Clone() const
{
return new ContourModelReader(*this);
}
void mitk::ContourModelReader::ReadPoints(mitk::ContourModel::Pointer newContourModel,
- TiXmlElement *currentTimeSeries,
+ const tinyxml2::XMLElement *currentTimeSeries,
unsigned int currentTimeStep)
{
// check if the timesteps in contourModel have to be expanded
if (currentTimeStep != newContourModel->GetTimeSteps())
{
newContourModel->Expand(currentTimeStep + 1);
}
// read all points within controlPoints tag
if (currentTimeSeries->FirstChildElement("controlPoints")->FirstChildElement("point") != nullptr)
{
- for (TiXmlElement *currentPoint =
+ for (auto *currentPoint =
currentTimeSeries->FirstChildElement("controlPoints")->FirstChildElement("point")->ToElement();
currentPoint != nullptr;
currentPoint = currentPoint->NextSiblingElement())
{
double x(0.0);
double y(0.0);
double z(0.0);
x = atof(currentPoint->FirstChildElement("x")->GetText());
y = atof(currentPoint->FirstChildElement("y")->GetText());
z = atof(currentPoint->FirstChildElement("z")->GetText());
int isActivePoint;
currentPoint->QueryIntAttribute("isActive", &isActivePoint);
mitk::Point3D point;
mitk::FillVector3D(point, x, y, z);
newContourModel->AddVertex(point, isActivePoint, currentTimeStep);
}
}
else
{
// nothing to read
}
}
diff --git a/Modules/ContourModel/IO/mitkContourModelReader.h b/Modules/ContourModel/IO/mitkContourModelReader.h
index bbeae0a7ec..f91298ae2c 100644
--- a/Modules/ContourModel/IO/mitkContourModelReader.h
+++ b/Modules/ContourModel/IO/mitkContourModelReader.h
@@ -1,56 +1,60 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef _MITK_CONTOURMODEL_READER__H_
#define _MITK_CONTOURMODEL_READER__H_
// MITK
#include <mitkAbstractFileReader.h>
#include <mitkBaseData.h>
#include <mitkContourModel.h>
#include <mitkMimeType.h>
#include <stack>
#include <string>
-#include <tinyxml.h>
#include <vtkXMLParser.h>
+namespace tinyxml2
+{
+ class XMLElement;
+}
+
namespace mitk
{
/**
* @brief
* @ingroup MitkContourModelModule
*/
class ContourModelReader : public mitk::AbstractFileReader
{
public:
ContourModelReader(const ContourModelReader &other);
ContourModelReader();
~ContourModelReader() override;
using AbstractFileReader::Read;
protected:
virtual void ReadPoints(mitk::ContourModel::Pointer newContourModel,
- TiXmlElement *currentTimeSeries,
+ const tinyxml2::XMLElement *currentTimeSeries,
unsigned int currentTimeStep);
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
private:
ContourModelReader *Clone() const override;
us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
};
}
#endif
diff --git a/Modules/ContourModel/IO/mitkContourModelSetReader.h b/Modules/ContourModel/IO/mitkContourModelSetReader.h
index 91e24180a1..3472efff46 100644
--- a/Modules/ContourModel/IO/mitkContourModelSetReader.h
+++ b/Modules/ContourModel/IO/mitkContourModelSetReader.h
@@ -1,54 +1,53 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef _MITK_ContourModelSetReader__H_
#define _MITK_ContourModelSetReader__H_
// MITK
#include <mitkAbstractFileReader.h>
#include <mitkBaseData.h>
#include <mitkContourModel.h>
#include <mitkContourModelSet.h>
#include <mitkMimeType.h>
#include <stack>
#include <string>
-#include <tinyxml.h>
#include <vtkXMLParser.h>
namespace mitk
{
/**
* @brief
* @ingroup MitkContourModelModule
*/
class ContourModelSetReader : public mitk::AbstractFileReader
{
public:
ContourModelSetReader(const ContourModelSetReader &other);
ContourModelSetReader();
~ContourModelSetReader() override;
using AbstractFileReader::Read;
protected:
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
private:
ContourModelSetReader *Clone() const override;
us::ServiceRegistration<mitk::IFileReader> m_ServiceReg;
};
}
#endif
diff --git a/Modules/ContourModel/IO/mitkContourModelSetWriter.cpp b/Modules/ContourModel/IO/mitkContourModelSetWriter.cpp
index c437dd022b..deb595a399 100644
--- a/Modules/ContourModel/IO/mitkContourModelSetWriter.cpp
+++ b/Modules/ContourModel/IO/mitkContourModelSetWriter.cpp
@@ -1,82 +1,85 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkContourModelSetWriter.h"
#include "mitkContourModelWriter.h"
#include <fstream>
#include <iostream>
#include <mitkCustomMimeType.h>
mitk::ContourModelSetWriter::ContourModelSetWriter() : AbstractFileWriter(ContourModelSet::GetStaticNameOfClass())
{
std::string category = "ContourModelSet File";
mitk::CustomMimeType customMimeType;
customMimeType.SetCategory(category);
customMimeType.AddExtension("cnt_set");
this->SetDescription(category);
this->SetMimeType(customMimeType);
RegisterService();
}
mitk::ContourModelSetWriter::ContourModelSetWriter(const mitk::ContourModelSetWriter &other) : AbstractFileWriter(other)
{
}
mitk::ContourModelSetWriter::~ContourModelSetWriter()
{
}
void mitk::ContourModelSetWriter::Write()
{
std::ostream *out;
std::ofstream outStream;
if (this->GetOutputStream())
{
out = this->GetOutputStream();
}
else
{
outStream.open(this->GetOutputLocation().c_str());
out = &outStream;
}
if (!out->good())
{
mitkThrow() << "Stream not good.";
}
+ *out << "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n";
+
// Use regular ContourModel writer to write each contour of the set to a single file.
// Just use a different file extension .cnt_set
- mitk::ContourModelWriter writer;
+ bool writeXMLHeader = false;
+ mitk::ContourModelWriter writer(writeXMLHeader);
mitk::ContourModelSet::ConstPointer contourModelSet = dynamic_cast<const mitk::ContourModelSet *>(this->GetInput());
//
// for each contour object set input of writer
//
for (int i = 0; i < contourModelSet->GetSize(); ++i)
{
const mitk::ContourModel *contour = contourModelSet->GetContourModelAt(i);
writer.SetInput(contour);
writer.SetOutputStream(this->GetOutputLocation(), out);
writer.Write();
}
}
mitk::ContourModelSetWriter *mitk::ContourModelSetWriter::Clone() const
{
return new ContourModelSetWriter(*this);
}
diff --git a/Modules/ContourModel/IO/mitkContourModelWriter.cpp b/Modules/ContourModel/IO/mitkContourModelWriter.cpp
index f41a1d83f4..8e7710a626 100644
--- a/Modules/ContourModel/IO/mitkContourModelWriter.cpp
+++ b/Modules/ContourModel/IO/mitkContourModelWriter.cpp
@@ -1,335 +1,335 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkContourModelWriter.h"
#include "mitkIOMimeTypes.h"
#include "mitkTimeGeometry.h"
#include <fstream>
#include <iostream>
#include <locale>
/*
* The xml file will look like:
*
* <?xml version="1.0" encoding="utf-8"?>
* <contourModel>
* <head>
* <geometryInfo>
* </geometryInfo>
* </head>
* <data>
* <timestep n="0">
* <controlPoints>
* <point>
* <x></x>
* <y></y>
* <z></z>
* </point>
* </controlPoint>
* </timestep>
* </data>
* </contourModel>
*/
//
// Initialization of the xml tags.
//
const char *mitk::ContourModelWriter::XML_CONTOURMODEL = "contourModel";
const char *mitk::ContourModelWriter::XML_HEAD = "head";
const char *mitk::ContourModelWriter::XML_GEOMETRY_INFO = "geometryInfo";
const char *mitk::ContourModelWriter::XML_DATA = "data";
const char *mitk::ContourModelWriter::XML_TIME_STEP = "timestep";
const char *mitk::ContourModelWriter::XML_CONTROL_POINTS = "controlPoints";
const char *mitk::ContourModelWriter::XML_POINT = "point";
const char *mitk::ContourModelWriter::XML_X = "x";
const char *mitk::ContourModelWriter::XML_Y = "y";
const char *mitk::ContourModelWriter::XML_Z = "z";
-mitk::ContourModelWriter::ContourModelWriter()
- : AbstractFileWriter(ContourModel::GetStaticNameOfClass()), m_IndentDepth(0), m_Indent(2)
+mitk::ContourModelWriter::ContourModelWriter(bool writeXMLHeader)
+ : AbstractFileWriter(ContourModel::GetStaticNameOfClass()), m_WriteXMLHeader(writeXMLHeader), m_IndentDepth(0), m_Indent(2)
{
std::string category = "Contour File";
mitk::CustomMimeType customMimeType;
customMimeType.SetCategory(category);
customMimeType.AddExtension("cnt");
this->SetDescription(category);
this->SetMimeType(customMimeType);
RegisterService();
}
mitk::ContourModelWriter::ContourModelWriter(const mitk::ContourModelWriter &other)
: AbstractFileWriter(other), m_IndentDepth(other.m_IndentDepth), m_Indent(other.m_Indent)
{
}
mitk::ContourModelWriter::~ContourModelWriter()
{
}
void mitk::ContourModelWriter::Write()
{
std::ostream *out;
std::ofstream outStream;
if (this->GetOutputStream())
{
out = this->GetOutputStream();
}
else
{
outStream.open(this->GetOutputLocation().c_str());
out = &outStream;
}
if (!out->good())
{
mitkThrow() << "Stream not good.";
}
std::locale previousLocale(out->getloc());
- std::locale I("C");
- out->imbue(I);
+ out->imbue(std::locale::classic());
/*+++++++++++ Here the actual xml writing begins +++++++++*/
/*++++ <?xml version="1.0" encoding="utf-8"?> ++++*/
- WriteXMLHeader(*out);
+ if (m_WriteXMLHeader)
+ WriteXMLHeader(*out);
//
// for each input object write its xml representation to
// the stream
//
mitk::ContourModel::ConstPointer contourModel = dynamic_cast<const mitk::ContourModel *>(this->GetInput());
assert(contourModel.IsNotNull());
WriteXML(contourModel.GetPointer(), *out);
out->imbue(previousLocale);
if (!out->good()) // some error during output
{
throw std::ios_base::failure("Some error during contour writing.");
}
}
mitk::ContourModelWriter *mitk::ContourModelWriter::Clone() const
{
return new ContourModelWriter(*this);
}
void mitk::ContourModelWriter::WriteXML(const mitk::ContourModel *contourModel, std::ostream &out)
{
/*++++ <contourModel> ++++*/
WriteStartElement(XML_CONTOURMODEL, out);
/*++++ <head> ++++*/
WriteStartElement(XML_HEAD, out);
/*++++ <geometryInfo> ++++*/
WriteStartElement(XML_GEOMETRY_INFO, out);
WriteGeometryInformation(contourModel->GetTimeGeometry(), out);
/*++++ </geometryInfo> ++++*/
WriteEndElement(XML_GEOMETRY_INFO, out);
/*++++ </head> ++++*/
WriteEndElement(XML_HEAD, out);
/*++++ <data> ++++*/
WriteStartElement(XML_DATA, out);
unsigned int timecount = contourModel->GetTimeSteps();
for (unsigned int i = 0; i < timecount; i++)
{
/*++++ <timestep> ++++*/
std::vector<std::string> at;
at.push_back("n");
std::vector<std::string> val;
val.push_back(ConvertToString(i));
at.push_back("isClosed");
val.push_back(ConvertToString(contourModel->IsClosed()));
WriteStartElementWithAttribut(XML_TIME_STEP, at, val, out);
/*++++ <controlPoints> ++++*/
WriteStartElement(XML_CONTROL_POINTS, out);
auto it = contourModel->IteratorBegin();
auto end = contourModel->IteratorEnd();
while (it != end)
{
mitk::ContourModel::VertexType *v = *it;
/*++++ <point> ++++*/
std::vector<std::string> attr;
attr.push_back("IsControlPoint");
std::vector<std::string> value;
value.push_back(ConvertToString(v->IsControlPoint));
WriteStartElementWithAttribut(XML_POINT, attr, value, out);
/*++++ <x> ++++*/
WriteStartElement(XML_X, out);
WriteCharacterData(ConvertToString(v->Coordinates[0]).c_str(), out);
/*++++ </x> ++++*/
WriteEndElement(XML_X, out, false);
/*++++ <y> ++++*/
WriteStartElement(XML_Y, out);
WriteCharacterData(ConvertToString(v->Coordinates[1]).c_str(), out);
/*++++ </y> ++++*/
WriteEndElement(XML_Y, out, false);
/*++++ <z> ++++*/
WriteStartElement(XML_Z, out);
WriteCharacterData(ConvertToString(v->Coordinates[2]).c_str(), out);
/*++++ </z> ++++*/
WriteEndElement(XML_Z, out, false);
/*++++ </point> ++++*/
WriteEndElement(XML_POINT, out);
it++;
}
/*++++ </controlPoints> ++++*/
WriteEndElement(XML_CONTROL_POINTS, out);
/*++++ </timestep> ++++*/
WriteEndElement(XML_TIME_STEP, out);
}
/*++++ </data> ++++*/
WriteEndElement(XML_DATA, out);
/*++++ </contourModel> ++++*/
WriteEndElement(XML_CONTOURMODEL, out);
}
void mitk::ContourModelWriter::WriteGeometryInformation(const mitk::TimeGeometry * /*geometry*/, std::ostream &out)
{
WriteCharacterData("<!-- geometry information -->", out);
}
template <typename T>
std::string mitk::ContourModelWriter::ConvertToString(T value)
{
std::ostringstream o;
std::locale I("C");
o.imbue(I);
if (o << value)
{
return o.str();
}
else
return "conversion error";
}
void mitk::ContourModelWriter::WriteXMLHeader(std::ostream &file)
{
file << "<?xml version=\"1.0\" encoding=\"utf-8\"?>";
}
void mitk::ContourModelWriter::WriteStartElement(const char *const tag, std::ostream &file)
{
file << std::endl;
WriteIndent(file);
file << '<' << tag << '>';
m_IndentDepth++;
}
void mitk::ContourModelWriter::WriteStartElementWithAttribut(const char *const tag,
std::vector<std::string> attributes,
std::vector<std::string> values,
std::ostream &file)
{
file << std::endl;
WriteIndent(file);
file << '<' << tag;
unsigned int attributesSize = attributes.size();
unsigned int valuesSize = values.size();
if (attributesSize == valuesSize)
{
auto attributesIt = attributes.begin();
auto end = attributes.end();
auto valuesIt = values.begin();
while (attributesIt != end)
{
file << ' ';
WriteCharacterData(*attributesIt, file);
file << '=' << '"';
WriteCharacterData(*valuesIt, file);
file << '"';
attributesIt++;
valuesIt++;
}
}
file << '>';
m_IndentDepth++;
}
void mitk::ContourModelWriter::WriteEndElement(const char *const tag, std::ostream &file, const bool &indent)
{
m_IndentDepth--;
if (indent)
{
file << std::endl;
WriteIndent(file);
}
file << '<' << '/' << tag << '>';
}
void mitk::ContourModelWriter::WriteCharacterData(const char *const data, std::ostream &file)
{
file << data;
}
void mitk::ContourModelWriter::WriteStartElement(std::string &tag, std::ostream &file)
{
WriteStartElement(tag.c_str(), file);
}
void mitk::ContourModelWriter::WriteEndElement(std::string &tag, std::ostream &file, const bool &indent)
{
WriteEndElement(tag.c_str(), file, indent);
}
void mitk::ContourModelWriter::WriteCharacterData(std::string &data, std::ostream &file)
{
WriteCharacterData(data.c_str(), file);
}
void mitk::ContourModelWriter::WriteIndent(std::ostream &file)
{
std::string spaces(m_IndentDepth * m_Indent, ' ');
file << spaces.c_str();
}
diff --git a/Modules/ContourModel/IO/mitkContourModelWriter.h b/Modules/ContourModel/IO/mitkContourModelWriter.h
index e338c4eee8..3a1b587533 100644
--- a/Modules/ContourModel/IO/mitkContourModelWriter.h
+++ b/Modules/ContourModel/IO/mitkContourModelWriter.h
@@ -1,169 +1,171 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef _MITK_CONTOURMODEL_WRITER__H_
#define _MITK_CONTOURMODEL_WRITER__H_
#include <mitkAbstractFileWriter.h>
#include <mitkContourModel.h>
// DEPRECATED
#include <mitkTimeGeometry.h>
namespace mitk
{
/**
* @brief XML-based writer for mitk::ContourModels
*
* XML-based writer for mitk::ContourModels. Multiple ContourModels can be written in
* a single XML file by simply setting multiple inputs to the filter.
*
* The xml file will look like:
*
* <?xml version="1.0" encoding="utf-8"?>
* <contourModel>
* <head>
* <geometryInfo>
* </geometryInfo>
* </head>
* <data>
* <timestep n="0">
* <controlPoints>
* <point>
* <x></x>
* <y></y>
* <z></z>
* </point>
* </controlPoint>
* </timestep>
* </data>
* </contourModel>
*
* @ingroup MitkContourModelModule
*/
class TimeSlicedGeometry;
class ContourModelWriter : public mitk::AbstractFileWriter
{
public:
- ContourModelWriter();
+ explicit ContourModelWriter(bool writeXMLHeader = true);
~ContourModelWriter() override;
using AbstractFileWriter::Write;
void Write() override;
protected:
ContourModelWriter(const ContourModelWriter &other);
mitk::ContourModelWriter *Clone() const override;
/**
* Converts an arbitrary type to a string. The type has to
* support the << operator. This works fine at least for integral
* data types as float, int, long etc.
* @param value the value to convert
* @returns the string representation of value
*/
template <typename T>
std::string ConvertToString(T value);
/**
* Writes an XML representation of the given point set to
* an outstream. The XML-Header an root node is not included!
* @param contourModel the point set to be converted to xml
* @param out the stream to write to.
*/
void WriteXML(const mitk::ContourModel *contourModel, std::ostream &out);
/**
* Writes the geometry information of the TimeGeometry to an outstream.
* The root tag is not included.
* @param geometry the TimeGeometry of the contour.
* @param out the stream to write to.
*/
void WriteGeometryInformation(const mitk::TimeGeometry *geometry, std::ostream &out);
/**
* Writes the geometry information of the TimeGeometry to an outstream.
* The root tag is not included.
* @param geometry the TimeGeometry of the contour.
* @param out the stream to write to.
*
* \deprecatedSince{2013_09} Please use TimeGeometry instead of TimeSlicedGeometry. For more information see
* http://www.mitk.org/Development/Refactoring%20of%20the%20Geometry%20Classes%20-%20Part%201
*/
DEPRECATED(void WriteGeometryInformation(const mitk::TimeSlicedGeometry *geometry, std::ostream &out));
/**
* Writes an standard xml header to the given stream.
* @param file the stream in which the header is written.
*/
void WriteXMLHeader(std::ostream &file);
/** Write a start element tag */
void WriteStartElement(const char *const tag, std::ostream &file);
void WriteStartElementWithAttribut(const char *const tag,
std::vector<std::string> attributes,
std::vector<std::string> values,
std::ostream &file);
/**
* Write an end element tag
* End-Elements following character data should pass indent = false.
*/
void WriteEndElement(const char *const tag, std::ostream &file, const bool &indent = true);
/** Write character data inside a tag. */
void WriteCharacterData(const char *const data, std::ostream &file);
/** Write a start element tag */
void WriteStartElement(std::string &tag, std::ostream &file);
/** Write an end element tag */
void WriteEndElement(std::string &tag, std::ostream &file, const bool &indent = true);
/** Write character data inside a tag. */
void WriteCharacterData(std::string &data, std::ostream &file);
/** Writes empty spaces to the stream according to m_IndentDepth and m_Indent */
void WriteIndent(std::ostream &file);
+ bool m_WriteXMLHeader;
+
unsigned int m_IndentDepth;
unsigned int m_Indent;
public:
static const char *XML_CONTOURMODEL;
static const char *XML_HEAD;
static const char *XML_GEOMETRY_INFO;
static const char *XML_DATA;
static const char *XML_TIME_STEP;
static const char *XML_CONTROL_POINTS;
static const char *XML_POINT;
static const char *XML_X;
static const char *XML_Y;
static const char *XML_Z;
};
}
#endif
diff --git a/Modules/Core/CMakeLists.txt b/Modules/Core/CMakeLists.txt
index 40e19fd8b4..b38af61df6 100644
--- a/Modules/Core/CMakeLists.txt
+++ b/Modules/Core/CMakeLists.txt
@@ -1,65 +1,77 @@
-
set(TOOL_CPPS "")
# temporary suppress warnings in the following files until image accessors are fully integrated.
set_source_files_properties( src/DataManagement/mitkImage.cpp COMPILE_FLAGS -DMITK_NO_DEPRECATED_WARNINGS )
set_source_files_properties( src/Controllers/mitkSliceNavigationController.cpp COMPILE_FLAGS -DMITK_NO_DEPRECATED_WARNINGS )
-MITK_CREATE_MODULE(
+#if(MSVC)
+# set(optional_private_package_depends psapi)
+#endif()
+
+mitk_create_module(
INCLUDE_DIRS
- PUBLIC ${MITK_BINARY_DIR}
- PRIVATE src/Algorithms src/Controllers src/DataManagement src/Interactions src/IO src/Rendering ${OPENGL_INCLUDE_DIR}
- DEPENDS PUBLIC mbilog CppMicroServices
+ PUBLIC
+ ${MITK_BINARY_DIR}
+ PRIVATE
+ src/Algorithms
+ src/Controllers
+ src/DataManagement
+ src/Interactions
+ src/IO
+ src/Rendering
+ DEPENDS
+ PUBLIC
+ mbilog
+ CppMicroServices
PACKAGE_DEPENDS
- PRIVATE tinyxml OpenGL
- PUBLIC ITK|ITKTransform+ITKImageGrid+ITKImageFeature+ITKIOImageBase+ITKIOHDF5+ITKIOLSM+ITKIOMRC+ITKIOBioRad+ITKIOGE+ITKIOStimulate+ITKIOBruker+ITKIOMINC
- # We privately use/link all ITK modules in order to support all IO, Transform, etc.
- # factories from ITK which are registered "automatically" via a factory manager.
- PRIVATE ITK
- PUBLIC VTK|FiltersTexture+FiltersParallel+ImagingStencil+ImagingMath+InteractionStyle+RenderingOpenGL2+RenderingVolumeOpenGL2+RenderingFreeType+RenderingLabel+InteractionWidgets+IOGeometry+IOXML
- PUBLIC Boost|boost
+ PUBLIC
+ Boost
+ ITK|IOImageBase+SpatialObjects+Statistics
+ #ITK|Statistics+Transform
+ VTK|FiltersTexture+FiltersParallel+ImagingStencil+ImagingMath+InteractionStyle+RenderingOpenGL2+RenderingVolumeOpenGL2+RenderingFreeType+RenderingLabel+InteractionWidgets+IOGeometry+IOXML
+ PRIVATE
+ ITK|IOBioRad+IOBMP+IOBruker+IOCSV+IOGDCM+IOGE+IOGIPL+IOHDF5+IOIPL+IOJPEG+IOLSM+IOMesh+IOMeta+IOMINC+IOMRC+IONIFTI+IONRRD+IOPNG+IOSiemens+IOSpatialObjects+IOStimulate+IOTIFF+IOTransformBase+IOTransformHDF5+IOTransformInsightLegacy+IOTransformMatlab+IOVTK+IOXML
+ tinyxml2
+ ${optional_private_package_depends}
# Do not automatically create CppMicroServices initialization code.
- # Because the VTK 6 "auto-init" functionality injects file-local static
+ # Because the VTK "auto-init" functionality injects file-local static
# initialization code in every cpp file which includes a VTK header,
# static initialization order becomes an issue again. For the Mitk
# core library, we need to ensure that the VTK static initialization stuff
# happens before the CppMicroServices initialization, since the latter
# might already use VTK code which needs to access VTK object factories.
# Hence, CppMicroServices initialization code is placed manually within
# the mitkCoreActivator.cpp file.
NO_INIT
)
if(NOT TARGET ${MODULE_TARGET})
message(SEND_ERROR "Core target ${MODULE_TARGET} does not exist")
endif()
+
function(_itk_create_factory_register_manager)
# In MITK_ITK_Config.cmake, we do *not* include ITK_USE_FILE, which
# prevents multiple registrations/unregistrations of ITK IO factories
# during library loading/unloading (of MITK libraries). However, we need
# "one" place where the IO factories are registered at
# least once. This could be the application executable, but every executable would
# need to take care of that itself. Instead, we allow the auto registration in the
# Mitk Core library.
set(NO_DIRECTORY_SCOPED_ITK_COMPILE_DEFINITION 1)
find_package(ITK)
include(${ITK_USE_FILE})
if(NOT ITK_NO_IO_FACTORY_REGISTER_MANAGER)
# We manually add the define which will be of target scope. MITK
# patches ITK_USE_FILE to remove the directory scoped compile
# definition since it would be propagated to other targets in the
# same directory scope but these targets might want to *not*
# use the ITK factory manager stuff.
target_compile_definitions(${MODULE_TARGET} PRIVATE ITK_IO_FACTORY_REGISTER_MANAGER)
endif()
endfunction()
_itk_create_factory_register_manager()
-if(MSVC_IDE OR MSVC_VERSION)
- target_link_libraries(${MODULE_TARGET} PRIVATE psapi.lib)
-endif()
-
if(BUILD_TESTING)
add_subdirectory(TestingHelper)
add_subdirectory(test)
endif()
diff --git a/Modules/Core/TestingHelper/CMakeLists.txt b/Modules/Core/TestingHelper/CMakeLists.txt
index c1d32c6cfd..ba38e5b698 100644
--- a/Modules/Core/TestingHelper/CMakeLists.txt
+++ b/Modules/Core/TestingHelper/CMakeLists.txt
@@ -1,7 +1,6 @@
mitk_create_module(
DEPENDS PUBLIC MitkCore
PACKAGE_DEPENDS
- PUBLIC CppUnit
- PRIVATE VTK|IOImage+TestingRendering tinyxml OpenGL
+ PUBLIC CppUnit tinyxml2
+ PRIVATE VTK|IOImage+TestingRendering
)
-
diff --git a/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp b/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp
index dea87c3ef7..92578ca3cf 100644
--- a/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp
+++ b/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp
@@ -1,432 +1,429 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include <mitkIOUtil.h>
#include <mitkInteractionEventConst.h>
#include <mitkInteractionTestHelper.h>
#include <mitkPlaneGeometryDataMapper2D.h>
#include <mitkStandaloneDataStorage.h>
// VTK
#include <vtkCamera.h>
#include <vtkRenderWindowInteractor.h>
// us
#include <usGetModuleContext.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
mitk::InteractionTestHelper::InteractionTestHelper(const std::string &interactionXmlFilePath)
: m_InteractionFilePath(interactionXmlFilePath)
{
this->Initialize(interactionXmlFilePath);
}
void mitk::InteractionTestHelper::Initialize(const std::string &interactionXmlFilePath)
{
- // TiXmlDocument document(interactionXmlPath.c_str());
- TiXmlDocument document(interactionXmlFilePath);
- bool loadOkay = document.LoadFile();
- if (loadOkay)
+ tinyxml2::XMLDocument document;
+ if (tinyxml2::XML_SUCCESS == document.LoadFile(interactionXmlFilePath.c_str()))
{
// get RenderingManager instance
auto rm = mitk::RenderingManager::GetInstance();
// create data storage
m_DataStorage = mitk::StandaloneDataStorage::New();
// for each renderer found create a render window and configure
- for (TiXmlElement *element = document.FirstChildElement(mitk::InteractionEventConst::xmlTagInteractions())
- ->FirstChildElement(mitk::InteractionEventConst::xmlTagConfigRoot())
- ->FirstChildElement(mitk::InteractionEventConst::xmlTagRenderer());
+ for (auto *element = document.FirstChildElement(mitk::InteractionEventConst::xmlTagInteractions().c_str())
+ ->FirstChildElement(mitk::InteractionEventConst::xmlTagConfigRoot().c_str())
+ ->FirstChildElement(mitk::InteractionEventConst::xmlTagRenderer().c_str());
element != nullptr;
- element = element->NextSiblingElement(mitk::InteractionEventConst::xmlTagRenderer()))
+ element = element->NextSiblingElement(mitk::InteractionEventConst::xmlTagRenderer().c_str()))
{
// get name of renderer
const char *rendererName =
element->Attribute(mitk::InteractionEventConst::xmlEventPropertyRendererName().c_str());
// get view direction
mitk::SliceNavigationController::ViewDirection viewDirection = mitk::SliceNavigationController::Axial;
- if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyViewDirection()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyViewDirection().c_str()) != nullptr)
{
int viewDirectionNum =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyViewDirection())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyViewDirection().c_str()));
viewDirection = static_cast<mitk::SliceNavigationController::ViewDirection>(viewDirectionNum);
}
// get mapper slot id
mitk::BaseRenderer::MapperSlotId mapperID = mitk::BaseRenderer::Standard2D;
- if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str()) != nullptr)
{
int mapperIDNum =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str()));
mapperID = static_cast<mitk::BaseRenderer::MapperSlotId>(mapperIDNum);
}
// Get Size of Render Windows
int size[3];
size[0] = size[1] = size[2] = 0;
- if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeX()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeX().c_str()) != nullptr)
{
- size[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeX())->c_str());
+ size[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeX().c_str()));
}
- if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeY()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeY().c_str()) != nullptr)
{
- size[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeY())->c_str());
+ size[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeY().c_str()));
}
- if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeZ()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeZ().c_str()) != nullptr)
{
- size[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeZ())->c_str());
+ size[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeZ().c_str()));
}
// create renderWindow, renderer and dispatcher
auto rw = RenderWindow::New(nullptr, rendererName); // VtkRenderWindow is created within constructor if nullptr
if (size[0] != 0 && size[1] != 0)
{
rw->SetSize(size[0], size[1]);
rw->GetRenderer()->Resize(size[0], size[1]);
}
// set storage of renderer
rw->GetRenderer()->SetDataStorage(m_DataStorage);
// set view direction to axial
rw->GetSliceNavigationController()->SetDefaultViewDirection(viewDirection);
// set renderer to render 2D
rw->GetRenderer()->SetMapperID(mapperID);
rw->GetRenderer()->PrepareRender();
// Some more magic for the 3D render window case:
// Camera view direction, position and focal point
if (mapperID == mitk::BaseRenderer::Standard3D)
{
- if (element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str()) != nullptr)
{
double cameraFocalPoint[3];
cameraFocalPoint[0] =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str()));
cameraFocalPoint[1] =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointY())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointY().c_str()));
cameraFocalPoint[2] =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointZ())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointZ().c_str()));
rw->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetFocalPoint(cameraFocalPoint);
}
- if (element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str()) != nullptr)
{
double cameraPosition[3];
- cameraPosition[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX())->c_str());
- cameraPosition[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionY())->c_str());
- cameraPosition[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionZ())->c_str());
+ cameraPosition[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str()));
+ cameraPosition[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionY().c_str()));
+ cameraPosition[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionZ().c_str()));
rw->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetPosition(cameraPosition);
}
- if (element->Attribute(mitk::InteractionEventConst::xmlViewUpX()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str()) != nullptr)
{
double viewUp[3];
- viewUp[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpX())->c_str());
- viewUp[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpY())->c_str());
- viewUp[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpZ())->c_str());
+ viewUp[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str()));
+ viewUp[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpY().c_str()));
+ viewUp[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpZ().c_str()));
rw->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetViewUp(viewUp);
}
}
rw->GetVtkRenderWindow()->Render();
rw->GetVtkRenderWindow()->WaitForCompletion();
// connect SliceNavigationControllers to timestep changed event of TimeNavigationController
rw->GetSliceNavigationController()->ConnectGeometryTimeEvent(rm->GetTimeNavigationController(), false);
rm->GetTimeNavigationController()->ConnectGeometryTimeEvent(rw->GetSliceNavigationController(), false);
// add to list of kown render windows
m_RenderWindowList.push_back(rw);
}
// TODO: check the following lines taken from QmitkStdMultiWidget and adapt them to be executed in our code here.
// mitkWidget1->GetSliceNavigationController()
// ->ConnectGeometrySendEvent(mitk::BaseRenderer::GetInstance(mitkWidget4->GetRenderWindow()));
//########### register display interactor to handle scroll events ##################
// use MouseModeSwitcher to ensure that the statemachine of DisplayInteractor is loaded correctly
m_MouseModeSwitcher = mitk::MouseModeSwitcher::New();
}
else
{
mitkThrow() << "Can not load interaction xml file <" << m_InteractionFilePath << ">";
}
// WARNING assumes a 3D window exists !!!!
this->AddDisplayPlaneSubTree();
}
mitk::InteractionTestHelper::~InteractionTestHelper()
{
mitk::RenderingManager *rm = mitk::RenderingManager::GetInstance();
// unregister renderers
auto it = m_RenderWindowList.begin();
auto end = m_RenderWindowList.end();
for (; it != end; ++it)
{
rm->GetTimeNavigationController()->Disconnect((*it)->GetSliceNavigationController());
(*it)->GetSliceNavigationController()->Disconnect(rm->GetTimeNavigationController());
mitk::BaseRenderer::RemoveInstance((*it)->GetVtkRenderWindow());
}
rm->RemoveAllObservers();
}
mitk::DataStorage::Pointer mitk::InteractionTestHelper::GetDataStorage()
{
return m_DataStorage;
}
void mitk::InteractionTestHelper::AddNodeToStorage(mitk::DataNode::Pointer node)
{
this->m_DataStorage->Add(node);
this->Set3dCameraSettings();
}
void mitk::InteractionTestHelper::PlaybackInteraction()
{
mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage);
// load events if not loaded yet
if (m_Events.empty())
this->LoadInteraction();
auto it = m_RenderWindowList.begin();
auto end = m_RenderWindowList.end();
for (; it != end; ++it)
{
(*it)->GetRenderer()->PrepareRender();
(*it)->GetVtkRenderWindow()->Render();
(*it)->GetVtkRenderWindow()->WaitForCompletion();
}
mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage);
it = m_RenderWindowList.begin();
for (; it != end; ++it)
{
(*it)->GetVtkRenderWindow()->Render();
(*it)->GetVtkRenderWindow()->WaitForCompletion();
}
// mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll();
// playback all events in queue
for (unsigned long i = 0; i < m_Events.size(); ++i)
{
// let dispatcher of sending renderer process the event
m_Events.at(i)->GetSender()->GetDispatcher()->ProcessEvent(m_Events.at(i));
}
if (false)
{
it--;
(*it)->GetVtkRenderWindow()->GetInteractor()->Start();
}
}
void mitk::InteractionTestHelper::LoadInteraction()
{
// load interaction pattern from xml file
std::ifstream xmlStream(m_InteractionFilePath.c_str());
mitk::XML2EventParser parser(xmlStream);
m_Events = parser.GetInteractions();
xmlStream.close();
// Avoid VTK warning: Trying to delete object with non-zero reference count.
parser.SetReferenceCount(0);
}
void mitk::InteractionTestHelper::SetTimeStep(int newTimeStep)
{
mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage);
bool timeStepIsvalid =
mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetCreatedWorldGeometry()->IsValidTimeStep(
newTimeStep);
if (timeStepIsvalid)
{
mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->SetPos(newTimeStep);
}
}
mitk::RenderWindow *mitk::InteractionTestHelper::GetRenderWindowByName(const std::string &name)
{
auto it = m_RenderWindowList.begin();
auto end = m_RenderWindowList.end();
for (; it != end; ++it)
{
if (name.compare((*it)->GetRenderer()->GetName()) == 0)
return (*it).GetPointer();
}
return nullptr;
}
mitk::RenderWindow *mitk::InteractionTestHelper::GetRenderWindowByDefaultViewDirection(
mitk::SliceNavigationController::ViewDirection viewDirection)
{
auto it = m_RenderWindowList.begin();
auto end = m_RenderWindowList.end();
for (; it != end; ++it)
{
if (viewDirection == (*it)->GetSliceNavigationController()->GetDefaultViewDirection())
return (*it).GetPointer();
}
return nullptr;
}
mitk::RenderWindow *mitk::InteractionTestHelper::GetRenderWindow(unsigned int index)
{
if (index < m_RenderWindowList.size())
{
return m_RenderWindowList.at(index).GetPointer();
}
else
{
return nullptr;
}
}
void mitk::InteractionTestHelper::AddDisplayPlaneSubTree()
{
// add the displayed planes of the multiwidget to a node to which the subtree
// @a planesSubTree points ...
mitk::PlaneGeometryDataMapper2D::Pointer mapper;
mitk::IntProperty::Pointer layer = mitk::IntProperty::New(1000);
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetProperty("name", mitk::StringProperty::New("Widgets"));
node->SetProperty("helper object", mitk::BoolProperty::New(true));
m_DataStorage->Add(node);
for (auto it : m_RenderWindowList)
{
if (it->GetRenderer()->GetMapperID() == BaseRenderer::Standard3D)
continue;
// ... of widget 1
mitk::DataNode::Pointer planeNode1 =
(mitk::BaseRenderer::GetInstance(it->GetVtkRenderWindow()))->GetCurrentWorldPlaneGeometryNode();
planeNode1->SetProperty("visible", mitk::BoolProperty::New(true));
planeNode1->SetProperty("name", mitk::StringProperty::New("widget1Plane"));
planeNode1->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false));
planeNode1->SetProperty("helper object", mitk::BoolProperty::New(true));
planeNode1->SetProperty("layer", layer);
planeNode1->SetColor(1.0, 0.0, 0.0);
mapper = mitk::PlaneGeometryDataMapper2D::New();
planeNode1->SetMapper(mitk::BaseRenderer::Standard2D, mapper);
m_DataStorage->Add(planeNode1, node);
}
}
void mitk::InteractionTestHelper::Set3dCameraSettings()
{
- TiXmlDocument document(m_InteractionFilePath);
- bool loadOkay = document.LoadFile();
- if (loadOkay)
+ tinyxml2::XMLDocument document;
+ if (tinyxml2::XML_SUCCESS == document.LoadFile(m_InteractionFilePath.c_str()))
{
// for each renderer found create a render window and configure
- for (TiXmlElement *element = document.FirstChildElement(mitk::InteractionEventConst::xmlTagInteractions())
- ->FirstChildElement(mitk::InteractionEventConst::xmlTagConfigRoot())
- ->FirstChildElement(mitk::InteractionEventConst::xmlTagRenderer());
+ for (auto *element = document.FirstChildElement(mitk::InteractionEventConst::xmlTagInteractions().c_str())
+ ->FirstChildElement(mitk::InteractionEventConst::xmlTagConfigRoot().c_str())
+ ->FirstChildElement(mitk::InteractionEventConst::xmlTagRenderer().c_str());
element != nullptr;
- element = element->NextSiblingElement(mitk::InteractionEventConst::xmlTagRenderer()))
+ element = element->NextSiblingElement(mitk::InteractionEventConst::xmlTagRenderer().c_str()))
{
// get name of renderer
const char *rendererName =
element->Attribute(mitk::InteractionEventConst::xmlEventPropertyRendererName().c_str());
// get mapper slot id
mitk::BaseRenderer::MapperSlotId mapperID = mitk::BaseRenderer::Standard2D;
- if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str()) != nullptr)
{
int mapperIDNum =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str()));
mapperID = static_cast<mitk::BaseRenderer::MapperSlotId>(mapperIDNum);
}
if (mapperID == mitk::BaseRenderer::Standard3D)
{
RenderWindow *namedRenderer = nullptr;
for (auto it : m_RenderWindowList)
{
if (strcmp(it->GetRenderer()->GetName(), rendererName) == 0)
{
namedRenderer = it.GetPointer();
break;
}
}
if (namedRenderer == nullptr)
{
MITK_ERROR << "No match for render window was found.";
return;
}
namedRenderer->GetRenderer()->PrepareRender();
- if (element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str()) != nullptr)
{
double cameraFocalPoint[3];
cameraFocalPoint[0] =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str()));
cameraFocalPoint[1] =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointY())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointY().c_str()));
cameraFocalPoint[2] =
- std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointZ())->c_str());
+ std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointZ().c_str()));
namedRenderer->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetFocalPoint(cameraFocalPoint);
}
- if (element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str()) != nullptr)
{
double cameraPosition[3];
- cameraPosition[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX())->c_str());
- cameraPosition[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionY())->c_str());
- cameraPosition[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionZ())->c_str());
+ cameraPosition[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str()));
+ cameraPosition[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionY().c_str()));
+ cameraPosition[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionZ().c_str()));
namedRenderer->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetPosition(cameraPosition);
}
- if (element->Attribute(mitk::InteractionEventConst::xmlViewUpX()) != nullptr)
+ if (element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str()) != nullptr)
{
double viewUp[3];
- viewUp[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpX())->c_str());
- viewUp[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpY())->c_str());
- viewUp[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpZ())->c_str());
+ viewUp[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str()));
+ viewUp[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpY().c_str()));
+ viewUp[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpZ().c_str()));
namedRenderer->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetViewUp(viewUp);
}
namedRenderer->GetVtkRenderWindow()->Render();
}
}
}
}
diff --git a/Modules/Core/include/mitkGeometryDataReaderService.h b/Modules/Core/include/mitkGeometryDataReaderService.h
index 1c7f8e23cb..aa95947ed4 100644
--- a/Modules/Core/include/mitkGeometryDataReaderService.h
+++ b/Modules/Core/include/mitkGeometryDataReaderService.h
@@ -1,61 +1,59 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkGeometryDataReaderService_h
#define mitkGeometryDataReaderService_h
// MITK
#include <mitkAbstractFileReader.h>
#include <mitkGeometryData.h>
-class TiXmlElement;
-
namespace mitk
{
/**
* @internal
*
* @brief reads XML representations of mitk::GeometryData from a file/stream.
*
* To be used via IOUtil.
*
* Reader for XML files containing one or multiple XML represenations of
* mitk::GeometryData. If multiple mitk::GeometryData objects are stored in one file,
* these are assigned to multiple BaseData objects.
*
* @sa Geometry3DToXML
*
* @ingroup IO
*/
class GeometryDataReaderService : public AbstractFileReader
{
public:
GeometryDataReaderService();
~GeometryDataReaderService() override;
using AbstractFileReader::Read;
/**
* @brief Provides the MIME type for reader and writer.
*/
static CustomMimeType GEOMETRY_DATA_MIMETYPE();
protected:
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
private:
GeometryDataReaderService(const GeometryDataReaderService &other);
GeometryDataReaderService *Clone() const override;
};
}
#endif
diff --git a/Modules/Core/include/mitkGeometryDataWriterService.h b/Modules/Core/include/mitkGeometryDataWriterService.h
index 6544cd8f4e..6de0ddabd4 100644
--- a/Modules/Core/include/mitkGeometryDataWriterService.h
+++ b/Modules/Core/include/mitkGeometryDataWriterService.h
@@ -1,55 +1,52 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkGeometryDataWriterService_h
#define mitkGeometryDataWriterService_h
#include <mitkAbstractFileWriter.h>
#include <mitkGeometryData.h>
-// forward
-class TiXmlNode;
-
namespace mitk
{
// forward
class Geometry3D;
/**
* @internal
*
* @brief XML-based writer for mitk::GeometryData
*
* XML-based writer for mitk::GeometryData. Multiple GeometryData instances
* can be written in a single XML file by simply setting multiple inputs to the filter.
*
* @sa Geometry3DToXML
*
* @ingroup IO
*/
class GeometryDataWriterService : public AbstractFileWriter
{
public:
GeometryDataWriterService();
~GeometryDataWriterService() override;
using AbstractFileWriter::Write;
void Write() override;
private:
GeometryDataWriterService(const GeometryDataWriterService &other);
mitk::GeometryDataWriterService *Clone() const override;
};
}
#endif
diff --git a/Modules/Core/include/mitkPlaneOrientationProperty.h b/Modules/Core/include/mitkPlaneOrientationProperty.h
index 54798b7f00..3d97490348 100644
--- a/Modules/Core/include/mitkPlaneOrientationProperty.h
+++ b/Modules/Core/include/mitkPlaneOrientationProperty.h
@@ -1,122 +1,122 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITK_PLANE_DECORATION_PROPERTY__H
#define MITK_PLANE_DECORATION_PROPERTY__H
#include "mitkEnumerationProperty.h"
namespace mitk
{
#ifdef _MSC_VER
#pragma warning(push)
#pragma warning(disable : 4522)
#endif
/**
* Property which controls whether 2D line representation of a PlaneGeometry
* should have small arrows at both ends to indicate the orientation of
* the plane, and whether the arrows should be oriented in the direction of
* the plane's normal or against it.
*
* Valid values of the enumeration property are
* - PLANE_DECORATION_NONE (no arrows)
* - PLANE_DECORATION_POSITIVE_ORIENTATION (arrows pointing upwards)
* - PLANE_DECORATION_NEGATIVE_ORIENTATION (arrows pointing downwards)
*
* See also mitk::PlaneGeometryDataMapper2D::DrawOrientationArrow()
*/
class MITKCORE_EXPORT PlaneOrientationProperty : public EnumerationProperty
{
public:
mitkClassMacro(PlaneOrientationProperty, EnumerationProperty);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- mitkNewMacro1Param(PlaneOrientationProperty, const IdType &);
+ mitkNewMacro1Param(PlaneOrientationProperty, const IdType &);
mitkNewMacro1Param(PlaneOrientationProperty, const std::string &);
enum
{
PLANE_DECORATION_NONE,
PLANE_DECORATION_POSITIVE_ORIENTATION,
PLANE_DECORATION_NEGATIVE_ORIENTATION
};
/**
* Returns the state of plane decoration.
*/
virtual int GetPlaneDecoration();
/**
* Sets the decoration type to no decoration.
*/
virtual void SetPlaneDecorationToNone();
/**
* Sets the decoration type to arrows in positive plane direction.
*/
virtual void SetPlaneDecorationToPositiveOrientation();
/**
* Sets the decoration type to arrows in negative plane direction.
*/
virtual void SetPlaneDecorationToNegativeOrientation();
using BaseProperty::operator=;
protected:
/**
* Constructor. Sets the decoration type to none.
*/
PlaneOrientationProperty();
/**
* Constructor. Sets the decoration type to the given value. If it is not
* valid, the interpolation is set to none
*/
PlaneOrientationProperty(const IdType &value);
/**
* Constructor. Sets the decoration type to the given value. If it is not
* valid, the representation is set to none
*/
PlaneOrientationProperty(const std::string &value);
/**
* this function is overridden as protected, so that the user may not add
* additional invalid types.
*/
bool AddEnum(const std::string &name, const IdType &id) override;
/**
* Adds the standard enumeration types with corresponding strings.
*/
virtual void AddDecorationTypes();
private:
// purposely not implemented
PlaneOrientationProperty &operator=(const PlaneOrientationProperty &);
itk::LightObject::Pointer InternalClone() const override;
};
#ifdef _MSC_VER
#pragma warning(pop)
#endif
} // end of namespace mitk
#endif
diff --git a/Modules/Core/src/IO/mitkGeometry3DToXML.cpp b/Modules/Core/src/IO/mitkGeometry3DToXML.cpp
index c611eac6c7..e9ee434cf7 100644
--- a/Modules/Core/src/IO/mitkGeometry3DToXML.cpp
+++ b/Modules/Core/src/IO/mitkGeometry3DToXML.cpp
@@ -1,236 +1,242 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkGeometry3DToXML.h"
#include <mitkLexicalCast.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
-TiXmlElement *mitk::Geometry3DToXML::ToXML(const Geometry3D *geom3D)
+#include <array>
+
+tinyxml2::XMLElement *mitk::Geometry3DToXML::ToXML(tinyxml2::XMLDocument& doc, const Geometry3D *geom3D)
{
assert(geom3D);
// really serialize
const AffineTransform3D *transform = geom3D->GetIndexToWorldTransform();
// get transform parameters that would need to be serialized
AffineTransform3D::MatrixType matrix = transform->GetMatrix();
AffineTransform3D::OffsetType offset = transform->GetOffset();
bool isImageGeometry = geom3D->GetImageGeometry();
BaseGeometry::BoundsArrayType bounds = geom3D->GetBounds();
// create XML file
// construct XML tree describing the geometry
- auto *geomElem = new TiXmlElement("Geometry3D");
- geomElem->SetAttribute("ImageGeometry", isImageGeometry ? "true" : "false");
+ auto *geomElem = doc.NewElement("Geometry3D");
+ geomElem->SetAttribute("ImageGeometry", isImageGeometry);
geomElem->SetAttribute("FrameOfReferenceID", geom3D->GetFrameOfReferenceID());
// coefficients are matrix[row][column]!
- auto *matrixElem = new TiXmlElement("IndexToWorld");
+ auto *matrixElem = doc.NewElement("IndexToWorld");
matrixElem->SetAttribute("type", "Matrix3x3");
- matrixElem->SetAttribute("m_0_0", boost::lexical_cast<std::string>(matrix[0][0]));
- matrixElem->SetAttribute("m_0_1", boost::lexical_cast<std::string>(matrix[0][1]));
- matrixElem->SetAttribute("m_0_2", boost::lexical_cast<std::string>(matrix[0][2]));
- matrixElem->SetAttribute("m_1_0", boost::lexical_cast<std::string>(matrix[1][0]));
- matrixElem->SetAttribute("m_1_1", boost::lexical_cast<std::string>(matrix[1][1]));
- matrixElem->SetAttribute("m_1_2", boost::lexical_cast<std::string>(matrix[1][2]));
- matrixElem->SetAttribute("m_2_0", boost::lexical_cast<std::string>(matrix[2][0]));
- matrixElem->SetAttribute("m_2_1", boost::lexical_cast<std::string>(matrix[2][1]));
- matrixElem->SetAttribute("m_2_2", boost::lexical_cast<std::string>(matrix[2][2]));
- geomElem->LinkEndChild(matrixElem);
-
- auto *offsetElem = new TiXmlElement("Offset");
+ matrixElem->SetAttribute("m_0_0", boost::lexical_cast<std::string>(matrix[0][0]).c_str());
+ matrixElem->SetAttribute("m_0_1", boost::lexical_cast<std::string>(matrix[0][1]).c_str());
+ matrixElem->SetAttribute("m_0_2", boost::lexical_cast<std::string>(matrix[0][2]).c_str());
+ matrixElem->SetAttribute("m_1_0", boost::lexical_cast<std::string>(matrix[1][0]).c_str());
+ matrixElem->SetAttribute("m_1_1", boost::lexical_cast<std::string>(matrix[1][1]).c_str());
+ matrixElem->SetAttribute("m_1_2", boost::lexical_cast<std::string>(matrix[1][2]).c_str());
+ matrixElem->SetAttribute("m_2_0", boost::lexical_cast<std::string>(matrix[2][0]).c_str());
+ matrixElem->SetAttribute("m_2_1", boost::lexical_cast<std::string>(matrix[2][1]).c_str());
+ matrixElem->SetAttribute("m_2_2", boost::lexical_cast<std::string>(matrix[2][2]).c_str());
+ geomElem->InsertEndChild(matrixElem);
+
+ auto *offsetElem = doc.NewElement("Offset");
offsetElem->SetAttribute("type", "Vector3D");
- offsetElem->SetAttribute("x", boost::lexical_cast<std::string>(offset[0]));
- offsetElem->SetAttribute("y", boost::lexical_cast<std::string>(offset[1]));
- offsetElem->SetAttribute("z", boost::lexical_cast<std::string>(offset[2]));
- geomElem->LinkEndChild(offsetElem);
+ offsetElem->SetAttribute("x", boost::lexical_cast<std::string>(offset[0]).c_str());
+ offsetElem->SetAttribute("y", boost::lexical_cast<std::string>(offset[1]).c_str());
+ offsetElem->SetAttribute("z", boost::lexical_cast<std::string>(offset[2]).c_str());
+ geomElem->InsertEndChild(offsetElem);
- auto *boundsElem = new TiXmlElement("Bounds");
- auto *boundsMinElem = new TiXmlElement("Min");
+ auto *boundsElem = doc.NewElement("Bounds");
+ auto *boundsMinElem = doc.NewElement("Min");
boundsMinElem->SetAttribute("type", "Vector3D");
- boundsMinElem->SetAttribute("x", boost::lexical_cast<std::string>(bounds[0]));
- boundsMinElem->SetAttribute("y", boost::lexical_cast<std::string>(bounds[2]));
- boundsMinElem->SetAttribute("z", boost::lexical_cast<std::string>(bounds[4]));
- boundsElem->LinkEndChild(boundsMinElem);
- auto *boundsMaxElem = new TiXmlElement("Max");
+ boundsMinElem->SetAttribute("x", boost::lexical_cast<std::string>(bounds[0]).c_str());
+ boundsMinElem->SetAttribute("y", boost::lexical_cast<std::string>(bounds[2]).c_str());
+ boundsMinElem->SetAttribute("z", boost::lexical_cast<std::string>(bounds[4]).c_str());
+ boundsElem->InsertEndChild(boundsMinElem);
+ auto *boundsMaxElem = doc.NewElement("Max");
boundsMaxElem->SetAttribute("type", "Vector3D");
- boundsMaxElem->SetAttribute("x", boost::lexical_cast<std::string>(bounds[1]));
- boundsMaxElem->SetAttribute("y", boost::lexical_cast<std::string>(bounds[3]));
- boundsMaxElem->SetAttribute("z", boost::lexical_cast<std::string>(bounds[5]));
- boundsElem->LinkEndChild(boundsMaxElem);
- geomElem->LinkEndChild(boundsElem);
+ boundsMaxElem->SetAttribute("x", boost::lexical_cast<std::string>(bounds[1]).c_str());
+ boundsMaxElem->SetAttribute("y", boost::lexical_cast<std::string>(bounds[3]).c_str());
+ boundsMaxElem->SetAttribute("z", boost::lexical_cast<std::string>(bounds[5]).c_str());
+ boundsElem->InsertEndChild(boundsMaxElem);
+ geomElem->InsertEndChild(boundsElem);
return geomElem;
}
-mitk::Geometry3D::Pointer mitk::Geometry3DToXML::FromXML(TiXmlElement *geometryElement)
+mitk::Geometry3D::Pointer mitk::Geometry3DToXML::FromXML(const tinyxml2::XMLElement *geometryElement)
{
if (!geometryElement)
{
MITK_ERROR << "Cannot deserialize Geometry3D from nullptr.";
return nullptr;
}
AffineTransform3D::MatrixType matrix;
AffineTransform3D::OffsetType offset;
bool isImageGeometry(false);
unsigned int frameOfReferenceID(0);
BaseGeometry::BoundsArrayType bounds;
- if (TIXML_SUCCESS != geometryElement->QueryUnsignedAttribute("FrameOfReferenceID", &frameOfReferenceID))
+ if (tinyxml2::XML_SUCCESS != geometryElement->QueryUnsignedAttribute("FrameOfReferenceID", &frameOfReferenceID))
{
MITK_WARN << "Missing FrameOfReference for Geometry3D.";
}
- if (TIXML_SUCCESS != geometryElement->QueryBoolAttribute("ImageGeometry", &isImageGeometry))
+ if (tinyxml2::XML_SUCCESS != geometryElement->QueryBoolAttribute("ImageGeometry", &isImageGeometry))
{
MITK_WARN << "Missing bool ImageGeometry for Geometry3D.";
}
// matrix
- if (TiXmlElement *matrixElem = geometryElement->FirstChildElement("IndexToWorld")->ToElement())
+ if (auto *matrixElem = geometryElement->FirstChildElement("IndexToWorld"))
{
bool matrixComplete = true;
for (unsigned int r = 0; r < 3; ++r)
{
for (unsigned int c = 0; c < 3; ++c)
{
std::stringstream element_namer;
element_namer << "m_" << r << "_" << c;
- std::string string_value;
- if (TIXML_SUCCESS == matrixElem->QueryStringAttribute(element_namer.str().c_str(), &string_value))
+ const char* string_value = matrixElem->Attribute(element_namer.str().c_str());
+ if (nullptr != string_value)
{
try
{
matrix[r][c] = boost::lexical_cast<double>(string_value);
}
catch ( const boost::bad_lexical_cast &e )
{
MITK_ERROR << "Could not parse '" << string_value << "' as number: " << e.what();
return nullptr;
}
}
else
{
matrixComplete = false;
}
}
}
if (!matrixComplete)
{
MITK_ERROR << "Could not parse all Geometry3D matrix coefficients!";
return nullptr;
}
}
else
{
MITK_ERROR << "Parse error: expected Matrix3x3 child below Geometry3D node";
return nullptr;
}
// offset
- if (TiXmlElement *offsetElem = geometryElement->FirstChildElement("Offset")->ToElement())
+ if (auto *offsetElem = geometryElement->FirstChildElement("Offset"))
{
- bool vectorComplete = true;
- std::string offset_string[3];
- vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("x", &offset_string[0]);
- vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("y", &offset_string[1]);
- vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("z", &offset_string[2]);
+ std::array<const char*, 3> offset_string = {
+ offsetElem->Attribute("x"),
+ offsetElem->Attribute("y"),
+ offsetElem->Attribute("z")
+ };
- if (!vectorComplete)
+ if (nullptr == offset_string[0] || nullptr == offset_string[1] || nullptr == offset_string[2])
{
MITK_ERROR << "Could not parse complete Geometry3D offset!";
return nullptr;
}
for (unsigned int d = 0; d < 3; ++d)
try
{
offset[d] = boost::lexical_cast<double>(offset_string[d]);
}
catch ( const boost::bad_lexical_cast &e )
{
MITK_ERROR << "Could not parse '" << offset_string[d] << "' as number: " << e.what();
return nullptr;
}
}
else
{
MITK_ERROR << "Parse error: expected Offset3D child below Geometry3D node";
return nullptr;
}
// bounds
- if (TiXmlElement *boundsElem = geometryElement->FirstChildElement("Bounds")->ToElement())
+ if (auto *boundsElem = geometryElement->FirstChildElement("Bounds"))
{
- bool vectorsComplete(true);
- std::string bounds_string[6];
- if (TiXmlElement *minElem = boundsElem->FirstChildElement("Min")->ToElement())
+ bool vectorsComplete;
+ std::array<const char*, 6> bounds_string;
+ if (auto* minElem = boundsElem->FirstChildElement("Min"))
{
- vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("x", &bounds_string[0]);
- vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("y", &bounds_string[2]);
- vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("z", &bounds_string[4]);
+ bounds_string[0] = minElem->Attribute("x");
+ bounds_string[2] = minElem->Attribute("y");
+ bounds_string[4] = minElem->Attribute("z");
+
+ vectorsComplete = !(nullptr == bounds_string[0] || nullptr == bounds_string[2] || nullptr == bounds_string[4]);
}
else
{
vectorsComplete = false;
}
- if (TiXmlElement *maxElem = boundsElem->FirstChildElement("Max")->ToElement())
+ if (auto *maxElem = boundsElem->FirstChildElement("Max"))
{
- vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("x", &bounds_string[1]);
- vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("y", &bounds_string[3]);
- vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("z", &bounds_string[5]);
+ bounds_string[1] = maxElem->Attribute("x");
+ bounds_string[3] = maxElem->Attribute("y");
+ bounds_string[5] = maxElem->Attribute("z");
+
+ vectorsComplete = !(nullptr == bounds_string[1] || nullptr == bounds_string[3] || nullptr == bounds_string[5]);
}
else
{
vectorsComplete = false;
}
if (!vectorsComplete)
{
MITK_ERROR << "Could not parse complete Geometry3D bounds!";
return nullptr;
}
for (unsigned int d = 0; d < 6; ++d)
try
{
bounds[d] = boost::lexical_cast<double>(bounds_string[d]);
}
catch ( const boost::bad_lexical_cast &e )
{
MITK_ERROR << "Could not parse '" << bounds_string[d] << "' as number: " << e.what();
return nullptr;
}
}
// build GeometryData from matrix/offset
AffineTransform3D::Pointer newTransform = AffineTransform3D::New();
newTransform->SetMatrix(matrix);
newTransform->SetOffset(offset);
Geometry3D::Pointer newGeometry = Geometry3D::New();
newGeometry->SetFrameOfReferenceID(frameOfReferenceID);
newGeometry->SetImageGeometry(isImageGeometry);
newGeometry->SetIndexToWorldTransform(newTransform);
newGeometry->SetBounds(bounds);
return newGeometry;
}
diff --git a/Modules/Core/src/IO/mitkGeometry3DToXML.h b/Modules/Core/src/IO/mitkGeometry3DToXML.h
index d0cd9d0f6d..ef3a2454eb 100644
--- a/Modules/Core/src/IO/mitkGeometry3DToXML.h
+++ b/Modules/Core/src/IO/mitkGeometry3DToXML.h
@@ -1,51 +1,55 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkGeometry3DToXML_h
#define mitkGeometry3DToXML_h
// MITK
#include "mitkGeometry3D.h"
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
/**
* @internal
*
* @brief Helper for Geometry3D related I/O classes.
*
* Creates TinyXML elements (blocks) that describe a Geometry3D.
* Also offers a method to read such blocks and create a corresponding Geometry3D.
*
* @sa GeometryDataReaderService, GeometryDataWriterService, PointSetWriterService, PointSetReaderService
*
* @ingroup IO
*/
class Geometry3DToXML
{
public:
/**
* @brief Serialize given geometry to XML.
*/
- static TiXmlElement *ToXML(const Geometry3D *geometry);
+ static tinyxml2::XMLElement *ToXML(tinyxml2::XMLDocument& doc, const Geometry3D *geometry);
/**
* @brief Create a Geometry3D from XML.
* Interprets only the format created by ToXML().
*/
- static Geometry3D::Pointer FromXML(TiXmlElement *node);
+ static Geometry3D::Pointer FromXML(const tinyxml2::XMLElement *node);
};
}
#endif
diff --git a/Modules/Core/src/IO/mitkGeometryDataReaderService.cpp b/Modules/Core/src/IO/mitkGeometryDataReaderService.cpp
index 0b13ffe89c..8731ae70e8 100644
--- a/Modules/Core/src/IO/mitkGeometryDataReaderService.cpp
+++ b/Modules/Core/src/IO/mitkGeometryDataReaderService.cpp
@@ -1,112 +1,113 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include "mitkGeometryDataReaderService.h"
#include "mitkGeometry3DToXML.h"
#include "mitkIOMimeTypes.h"
#include "mitkProportionalTimeGeometryToXML.h"
// STL
#include <mitkLocaleSwitch.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
mitk::GeometryDataReaderService::GeometryDataReaderService()
: AbstractFileReader(IOMimeTypes::GEOMETRY_DATA_MIMETYPE(), "MITK Geometry Data Reader")
{
RegisterService();
}
mitk::GeometryDataReaderService::~GeometryDataReaderService()
{
}
std::vector<itk::SmartPointer<mitk::BaseData>> mitk::GeometryDataReaderService::DoRead()
{
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
std::vector<itk::SmartPointer<BaseData>> result;
InputStream stream(this);
- TiXmlDocument doc;
- stream >> doc;
+ std::string s(std::istreambuf_iterator<char>{stream.rdbuf()}, std::istreambuf_iterator<char>());
+ tinyxml2::XMLDocument doc;
+ doc.Parse(s.c_str(), s.size());
if (!doc.Error())
{
- TiXmlHandle docHandle(&doc);
+ tinyxml2::XMLHandle docHandle(&doc);
- for (TiXmlElement *geomDataElement = docHandle.FirstChildElement("GeometryData").ToElement();
+ for (auto *geomDataElement = docHandle.FirstChildElement("GeometryData").ToElement();
geomDataElement != nullptr;
geomDataElement = geomDataElement->NextSiblingElement())
{
- for (TiXmlElement *currentElement = geomDataElement->FirstChildElement(); currentElement != nullptr;
+ for (auto *currentElement = geomDataElement->FirstChildElement(); currentElement != nullptr;
currentElement = currentElement->NextSiblingElement())
{
// different geometries could have been serialized from a GeometryData
// object:
std::string tagName = currentElement->Value();
if (tagName == "Geometry3D")
{
Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement);
if (restoredGeometry.IsNotNull())
{
GeometryData::Pointer newGeometryData = GeometryData::New();
newGeometryData->SetGeometry(restoredGeometry);
result.push_back(newGeometryData.GetPointer());
}
else
{
MITK_ERROR << "Invalid <Geometry3D> tag encountered. Skipping.";
}
}
else if (tagName == "ProportionalTimeGeometry")
{
ProportionalTimeGeometry::Pointer restoredTimeGeometry =
ProportionalTimeGeometryToXML::FromXML(currentElement);
if (restoredTimeGeometry.IsNotNull())
{
GeometryData::Pointer newGeometryData = GeometryData::New();
newGeometryData->SetTimeGeometry(restoredTimeGeometry);
result.push_back(newGeometryData.GetPointer());
}
else
{
MITK_ERROR << "Invalid <ProportionalTimeGeometry> tag encountered. Skipping.";
}
}
} // for child of <GeometryData>
} // for <GeometryData>
}
else
{
- mitkThrow() << "Parsing error at line " << doc.ErrorRow() << ", col " << doc.ErrorCol() << ": " << doc.ErrorDesc();
+ mitkThrow() << doc.ErrorStr();
}
if (result.empty())
{
mitkThrow() << "Did not read a single GeometryData object from input.";
}
return result;
}
mitk::GeometryDataReaderService::GeometryDataReaderService(const mitk::GeometryDataReaderService &other)
: mitk::AbstractFileReader(other)
{
}
mitk::GeometryDataReaderService *mitk::GeometryDataReaderService::Clone() const
{
return new GeometryDataReaderService(*this);
}
diff --git a/Modules/Core/src/IO/mitkGeometryDataWriterService.cpp b/Modules/Core/src/IO/mitkGeometryDataWriterService.cpp
index 1ca99cb8d0..57f02597a9 100644
--- a/Modules/Core/src/IO/mitkGeometryDataWriterService.cpp
+++ b/Modules/Core/src/IO/mitkGeometryDataWriterService.cpp
@@ -1,91 +1,90 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkGeometryDataWriterService.h"
#include "mitkIOMimeTypes.h"
#include "mitkProportionalTimeGeometryToXML.h"
-#include <tinyxml.h>
+#include <tinyxml2.h>
#include <mitkLocaleSwitch.h>
mitk::GeometryDataWriterService::GeometryDataWriterService()
: AbstractFileWriter(
GeometryData::GetStaticNameOfClass(), IOMimeTypes::GEOMETRY_DATA_MIMETYPE(), "MITK Geometry Data Writer")
{
RegisterService();
}
mitk::GeometryDataWriterService::GeometryDataWriterService(const mitk::GeometryDataWriterService &other)
: AbstractFileWriter(other)
{
}
mitk::GeometryDataWriterService::~GeometryDataWriterService()
{
}
void mitk::GeometryDataWriterService::Write()
{
/* using the stream interface produces files without line breaks or indentation..
But before changing to file interface, need to understand the new I/O classes */
OutputStream out(this);
if (!out.good())
{
mitkThrow() << "Stream not good.";
}
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
// Open XML file using TinyXML,
// loop over all inputs,
// call appropriate serializing functions
- TiXmlDocument doc;
+ tinyxml2::XMLDocument doc;
+ doc.InsertEndChild(doc.NewDeclaration());
- auto *decl = new TiXmlDeclaration(
- "1.0", "UTF-8", ""); // TODO what to write here? encoding? standalone would mean that we provide a DTD somewhere...
- doc.LinkEndChild(decl);
-
- auto *rootNode = new TiXmlElement("GeometryData");
- doc.LinkEndChild(rootNode);
+ auto* rootNode = doc.NewElement("GeometryData");
+ doc.InsertEndChild(rootNode);
// note version info
- auto *version = new TiXmlElement("Version");
+ auto *version = doc.NewElement("Version");
version->SetAttribute("Writer", __FILE__);
version->SetAttribute("FileVersion", 1);
- rootNode->LinkEndChild(version);
+ rootNode->InsertEndChild(version);
const auto *data = static_cast<const GeometryData *>(this->GetInput());
const ProportionalTimeGeometry *timeGeometry(nullptr);
if ((timeGeometry = dynamic_cast<const ProportionalTimeGeometry *>(data->GetTimeGeometry())))
{
- TiXmlElement *timeGeometryElement = ProportionalTimeGeometryToXML::ToXML(timeGeometry);
- rootNode->LinkEndChild(timeGeometryElement);
+ auto *timeGeometryElement = ProportionalTimeGeometryToXML::ToXML(doc, timeGeometry);
+ rootNode->InsertEndChild(timeGeometryElement);
}
else
{
MITK_WARN << "Serializing GeometryData that does not have a valid ProportionalTimeGeometry! Not implemented!";
}
// Write out document
- out << doc;
+ tinyxml2::XMLPrinter printer;
+ doc.Print(&printer);
+ out << printer.CStr();
}
mitk::GeometryDataWriterService *mitk::GeometryDataWriterService::Clone() const
{
return new GeometryDataWriterService(*this);
}
diff --git a/Modules/Core/src/IO/mitkPointSetReaderService.cpp b/Modules/Core/src/IO/mitkPointSetReaderService.cpp
index 68cc84f562..63d3018782 100644
--- a/Modules/Core/src/IO/mitkPointSetReaderService.cpp
+++ b/Modules/Core/src/IO/mitkPointSetReaderService.cpp
@@ -1,275 +1,276 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include "mitkPointSetReaderService.h"
#include "mitkGeometry3DToXML.h"
#include "mitkIOMimeTypes.h"
#include "mitkProportionalTimeGeometry.h"
+#include <mitkLocaleSwitch.h>
// STL
#include <fstream>
#include <iostream>
-#include <mitkLocaleSwitch.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
mitk::PointSetReaderService::PointSetReaderService()
: AbstractFileReader(CustomMimeType(IOMimeTypes::POINTSET_MIMETYPE()), "MITK Point Set Reader")
{
RegisterService();
}
mitk::PointSetReaderService::~PointSetReaderService()
{
}
std::vector<itk::SmartPointer<mitk::BaseData>> mitk::PointSetReaderService::DoRead()
{
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
std::vector<itk::SmartPointer<mitk::BaseData>> result;
InputStream stream(this);
- TiXmlDocument doc;
- stream >> doc;
+ std::string s(std::istreambuf_iterator<char>{stream.rdbuf()}, std::istreambuf_iterator<char>());
+ tinyxml2::XMLDocument doc;
+ doc.Parse(s.c_str(), s.size());
if (!doc.Error())
{
- TiXmlHandle docHandle(&doc);
+ tinyxml2::XMLHandle docHandle(&doc);
// unsigned int pointSetCounter(0);
- for (TiXmlElement *currentPointSetElement =
+ for (auto *currentPointSetElement =
docHandle.FirstChildElement("point_set_file").FirstChildElement("point_set").ToElement();
currentPointSetElement != nullptr;
currentPointSetElement = currentPointSetElement->NextSiblingElement())
{
mitk::PointSet::Pointer newPointSet = mitk::PointSet::New();
// time geometry assembled for addition after all points
// else the SetPoint method would already transform the points that we provide it
mitk::ProportionalTimeGeometry::Pointer timeGeometry = mitk::ProportionalTimeGeometry::New();
if (currentPointSetElement->FirstChildElement("time_series") != nullptr)
{
- for (TiXmlElement *currentTimeSeries = currentPointSetElement->FirstChildElement("time_series")->ToElement();
+ for (auto *currentTimeSeries = currentPointSetElement->FirstChildElement("time_series")->ToElement();
currentTimeSeries != nullptr;
currentTimeSeries = currentTimeSeries->NextSiblingElement())
{
unsigned int currentTimeStep(0);
- TiXmlElement *currentTimeSeriesID = currentTimeSeries->FirstChildElement("time_series_id");
+ auto *currentTimeSeriesID = currentTimeSeries->FirstChildElement("time_series_id");
currentTimeStep = atoi(currentTimeSeriesID->GetText());
timeGeometry->Expand(currentTimeStep + 1); // expand (default to identity) in any case
- TiXmlElement *geometryElem = currentTimeSeries->FirstChildElement("Geometry3D");
+ auto *geometryElem = currentTimeSeries->FirstChildElement("Geometry3D");
if (geometryElem)
{
Geometry3D::Pointer geometry = Geometry3DToXML::FromXML(geometryElem);
if (geometry.IsNotNull())
{
timeGeometry->SetTimeStepGeometry(geometry, currentTimeStep);
}
else
{
MITK_ERROR << "Could not deserialize Geometry3D element.";
}
}
else
{
MITK_WARN << "Fallback to legacy behavior: defining PointSet geometry as identity";
}
newPointSet = this->ReadPoints(newPointSet, currentTimeSeries, currentTimeStep);
}
}
else
{
newPointSet = this->ReadPoints(newPointSet, currentPointSetElement, 0);
}
newPointSet->SetTimeGeometry(timeGeometry);
result.push_back(newPointSet.GetPointer());
}
}
else
{
- mitkThrow() << "Parsing error at line " << doc.ErrorRow() << ", col " << doc.ErrorCol() << ": " << doc.ErrorDesc();
+ mitkThrow() << doc.ErrorStr();
}
return result;
}
-mitk::BaseGeometry::Pointer mitk::PointSetReaderService::ReadGeometry(TiXmlElement *parentElement)
+mitk::BaseGeometry::Pointer mitk::PointSetReaderService::ReadGeometry(tinyxml2::XMLElement *parentElement)
{
- TiXmlElement *geometryElem = parentElement->FirstChildElement("geometry3d");
+ auto *geometryElem = parentElement->FirstChildElement("geometry3d");
if (!geometryElem)
return nullptr;
// data to generate
AffineTransform3D::MatrixType matrix;
AffineTransform3D::OffsetType offset;
bool isImageGeometry(false);
unsigned int frameOfReferenceID(0);
BaseGeometry::BoundsArrayType bounds;
bool somethingMissing(false);
// find data in xml structure
- TiXmlElement *imageGeometryElem = geometryElem->FirstChildElement("image_geometry");
+ auto *imageGeometryElem = geometryElem->FirstChildElement("image_geometry");
if (imageGeometryElem)
{
std::string igs = imageGeometryElem->GetText();
isImageGeometry = igs == "true" || igs == "TRUE" || igs == "1";
}
else
somethingMissing = true;
- TiXmlElement *frameOfReferenceElem = geometryElem->FirstChildElement("frame_of_reference_id");
+ auto *frameOfReferenceElem = geometryElem->FirstChildElement("frame_of_reference_id");
if (frameOfReferenceElem)
{
frameOfReferenceID = atoi(frameOfReferenceElem->GetText());
}
else
somethingMissing = true;
- TiXmlElement *indexToWorldElem = geometryElem->FirstChildElement("index_to_world");
+ auto *indexToWorldElem = geometryElem->FirstChildElement("index_to_world");
if (indexToWorldElem)
{
- TiXmlElement *matrixElem = indexToWorldElem->FirstChildElement("matrix3x3");
- TiXmlElement *offsetElem = indexToWorldElem->FirstChildElement("offset");
+ auto *matrixElem = indexToWorldElem->FirstChildElement("matrix3x3");
+ auto *offsetElem = indexToWorldElem->FirstChildElement("offset");
if (indexToWorldElem && offsetElem)
{
- TiXmlElement *col0 = matrixElem->FirstChildElement("column_0");
- TiXmlElement *col1 = matrixElem->FirstChildElement("column_1");
- TiXmlElement *col2 = matrixElem->FirstChildElement("column_2");
+ auto*col0 = matrixElem->FirstChildElement("column_0");
+ auto*col1 = matrixElem->FirstChildElement("column_1");
+ auto*col2 = matrixElem->FirstChildElement("column_2");
if (col0 && col1 && col2)
{
- somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("x", &matrix[0][0]);
- somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("y", &matrix[1][0]);
- somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("z", &matrix[2][0]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col0->QueryDoubleAttribute("x", &matrix[0][0]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col0->QueryDoubleAttribute("y", &matrix[1][0]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col0->QueryDoubleAttribute("z", &matrix[2][0]);
- somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("x", &matrix[0][1]);
- somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("y", &matrix[1][1]);
- somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("z", &matrix[2][1]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col1->QueryDoubleAttribute("x", &matrix[0][1]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col1->QueryDoubleAttribute("y", &matrix[1][1]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col1->QueryDoubleAttribute("z", &matrix[2][1]);
- somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("x", &matrix[0][2]);
- somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("y", &matrix[1][2]);
- somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("z", &matrix[2][2]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col2->QueryDoubleAttribute("x", &matrix[0][2]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col2->QueryDoubleAttribute("y", &matrix[1][2]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != col2->QueryDoubleAttribute("z", &matrix[2][2]);
}
else
somethingMissing = true;
- somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("x", &offset[0]);
- somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("y", &offset[1]);
- somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("z", &offset[2]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != offsetElem->QueryDoubleAttribute("x", &offset[0]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != offsetElem->QueryDoubleAttribute("y", &offset[1]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != offsetElem->QueryDoubleAttribute("z", &offset[2]);
}
else
somethingMissing = true;
- TiXmlElement *boundsElem = geometryElem->FirstChildElement("bounds");
+ auto *boundsElem = geometryElem->FirstChildElement("bounds");
if (boundsElem)
{
- TiXmlElement *minBoundsElem = boundsElem->FirstChildElement("min");
- TiXmlElement *maxBoundsElem = boundsElem->FirstChildElement("max");
+ auto *minBoundsElem = boundsElem->FirstChildElement("min");
+ auto *maxBoundsElem = boundsElem->FirstChildElement("max");
if (minBoundsElem && maxBoundsElem)
{
- somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("x", &bounds[0]);
- somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("y", &bounds[2]);
- somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("z", &bounds[4]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != minBoundsElem->QueryDoubleAttribute("x", &bounds[0]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != minBoundsElem->QueryDoubleAttribute("y", &bounds[2]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != minBoundsElem->QueryDoubleAttribute("z", &bounds[4]);
- somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("x", &bounds[1]);
- somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("y", &bounds[3]);
- somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("z", &bounds[5]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("x", &bounds[1]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("y", &bounds[3]);
+ somethingMissing |= tinyxml2::XML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("z", &bounds[5]);
}
else
somethingMissing = true;
}
else
somethingMissing = true;
}
else
somethingMissing = true;
if (somethingMissing)
{
MITK_ERROR << "XML structure of geometry inside a PointSet file broken. Refusing to build Geometry3D";
return nullptr;
}
else
{
Geometry3D::Pointer g = Geometry3D::New();
g->SetImageGeometry(isImageGeometry);
g->SetFrameOfReferenceID(frameOfReferenceID);
g->SetBounds(bounds);
AffineTransform3D::Pointer transform = AffineTransform3D::New();
transform->SetMatrix(matrix);
transform->SetOffset(offset);
g->SetIndexToWorldTransform(transform);
return g.GetPointer();
}
}
mitk::PointSet::Pointer mitk::PointSetReaderService::ReadPoints(mitk::PointSet::Pointer newPointSet,
- TiXmlElement *currentTimeSeries,
+ tinyxml2::XMLElement *currentTimeSeries,
unsigned int currentTimeStep)
{
if (currentTimeSeries->FirstChildElement("point") != nullptr)
{
- for (TiXmlElement *currentPoint = currentTimeSeries->FirstChildElement("point")->ToElement(); currentPoint != nullptr;
+ for (auto *currentPoint = currentTimeSeries->FirstChildElement("point"); currentPoint != nullptr;
currentPoint = currentPoint->NextSiblingElement())
{
unsigned int id(0);
auto spec((mitk::PointSpecificationType)0);
double x(0.0);
double y(0.0);
double z(0.0);
id = atoi(currentPoint->FirstChildElement("id")->GetText());
if (currentPoint->FirstChildElement("specification") != nullptr)
{
spec = (mitk::PointSpecificationType)atoi(currentPoint->FirstChildElement("specification")->GetText());
}
x = atof(currentPoint->FirstChildElement("x")->GetText());
y = atof(currentPoint->FirstChildElement("y")->GetText());
z = atof(currentPoint->FirstChildElement("z")->GetText());
mitk::Point3D point;
mitk::FillVector3D(point, x, y, z);
newPointSet->SetPoint(id, point, spec, currentTimeStep);
}
}
else
{
if (currentTimeStep != newPointSet->GetTimeSteps() + 1)
{
newPointSet->Expand(currentTimeStep + 1); // expand time step series with empty time step
}
}
return newPointSet;
}
mitk::PointSetReaderService::PointSetReaderService(const mitk::PointSetReaderService &other)
: mitk::AbstractFileReader(other)
{
}
mitk::PointSetReaderService *mitk::PointSetReaderService::Clone() const
{
return new mitk::PointSetReaderService(*this);
}
diff --git a/Modules/Core/src/IO/mitkPointSetReaderService.h b/Modules/Core/src/IO/mitkPointSetReaderService.h
index 5aba51b592..f72bc23fdb 100644
--- a/Modules/Core/src/IO/mitkPointSetReaderService.h
+++ b/Modules/Core/src/IO/mitkPointSetReaderService.h
@@ -1,62 +1,65 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef _MITK_POINT_SET_READER_SERVICE__H_
#define _MITK_POINT_SET_READER_SERVICE__H_
// MITK
#include <mitkAbstractFileReader.h>
#include <mitkPointSet.h>
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLElement;
+}
namespace mitk
{
/**
* @internal
*
* @brief reads xml representations of mitk::PointSets from a file
*
* Reader for xml files containing one or multiple xml represenations of
* mitk::PointSet. If multiple mitk::PointSet objects are stored in one file,
* these are assigned to multiple BaseData objects.
*
* The reader is able to read the old 3D Pointsets without the "specification" and "timeseries" tags and the new 4D
* Pointsets.
*
* @ingroup IO
*/
class PointSetReaderService : public AbstractFileReader
{
public:
PointSetReaderService();
~PointSetReaderService() override;
using AbstractFileReader::Read;
protected:
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
private:
PointSetReaderService(const PointSetReaderService &other);
- mitk::BaseGeometry::Pointer ReadGeometry(TiXmlElement *parentElement);
+ mitk::BaseGeometry::Pointer ReadGeometry(tinyxml2::XMLElement *parentElement);
mitk::PointSet::Pointer ReadPoints(mitk::PointSet::Pointer newPointSet,
- TiXmlElement *currentTimeSeries,
+ tinyxml2::XMLElement *currentTimeSeries,
unsigned int currentTimeStep);
PointSetReaderService *Clone() const override;
};
}
#endif
diff --git a/Modules/Core/src/IO/mitkPointSetWriterService.cpp b/Modules/Core/src/IO/mitkPointSetWriterService.cpp
index 30a5d25dcc..63e99ad061 100644
--- a/Modules/Core/src/IO/mitkPointSetWriterService.cpp
+++ b/Modules/Core/src/IO/mitkPointSetWriterService.cpp
@@ -1,182 +1,179 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPointSetWriterService.h"
#include "mitkGeometry3DToXML.h"
#include "mitkIOMimeTypes.h"
#include "mitkLocaleSwitch.h"
#include "mitkGeometry3D.h"
-#include <tinyxml.h>
-
#include <fstream>
#include <iostream>
#include <locale>
+#include <tinyxml2.h>
+
//
// Initialization of the xml tags.
//
const std::string mitk::PointSetWriterService::XML_POINT_SET_FILE = "point_set_file";
const std::string mitk::PointSetWriterService::XML_FILE_VERSION = "file_version";
const std::string mitk::PointSetWriterService::XML_POINT_SET = "point_set";
const std::string mitk::PointSetWriterService::XML_TIME_SERIES = "time_series";
const std::string mitk::PointSetWriterService::XML_TIME_SERIES_ID = "time_series_id";
const std::string mitk::PointSetWriterService::XML_POINT = "point";
const std::string mitk::PointSetWriterService::XML_ID = "id";
const std::string mitk::PointSetWriterService::XML_SPEC = "specification";
const std::string mitk::PointSetWriterService::XML_X = "x";
const std::string mitk::PointSetWriterService::XML_Y = "y";
const std::string mitk::PointSetWriterService::XML_Z = "z";
const std::string mitk::PointSetWriterService::VERSION_STRING = "0.1";
mitk::PointSetWriterService::PointSetWriterService()
: AbstractFileWriter(
PointSet::GetStaticNameOfClass(), CustomMimeType(IOMimeTypes::POINTSET_MIMETYPE()), "MITK Point Set Writer")
{
RegisterService();
}
mitk::PointSetWriterService::PointSetWriterService(const mitk::PointSetWriterService &other) : AbstractFileWriter(other)
{
}
mitk::PointSetWriterService::~PointSetWriterService()
{
}
void mitk::PointSetWriterService::Write()
{
mitk::LocaleSwitch localeC("C");
- TiXmlDocument doc;
-
- auto *decl = new TiXmlDeclaration(
- "1.0", "UTF-8", ""); // TODO what to write here? encoding? standalone would mean that we provide a DTD somewhere...
- doc.LinkEndChild(decl);
+ tinyxml2::XMLDocument doc;
+ doc.InsertEndChild(doc.NewDeclaration());
- auto *rootNode = new TiXmlElement(XML_POINT_SET_FILE);
- doc.LinkEndChild(rootNode);
+ auto *rootNode = doc.NewElement(XML_POINT_SET_FILE.c_str());
+ doc.InsertEndChild(rootNode);
- auto *versionNode = new TiXmlElement(XML_FILE_VERSION);
- auto *versionText = new TiXmlText(VERSION_STRING);
- versionNode->LinkEndChild(versionText);
- rootNode->LinkEndChild(versionNode);
+ auto *versionNode = doc.NewElement(XML_FILE_VERSION.c_str());
+ auto *versionText = doc.NewText(VERSION_STRING.c_str());
+ versionNode->InsertEndChild(versionText);
+ rootNode->InsertEndChild(versionNode);
- TiXmlElement *pointSetNode = ToXML(static_cast<const PointSet *>(this->GetInput()));
+ auto *pointSetNode = ToXML(doc, static_cast<const PointSet *>(this->GetInput()));
if (!pointSetNode)
{
mitkThrow() << "Serialization error during PointSet writing.";
}
- rootNode->LinkEndChild(pointSetNode);
+ rootNode->InsertEndChild(pointSetNode);
// out << doc; // streaming of TinyXML write no new-lines,
// rendering XML files unreadable (for humans)
LocalFile f(this);
- if (!doc.SaveFile(f.GetFileName()))
+ if (tinyxml2::XML_SUCCESS != doc.SaveFile(f.GetFileName().c_str()))
{
mitkThrow() << "Some error during point set writing.";
}
}
mitk::PointSetWriterService *mitk::PointSetWriterService::Clone() const
{
return new PointSetWriterService(*this);
}
-TiXmlElement *mitk::PointSetWriterService::ToXML(const mitk::PointSet *pointSet)
+tinyxml2::XMLElement *mitk::PointSetWriterService::ToXML(tinyxml2::XMLDocument& doc, const mitk::PointSet *pointSet)
{
// the following is rather bloated and could be expressed in more compact XML
// (e.g. using attributes instead of tags for x/y/z). The current format is
// kept to be compatible with the previous writer.
- auto *pointSetElement = new TiXmlElement(XML_POINT_SET);
+ auto *pointSetElement = doc.NewElement(XML_POINT_SET.c_str());
unsigned int timecount = pointSet->GetTimeSteps();
for (unsigned int i = 0; i < timecount; i++)
{
- auto *timeSeriesElement = new TiXmlElement(XML_TIME_SERIES);
- pointSetElement->LinkEndChild(timeSeriesElement);
+ auto *timeSeriesElement = doc.NewElement(XML_TIME_SERIES.c_str());
+ pointSetElement->InsertEndChild(timeSeriesElement);
- auto *timeSeriesIDElement = new TiXmlElement(XML_TIME_SERIES_ID);
- timeSeriesElement->LinkEndChild(timeSeriesIDElement);
- TiXmlText *timeSeriesIDText = new TiXmlText(ConvertToString(i));
- timeSeriesIDElement->LinkEndChild(timeSeriesIDText);
+ auto *timeSeriesIDElement = doc.NewElement(XML_TIME_SERIES_ID.c_str());
+ timeSeriesElement->InsertEndChild(timeSeriesIDElement);
+ auto *timeSeriesIDText = doc.NewText(ConvertToString(i).c_str());
+ timeSeriesIDElement->InsertEndChild(timeSeriesIDText);
PointSet::PointsContainer *pointsContainer = pointSet->GetPointSet(i)->GetPoints();
PointSet::PointsContainer::Iterator it;
auto *geometry = dynamic_cast<Geometry3D *>(pointSet->GetGeometry(i));
if (geometry == nullptr)
{
MITK_WARN << "Writing a PointSet with something other that a Geometry3D. This is not foreseen and not handled.";
// we'll continue anyway, this imitates previous behavior
}
else
{
- TiXmlElement *geometryElement = Geometry3DToXML::ToXML(geometry);
- timeSeriesElement->LinkEndChild(geometryElement);
+ auto *geometryElement = Geometry3DToXML::ToXML(doc, geometry);
+ timeSeriesElement->InsertEndChild(geometryElement);
}
for (it = pointsContainer->Begin(); it != pointsContainer->End(); ++it)
{
- auto *pointElement = new TiXmlElement(XML_POINT);
- timeSeriesElement->LinkEndChild(pointElement);
+ auto *pointElement = doc.NewElement(XML_POINT.c_str());
+ timeSeriesElement->InsertEndChild(pointElement);
- auto *pointIDElement = new TiXmlElement(XML_ID);
- TiXmlText *pointIDText = new TiXmlText(ConvertToString(it->Index()));
- pointIDElement->LinkEndChild(pointIDText);
- pointElement->LinkEndChild(pointIDElement);
+ auto *pointIDElement = doc.NewElement(XML_ID.c_str());
+ auto *pointIDText = doc.NewText(ConvertToString(it->Index()).c_str());
+ pointIDElement->InsertEndChild(pointIDText);
+ pointElement->InsertEndChild(pointIDElement);
mitk::PointSet::PointType point = it->Value();
- auto *pointSpecElement = new TiXmlElement(XML_SPEC);
- TiXmlText *pointSpecText = new TiXmlText(ConvertToString(pointSet->GetSpecificationTypeInfo(it->Index(), i)));
- pointSpecElement->LinkEndChild(pointSpecText);
- pointElement->LinkEndChild(pointSpecElement);
-
- auto *pointXElement = new TiXmlElement(XML_X);
- TiXmlText *pointXText = new TiXmlText(ConvertToString(point[0]));
- pointXElement->LinkEndChild(pointXText);
- pointElement->LinkEndChild(pointXElement);
-
- auto *pointYElement = new TiXmlElement(XML_Y);
- TiXmlText *pointYText = new TiXmlText(ConvertToString(point[1]));
- pointYElement->LinkEndChild(pointYText);
- pointElement->LinkEndChild(pointYElement);
-
- auto *pointZElement = new TiXmlElement(XML_Z);
- TiXmlText *pointZText = new TiXmlText(ConvertToString(point[2]));
- pointZElement->LinkEndChild(pointZText);
- pointElement->LinkEndChild(pointZElement);
+ auto *pointSpecElement = doc.NewElement(XML_SPEC.c_str());
+ auto *pointSpecText = doc.NewText(ConvertToString(pointSet->GetSpecificationTypeInfo(it->Index(), i)).c_str());
+ pointSpecElement->InsertEndChild(pointSpecText);
+ pointElement->InsertEndChild(pointSpecElement);
+
+ auto *pointXElement = doc.NewElement(XML_X.c_str());
+ auto *pointXText = doc.NewText(ConvertToString(point[0]).c_str());
+ pointXElement->InsertEndChild(pointXText);
+ pointElement->InsertEndChild(pointXElement);
+
+ auto *pointYElement = doc.NewElement(XML_Y.c_str());
+ auto *pointYText = doc.NewText(ConvertToString(point[1]).c_str());
+ pointYElement->InsertEndChild(pointYText);
+ pointElement->InsertEndChild(pointYElement);
+
+ auto *pointZElement = doc.NewElement(XML_Z.c_str());
+ auto *pointZText = doc.NewText(ConvertToString(point[2]).c_str());
+ pointZElement->InsertEndChild(pointZText);
+ pointElement->InsertEndChild(pointZElement);
}
}
return pointSetElement;
}
template <typename T>
std::string mitk::PointSetWriterService::ConvertToString(T value)
{
std::ostringstream o;
std::locale I("C");
o.imbue(I);
if (o << std::setprecision(12) << value)
{
return o.str();
}
else
{
return "conversion error";
}
}
diff --git a/Modules/Core/src/IO/mitkPointSetWriterService.h b/Modules/Core/src/IO/mitkPointSetWriterService.h
index b9b55d4aef..68aa0e99e7 100644
--- a/Modules/Core/src/IO/mitkPointSetWriterService.h
+++ b/Modules/Core/src/IO/mitkPointSetWriterService.h
@@ -1,71 +1,75 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef _MITK_POINT_SET_WRITER_SERVICE__H_
#define _MITK_POINT_SET_WRITER_SERVICE__H_
#include <mitkAbstractFileWriter.h>
#include <mitkPointSet.h>
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
class Geometry3D;
/**
* @internal
*
* @brief XML-based writer for mitk::PointSets
*
* XML-based writer for mitk::PointSet. Multiple PointSets can be written in
* a single XML file by simply setting multiple inputs to the filter.
*
* @todo This class would merit a XML library for maintainability or a denser format for performance.
*
* @ingroup IO
*/
class PointSetWriterService : public AbstractFileWriter
{
public:
PointSetWriterService();
~PointSetWriterService() override;
using AbstractFileWriter::Write;
void Write() override;
private:
PointSetWriterService(const PointSetWriterService &other);
mitk::PointSetWriterService *Clone() const override;
template <typename T>
std::string ConvertToString(T value);
- TiXmlElement *ToXML(const mitk::PointSet *pointSet);
+ tinyxml2::XMLElement *ToXML(tinyxml2::XMLDocument &doc, const mitk::PointSet *pointSet);
static const std::string XML_POINT_SET;
static const std::string XML_TIME_SERIES;
static const std::string XML_TIME_SERIES_ID;
static const std::string XML_POINT_SET_FILE;
static const std::string XML_FILE_VERSION;
static const std::string XML_POINT;
static const std::string XML_SPEC;
static const std::string XML_ID;
static const std::string XML_X;
static const std::string XML_Y;
static const std::string XML_Z;
static const std::string VERSION_STRING;
};
}
#endif
diff --git a/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp b/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp
index 6df438ad99..3b42888705 100644
--- a/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp
+++ b/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp
@@ -1,162 +1,164 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkProportionalTimeGeometryToXML.h"
#include "mitkGeometry3DToXML.h"
-#include <tinyxml.h>
-
#include <mitkLexicalCast.h>
-TiXmlElement *mitk::ProportionalTimeGeometryToXML::ToXML(const ProportionalTimeGeometry *timeGeom)
+#include <tinyxml2.h>
+
+tinyxml2::XMLElement *mitk::ProportionalTimeGeometryToXML::ToXML(tinyxml2::XMLDocument& doc, const ProportionalTimeGeometry *timeGeom)
{
assert(timeGeom);
- auto *timeGeomElem = new TiXmlElement("ProportionalTimeGeometry");
- timeGeomElem->SetAttribute("NumberOfTimeSteps", timeGeom->CountTimeSteps());
+ auto *timeGeomElem = doc.NewElement("ProportionalTimeGeometry");
+ timeGeomElem->SetAttribute("NumberOfTimeSteps", static_cast<int>(timeGeom->CountTimeSteps()));
// TinyXML cannot serialize infinity (default value for time step)
// So we guard this value and the first time point against serialization problems
// by not writing them. The reader can then tell that absence of those values
// means "keep the default values"
if (timeGeom->GetFirstTimePoint() != -std::numeric_limits<TimePointType>::max())
- timeGeomElem->SetAttribute("FirstTimePoint", boost::lexical_cast<std::string>(timeGeom->GetFirstTimePoint()));
+ timeGeomElem->SetAttribute("FirstTimePoint", boost::lexical_cast<std::string>(timeGeom->GetFirstTimePoint()).c_str());
if (timeGeom->GetStepDuration() != std::numeric_limits<TimePointType>::infinity())
- timeGeomElem->SetAttribute("StepDuration", boost::lexical_cast<std::string>(timeGeom->GetStepDuration()));
+ timeGeomElem->SetAttribute("StepDuration", boost::lexical_cast<std::string>(timeGeom->GetStepDuration()).c_str());
for (TimeStepType t = 0; t < timeGeom->CountTimeSteps(); ++t)
{
// add a node for the geometry of each time step
const Geometry3D *geom3D(nullptr);
if ((geom3D = dynamic_cast<const Geometry3D *>(timeGeom->GetGeometryForTimeStep(t).GetPointer())))
{
- TiXmlElement *geom3DElement = Geometry3DToXML::ToXML(geom3D);
- geom3DElement->SetAttribute("TimeStep", t); // mark order for us
- timeGeomElem->LinkEndChild(geom3DElement);
+ auto *geom3DElement = Geometry3DToXML::ToXML(doc, geom3D);
+ geom3DElement->SetAttribute("TimeStep", static_cast<int>(t)); // mark order for us
+ timeGeomElem->InsertEndChild(geom3DElement);
}
else
{
MITK_WARN << "Serializing a ProportionalTimeGeometry that contains something other than Geometry3D!"
<< " (in time step " << t << ")"
<< " File will miss information!";
}
}
return timeGeomElem;
}
-mitk::ProportionalTimeGeometry::Pointer mitk::ProportionalTimeGeometryToXML::FromXML(TiXmlElement *timeGeometryElement)
+mitk::ProportionalTimeGeometry::Pointer mitk::ProportionalTimeGeometryToXML::FromXML(const tinyxml2::XMLElement *timeGeometryElement)
{
if (!timeGeometryElement)
{
MITK_ERROR << "Cannot deserialize ProportionalTimeGeometry from nullptr.";
return nullptr;
}
int numberOfTimeSteps = 0;
- if (TIXML_SUCCESS != timeGeometryElement->QueryIntAttribute("NumberOfTimeSteps", &numberOfTimeSteps))
+ if (tinyxml2::XML_SUCCESS != timeGeometryElement->QueryIntAttribute("NumberOfTimeSteps", &numberOfTimeSteps))
{
MITK_WARN << "<ProportionalTimeGeometry> found without NumberOfTimeSteps attribute. Counting...";
}
// might be missing!
TimePointType firstTimePoint;
- std::string firstTimePoint_s;
+ const char* firstTimePoint_s = nullptr;
TimePointType stepDuration;
- std::string stepDuration_s;
+ const char* stepDuration_s = nullptr;
try
{
- if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("FirstTimePoint", &firstTimePoint_s))
+ firstTimePoint_s = timeGeometryElement->Attribute("FirstTimePoint");
+ if (nullptr != firstTimePoint_s)
{
firstTimePoint = boost::lexical_cast<double>(firstTimePoint_s);
}
else
{
firstTimePoint = -std::numeric_limits<TimePointType>::max();
}
- if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("StepDuration", &stepDuration_s))
+ stepDuration_s = timeGeometryElement->Attribute("StepDuration");
+ if (nullptr != stepDuration_s)
{
stepDuration = boost::lexical_cast<double>(stepDuration_s);
}
else
{
stepDuration = std::numeric_limits<TimePointType>::infinity();
}
}
catch ( const boost::bad_lexical_cast &e )
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
// list of all geometries with their time steps
std::multimap<TimeStepType, BaseGeometry::Pointer> allReadGeometries;
int indexForUnlabeledTimeStep(-1);
- for (TiXmlElement *currentElement = timeGeometryElement->FirstChildElement(); currentElement != nullptr;
+ for (auto *currentElement = timeGeometryElement->FirstChildElement(); currentElement != nullptr;
currentElement = currentElement->NextSiblingElement())
{
// different geometries could have been inside a ProportionalTimeGeometry.
// By now, we only support Geometry3D
std::string tagName = currentElement->Value();
if (tagName == "Geometry3D")
{
Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement);
if (restoredGeometry.IsNotNull())
{
int timeStep(-1);
- if (TIXML_SUCCESS != currentElement->QueryIntAttribute("TimeStep", &timeStep))
+ if (tinyxml2::XML_SUCCESS != currentElement->QueryIntAttribute("TimeStep", &timeStep))
{
timeStep = indexForUnlabeledTimeStep--; // decrement index for next one
MITK_WARN << "Found <Geometry3D> without 'TimeStep' attribute in <ProportionalTimeGeometry>. No guarantees "
"on order anymore.";
}
if (allReadGeometries.count(static_cast<TimeStepType>(timeStep)) > 0)
{
MITK_WARN << "Found <Geometry3D> tags with identical 'TimeStep' attribute in <ProportionalTimeGeometry>. No "
"guarantees on order anymore.";
}
allReadGeometries.insert(std::make_pair(static_cast<TimeStepType>(timeStep), restoredGeometry.GetPointer()));
}
}
else
{
MITK_WARN << "Found unsupported tag <" << tagName << "> inside <ProportionalTimeGeometry>. Ignoring.";
}
}
// now add all BaseGeometries that were read to a new instance
// of ProportionalTimeGeometry
ProportionalTimeGeometry::Pointer newTimeGeometry = ProportionalTimeGeometry::New();
newTimeGeometry->SetFirstTimePoint(firstTimePoint);
newTimeGeometry->SetStepDuration(stepDuration);
newTimeGeometry->ReserveSpaceForGeometries(allReadGeometries.size());
TimeStepType t(0);
for (auto entry : allReadGeometries)
{
// We add items with newly assigned time steps.
// This avoids great confusion when a file contains
// bogus numbers.
newTimeGeometry->SetTimeStepGeometry(entry.second, t++);
}
// Need to re-calculate global bounding box.
// This is neither stored in a file, nor done by SetTimeStepGeometry
newTimeGeometry->UpdateBoundingBox();
return newTimeGeometry;
}
diff --git a/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.h b/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.h
index 5091a9a482..5ccd053619 100644
--- a/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.h
+++ b/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.h
@@ -1,51 +1,54 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkProportionalTimeGeometryToXML_h
#define mitkProportionalTimeGeometryToXML_h
-// MITK
#include "mitkProportionalTimeGeometry.h"
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
/**
* @internal
*
* @brief Helper for ProportionalTimeGeometry related I/O classes.
*
* Creates TinyXML elements (blocks) that describe a ProportionalTimeGeometry.
* Also offers a method to read such blocks and create a corresponding ProportionalTimeGeometry.
*
* @sa GeometryDataWriterService, GeometryDataReaderService, Geometry3DToXML
*
* @ingroup IO
*/
class ProportionalTimeGeometryToXML
{
public:
/**
* @brief Serialize given geometry to XML.
*/
- static TiXmlElement *ToXML(const ProportionalTimeGeometry *geometry);
+ static tinyxml2::XMLElement *ToXML(tinyxml2::XMLDocument& doc, const ProportionalTimeGeometry *geometry);
/**
* @brief Create a ProportionalTimeGeometry from XML.
* Interprets only the format created by ToXML().
*/
- static ProportionalTimeGeometry::Pointer FromXML(TiXmlElement *node);
+ static ProportionalTimeGeometry::Pointer FromXML(const tinyxml2::XMLElement *node);
};
}
#endif
diff --git a/Modules/Core/test/CMakeLists.txt b/Modules/Core/test/CMakeLists.txt
index d3d3321aed..dc8d4ee9b4 100644
--- a/Modules/Core/test/CMakeLists.txt
+++ b/Modules/Core/test/CMakeLists.txt
@@ -1,181 +1,181 @@
# The core tests need relaxed compiler flags...
# TODO fix core tests to compile without these additional no-error flags
if(MSVC_VERSION)
# disable deprecated warnings (they would lead to errors)
mitkFunctionCheckCAndCXXCompilerFlags("/wd4996" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
else()
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
endif()
MITK_CREATE_MODULE_TESTS()
if(TARGET ${TESTDRIVER})
- mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK|ITKThresholding+ITKTestKernel VTK|TestingRendering tinyxml)
+ mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK|IONRRD VTK|TestingRendering tinyxml2)
mitkAddCustomModuleTest(mitkVolumeCalculatorTest_Png2D-bw mitkVolumeCalculatorTest
${MITK_DATA_DIR}/Png2D-bw.png
${MITK_DATA_DIR}/Pic2DplusT.nrrd
)
mitkAddCustomModuleTest(mitkEventConfigTest_CreateObjectInDifferentWays mitkEventConfigTest
${MITK_SOURCE_DIR}/Modules/Core/test/resource/Interactions/StatemachineConfigTest.xml
)
mitkAddCustomModuleTest(mitkDataStorageTest_US4DCyl mitkDataStorageTest
${MITK_DATA_DIR}/US4DCyl.nrrd
)
mitkAddCustomModuleTest(mitkPointSetReaderTest mitkPointSetReaderTest
${MITK_DATA_DIR}/PointSetReaderTestData.mps
)
mitkAddCustomModuleTest(mitkImageTest_4DImageData mitkImageTest
${MITK_DATA_DIR}/US4DCyl.nrrd
)
mitkAddCustomModuleTest(mitkImageTest_2D+tImageData mitkImageTest
${MITK_DATA_DIR}/Pic2DplusT.nrrd
)
mitkAddCustomModuleTest(mitkImageTest_3DImageData mitkImageTest
${MITK_DATA_DIR}/Pic3D.nrrd
)
mitkAddCustomModuleTest(mitkImageEqualTest mitkImageEqualTest)
mitkAddCustomModuleTest(mitkImageTest_brainImage mitkImageTest
${MITK_DATA_DIR}/brain.mhd
)
mitkAddCustomModuleTest(mitkLevelWindowManagerTest mitkLevelWindowManagerTest
${MITK_DATA_DIR}/Pic3D.nrrd
)
mitkAddCustomModuleTest(mitkMultiComponentImageDataComparisonFilterTest mitkMultiComponentImageDataComparisonFilterTest
${MITK_DATA_DIR}/NrrdWritingTestImage.jpg
)
mitkAddCustomModuleTest(mitkImageToItkTest mitkImageToItkTest
${MITK_DATA_DIR}/Pic3D.nrrd
)
mitkAddCustomModuleTest(mitkImageSliceSelectorTest mitkImageSliceSelectorTest
${MITK_DATA_DIR}/Pic2DplusT.nrrd
)
mitkAddCustomModuleTest(mitkRotatedSlice4DTest mitkRotatedSlice4DTest
${MITK_DATA_DIR}/UltrasoundImages/4D_TEE_Data_MV.dcm
)
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_rgbaImage640x480 mitkImageVtkMapper2DTest
${MITK_DATA_DIR}/RenderingTestData/rgbaImage.png #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/rgbaImage640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3d640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3d640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3dColorBlue640x480 mitkImageVtkMapper2DColorTest #test for color property (=blue) Pic3D sagittal slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dColorBlue640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3dLevelWindow640x480 mitkImageVtkMapper2DLevelWindowTest #test for levelwindow property (=blood) #Pic3D sagittal slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dLevelWindowBlood640x480REF.png #corresponding reference #screenshot
)
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3dSwivel640x480 mitkImageVtkMapper2DSwivelTest #test for a randomly chosen Pic3D swivelled slice
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dSwivel640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_openMeAlone640x480 mitkPointSetVtkMapper2DTest
${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAlone640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_Pic3DPointSetForPic3D640x480 mitkPointSetVtkMapper2DImageTest
${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/RenderingTestData/PointSetForPic3D.mps #input point set and image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Pic3DPointSetForPic3D640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_openMeAloneGlyphType640x480 mitkPointSetVtkMapper2DGlyphTypeTest
${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAloneGlyphType640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_openMeAloneTransformed640x480 mitkPointSetVtkMapper2DTransformedPointsTest
${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAloneTransformedPoints640x480REF.png #corresponding reference screenshot
)
# Currently not working on windows because of a rendering timing issue
# see bug 18083 for details
if(NOT WIN32)
mitkAddCustomModuleRenderingTest(mitkSurfaceDepthSortingTransparency_StanfordBunnySTL640x480 mitkSurfaceDepthSortingTest
${MITK_DATA_DIR}/RenderingTestData/Stanford_bunny.stl
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Stanford_bunnySTLDepthSorting640x480REF.png)
endif()
# BUG 18695 - tests deactivated, because win 32 bit continuous renders images slightly different. TODO!
#Test reslice interpolation
#note: nearest mode is already tested by swivel test
#mitkAddCustomModuleRenderingTest(ResliceInterpolationIsLinear mitkImageVtkMapper2DResliceInterpolationPropertyTest
# 1 #linear
# ${MITK_DATA_DIR}/Pic3D.nrrd
# -V
# ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefLinear.png #corresponding reference screenshot LINEAR
#)
#mitkAddCustomModuleRenderingTest(ResliceInterpolationIsCubic mitkImageVtkMapper2DResliceInterpolationPropertyTest
# 3 #cubic
# ${MITK_DATA_DIR}/Pic3D.nrrd
# -V
# ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefCubic.png #corresponding reference screenshot CUBIC
#)
#End test reslice interpolation
# Testing of the rendering of binary images
#mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_binaryTestImage640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice
# ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage
# -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImage640x480REF.png #corresponding reference screenshot
#)
#mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_binaryTestImageWithRef640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice
# ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage
# -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImageWithRef640x480REF.png #corresponding reference screenshot
#)
# End of binary image tests
mitkAddCustomModuleRenderingTest(mitkSurfaceVtkMapper3DTest_TextureProperty mitkSurfaceVtkMapper3DTest
${MITK_DATA_DIR}/RenderingTestData/earth.jpg
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/texturedSphere640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2DTransferFunctionTest_Png2D-bw mitkImageVtkMapper2DTransferFunctionTest
${MITK_DATA_DIR}/Png2D-bw.png
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-TransferFunctionRGBImage640x480REF.png #corresponding reference screenshot
)
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2DOpacityTransferFunctionTest_Png2D-bw mitkImageVtkMapper2DOpacityTransferFunctionTest
${MITK_DATA_DIR}/Png2D-bw.png
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-OpacityTransferFunctionRGBImage640x480REF.png #corresponding reference screenshot
)
############################## DISABLED TESTS
mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2DLookupTableTest_Png2D-bw mitkImageVtkMapper2DLookupTableTest
${MITK_DATA_DIR}/Png2D-bw.png
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-LookupTableRGBImage640x480REF.png #corresponding reference screenshot
)
#mitkAddCustomModuleRenderingTest(mitkImageTest_color2DImage mitkImageTest
# ${MITK_DATA_DIR}/NrrdWritingTestImage.jpg
#)
#mitkAddCustomModuleRenderingTest(mitkNodeDependentPointSetInteractorTest mitkNodeDependentPointSetInteractorTest
# ${MITK_DATA_DIR}/Pic3D.pic.gz ${MITK_DATA_DIR}/BallBinary30x30x30.pic.gz
#)
mitkAddCustomModuleRenderingTest(mitkPlaneGeometryDataMapper2DTest mitkPlaneGeometryDataMapper2DTest
${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage
-V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/PlaneGeometryMapper640x480REF.png #corresponding reference screenshot
)
endif() # TARGET ${TESTDRIVER}
diff --git a/Modules/Core/test/mitkTinyXMLTest.cpp b/Modules/Core/test/mitkTinyXMLTest.cpp
index ddd251e473..392ab4384d 100644
--- a/Modules/Core/test/mitkTinyXMLTest.cpp
+++ b/Modules/Core/test/mitkTinyXMLTest.cpp
@@ -1,159 +1,162 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// Testing
#include "mitkTestFixture.h"
#include <mitkTestingMacros.h>
// std includes
#include <cmath>
#include <iomanip>
-#include <tinyxml.h>
+#include <tinyxml2.h>
// MITK includes
#include "mitkStringProperty.h"
#include <mitkNumericTypes.h>
// itksys
#include <itksys/SystemTools.hxx>
// VTK includes
#include <vtkDebugLeaks.h>
// vnl includes
#include <vnl/vnl_vector_fixed.hxx>
class mitkTinyXMLTestSuite : public mitk::TestFixture
{
CPPUNIT_TEST_SUITE(mitkTinyXMLTestSuite);
MITK_TEST(TestingFunctionSetupWorks_Success);
MITK_TEST(TestingReadValueFromSetupDocument_Success);
MITK_TEST(TestingReadOutValueWorks_Success);
MITK_TEST(TestDoubleValueWriteOut_Success);
MITK_TEST(TestDoubleValueWriteOutManyDecimalPlaces_Success);
CPPUNIT_TEST_SUITE_END();
private:
const std::string m_Filename = itksys::SystemTools::GetCurrentWorkingDirectory() + "/TinyXMLTest.txt";
const std::string m_ElementToStoreAttributeName = "DoubleTest";
const std::string m_AttributeToStoreName = "CommaValue";
- TiXmlDocument m_Document;
- TiXmlElement *m_DoubleTest;
+ tinyxml2::XMLDocument m_Document;
+ tinyxml2::XMLElement *m_DoubleTest;
double calcPrecision(const unsigned int requiredDecimalPlaces)
{
return pow(10.0, -1.0 * ((double)requiredDecimalPlaces));
}
bool Setup(double valueToWrite)
{
+ m_Document.Clear();
+ m_DoubleTest = nullptr;
+
// 1. create simple document
- auto decl = new TiXmlDeclaration("1.0", "", ""); // TODO what to write here? encoding? etc....
- m_Document.LinkEndChild(decl);
+ m_Document.InsertEndChild(m_Document.NewDeclaration());
- auto version = new TiXmlElement("Version");
+ auto *version = m_Document.NewElement("Version");
version->SetAttribute("Writer", __FILE__);
version->SetAttribute("CVSRevision", "$Revision: 17055 $");
version->SetAttribute("FileVersion", 1);
- m_Document.LinkEndChild(version);
+ m_Document.InsertEndChild(version);
// 2. store one element containing a double value with potentially many after comma digits.
- auto vElement = new TiXmlElement(m_ElementToStoreAttributeName);
- vElement->SetDoubleAttribute(m_AttributeToStoreName, valueToWrite);
- m_Document.LinkEndChild(vElement);
+ auto *vElement = m_Document.NewElement(m_ElementToStoreAttributeName.c_str());
+ vElement->SetAttribute(m_AttributeToStoreName.c_str(), valueToWrite);
+ m_Document.InsertEndChild(vElement);
// 3. store in file.
- return m_Document.SaveFile(m_Filename);
+ auto err = m_Document.SaveFile(m_Filename.c_str());
+ return tinyxml2::XML_SUCCESS == err;
}
public:
void setUp() override {}
void tearDown() override {}
void TestingFunctionSetupWorks_Success()
{
CPPUNIT_ASSERT_MESSAGE("Test if Setup correctly writes data to file", Setup(1.0));
}
int readValueFromSetupDocument(double &readOutValue)
{
- if (!m_Document.LoadFile(m_Filename))
+ if (tinyxml2::XML_SUCCESS != m_Document.LoadFile(m_Filename.c_str()))
{
CPPUNIT_ASSERT_MESSAGE("Test Setup failed, could not open file", false);
- return TIXML_NO_ATTRIBUTE;
+ return tinyxml2::XML_NO_ATTRIBUTE;
}
else
{
- m_DoubleTest = m_Document.FirstChildElement(m_ElementToStoreAttributeName);
- return m_DoubleTest->QueryDoubleAttribute(m_AttributeToStoreName, &readOutValue);
+ m_DoubleTest = m_Document.FirstChildElement(m_ElementToStoreAttributeName.c_str());
+ return m_DoubleTest->QueryDoubleAttribute(m_AttributeToStoreName.c_str(), &readOutValue);
}
}
void TestingReadValueFromSetupDocument_Success()
{
- if (!m_Document.LoadFile(m_Filename))
+ if (tinyxml2::XML_SUCCESS != m_Document.LoadFile(m_Filename.c_str()))
{
- CPPUNIT_ASSERT_MESSAGE("Test Setup failed, could not open file", !m_Document.LoadFile(m_Filename));
+ CPPUNIT_ASSERT_MESSAGE("Test Setup failed, could not open file", tinyxml2::XML_SUCCESS != m_Document.LoadFile(m_Filename.c_str()));
}
else
{
- m_DoubleTest = m_Document.FirstChildElement(m_ElementToStoreAttributeName);
+ m_DoubleTest = m_Document.FirstChildElement(m_ElementToStoreAttributeName.c_str());
CPPUNIT_ASSERT_MESSAGE("Test Setup could open file", m_DoubleTest != nullptr);
}
}
/**
* this first test ensures we can correctly readout values from the
* TinyXMLDocument.
*/
void TestingReadOutValueWorks_Success()
{
double readValue;
CPPUNIT_ASSERT_MESSAGE("checking if readout mechanism works.",
- TIXML_SUCCESS == readValueFromSetupDocument(readValue));
+ tinyxml2::XML_SUCCESS == readValueFromSetupDocument(readValue));
}
void TestDoubleValueWriteOut_Success()
{
const double valueToWrite = -1.123456;
const int validDigitsAfterComma = 6; // indicates the number of valid digits after comma of valueToWrite
const double neededPrecision = calcPrecision(validDigitsAfterComma + 1);
double readValue;
Setup(valueToWrite);
readValueFromSetupDocument(readValue);
CPPUNIT_ASSERT_MESSAGE("Testing if value valueToWrite equals readValue which was retrieved from TinyXML document",
mitk::Equal(valueToWrite, readValue, neededPrecision));
}
void TestDoubleValueWriteOutManyDecimalPlaces_Success()
{
const double valueToWrite = -1.12345678910111;
const int validDigitsAfterComma = 14; // indicates the number of valid digits after comma of valueToWrite
const double neededPrecision = calcPrecision(validDigitsAfterComma + 1);
double readValue;
Setup(valueToWrite);
readValueFromSetupDocument(readValue);
CPPUNIT_ASSERT_MESSAGE("Testing if value valueToWrite equals readValue which was retrieved from TinyXML document",
mitk::Equal(valueToWrite, readValue, neededPrecision));
}
};
MITK_TEST_SUITE_REGISTRATION(mitkTinyXML)
diff --git a/Modules/DICOM/CMakeLists.txt b/Modules/DICOM/CMakeLists.txt
index 98d7de357c..ebff7f5798 100644
--- a/Modules/DICOM/CMakeLists.txt
+++ b/Modules/DICOM/CMakeLists.txt
@@ -1,9 +1,9 @@
MITK_CREATE_MODULE(
DEPENDS MitkCore
PACKAGE_DEPENDS
- PUBLIC tinyxml GDCM
- PRIVATE ITK|ITKIOImageBase+ITKIOGDCM DCMTK
+ PUBLIC GDCM tinyxml2
+ PRIVATE DCMTK ITK|IOGDCM
)
add_subdirectory(test)
add_subdirectory(autoload/DICOMImageIO)
diff --git a/Modules/DICOM/autoload/DICOMImageIO/CMakeLists.txt b/Modules/DICOM/autoload/DICOMImageIO/CMakeLists.txt
index 53a0b7f3c2..147473ce52 100644
--- a/Modules/DICOM/autoload/DICOMImageIO/CMakeLists.txt
+++ b/Modules/DICOM/autoload/DICOMImageIO/CMakeLists.txt
@@ -1,6 +1,4 @@
MITK_CREATE_MODULE(
DEPENDS MitkCore MitkDICOM
- PACKAGE_DEPENDS
- PRIVATE ITK|ITKIOGDCM+ITKIOImageBase
AUTOLOAD_WITH MitkCore
)
diff --git a/Modules/DICOM/include/mitkDICOMReaderConfigurator.h b/Modules/DICOM/include/mitkDICOMReaderConfigurator.h
index e098ee4b85..00da6131c2 100644
--- a/Modules/DICOM/include/mitkDICOMReaderConfigurator.h
+++ b/Modules/DICOM/include/mitkDICOMReaderConfigurator.h
@@ -1,142 +1,145 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDICOMReaderConfigurator_h
#define mitkDICOMReaderConfigurator_h
#include "mitkClassicDICOMSeriesReader.h"
#include "mitkDICOMTagBasedSorter.h"
-// to put into private implementation
-#include "tinyxml.h"
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
/**
\ingroup DICOMModule
\brief Too-simple factory to create DICOMFileReader%s.
This class is able to instantiate and configure (where possible) DICOMFileReader%s from XML descriptions.
\note This is a bad factory example, because the factory is not extensible and needs to know all the specific readers. A flexible implementation should be provided in a future version.
In its current version, the XML input is meant to be structured like
\verbatim
<?xml version="1.0" standalone=no>
<DICOMFileReader
label="Example Reader"
description="Sort images by example tags"
class="DICOMITKSeriesGDCMReader"
fixTiltByShearing="true">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
</Distinguishing>
<Sorting>
<ImagePositionPatient/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMFileReader>
\endverbatim
The root-tag \c \<DICOMFileReader\> names the class to be instantiated, currently this can be one of
- DICOMITKSeriesGDCMReader
- ThreeDnTDICOMSeriesReader
Both classes bring simple configuration flags with them and a description of how images are sorted prior to loading.
Flag for DICOMITKSeriesGDCMReader:
<pre>fixTiltByShearing="true|false"</pre>
Determines whether a potential gantry tilt should be "fixed" by shearing the output image.
Flag for ThreeDnTDICOMSeriesReader:
<pre>group3DnT="true|false"</pre>
Determines whether images at the same spatial position should be interpreted as 3D+t images.
The tags \c \<Distinguishing\> and \c \<Sorting\> describe the basic loading strategy of both
reader mentioned above: first images are divided into incompatible groups (\c \<Distinguishing\>),
and afterwards the images within each group are sorted by means of DICOMSortCriterion, which
most commonly mentions a tag.
Tag element and group are interpreted as the exadecimal numbers
found all around the DICOM standard. The numbers can be prepended by a "0x" if this is preferred
by the programmer (but they are taken as hexadecimal in all cases).
\section DICOMReaderConfigurator_AboutTheFuture About the future evolution of this class
This first version is hard coded for the current state of the implementation.
If things should evolve in a way that needs us to splitt off readers for "old" versions,
time should be taken to refactor this class.
Basically, a serializer class should accompany each of the configurable classes. Such
serializer classes should be registered and discovered via micro-services (to support extensions).
A serializer should offer both methods to serialize a class and to desirialize it again.
A "version" attribute at the top-level tag should be used to distinguish versions.
Usually it should be enough to keep DE-serializers for all versions. Writers for the most
recent version should be enough.
*/
class MITKDICOM_EXPORT DICOMReaderConfigurator : public itk::LightObject
{
public:
mitkClassMacroItkParent( DICOMReaderConfigurator, itk::LightObject );
itkNewMacro( DICOMReaderConfigurator );
DICOMFileReader::Pointer CreateFromConfigFile(const std::string& filename) const;
DICOMFileReader::Pointer CreateFromUTF8ConfigString(const std::string& xmlContents) const;
std::string CreateConfigStringFromReader(DICOMFileReader::ConstPointer reader) const;
protected:
DICOMReaderConfigurator();
~DICOMReaderConfigurator() override;
private:
- DICOMFileReader::Pointer CreateFromTiXmlDocument(TiXmlDocument& doc) const;
- DICOMTag tagFromXMLElement(TiXmlElement*) const;
- std::string requiredStringAttribute(TiXmlElement* xmlElement, const std::string& key) const;
+ DICOMFileReader::Pointer CreateFromXMLDocument(tinyxml2::XMLDocument& doc) const;
+ DICOMTag tagFromXMLElement(const tinyxml2::XMLElement*) const;
+ std::string requiredStringAttribute(const tinyxml2::XMLElement* xmlElement, const std::string& key) const;
unsigned int hexStringToUInt(const std::string& s) const;
- ThreeDnTDICOMSeriesReader::Pointer ConfigureThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, TiXmlElement*) const;
- DICOMITKSeriesGDCMReader::Pointer ConfigureDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, TiXmlElement*) const;
- void ConfigureCommonPropertiesOfDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, TiXmlElement* element) const;
- void ConfigureCommonPropertiesOfThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, TiXmlElement* element) const;
+ ThreeDnTDICOMSeriesReader::Pointer ConfigureThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, const tinyxml2::XMLElement*) const;
+ DICOMITKSeriesGDCMReader::Pointer ConfigureDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, const tinyxml2::XMLElement*) const;
+ void ConfigureCommonPropertiesOfDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, const tinyxml2::XMLElement* element) const;
+ void ConfigureCommonPropertiesOfThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, const tinyxml2::XMLElement* element) const;
+
+ DICOMSortCriterion::Pointer CreateDICOMSortByTag(const tinyxml2::XMLElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const;
+ DICOMSortCriterion::Pointer CreateSortByImagePositionPatient(const tinyxml2::XMLElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const;
- DICOMSortCriterion::Pointer CreateDICOMSortByTag(TiXmlElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const;
- DICOMSortCriterion::Pointer CreateSortByImagePositionPatient(TiXmlElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const;
+ mitk::DICOMTagBasedSorter::Pointer CreateDICOMTagBasedSorter(const tinyxml2::XMLElement* element) const;
- mitk::DICOMTagBasedSorter::Pointer CreateDICOMTagBasedSorter(TiXmlElement* element) const;
+ tinyxml2::XMLElement* CreateConfigStringFromReader(tinyxml2::XMLDocument& doc, const DICOMITKSeriesGDCMReader* reader) const;
+ tinyxml2::XMLElement* CreateConfigStringFromReader(tinyxml2::XMLDocument& doc, const ThreeDnTDICOMSeriesReader* reader) const;
+ tinyxml2::XMLElement* CreateConfigStringFromReader(tinyxml2::XMLDocument& doc, const ClassicDICOMSeriesReader* reader) const;
- TiXmlElement* CreateConfigStringFromReader(const DICOMITKSeriesGDCMReader* reader) const;
- TiXmlElement* CreateConfigStringFromReader(const ThreeDnTDICOMSeriesReader* reader) const;
- TiXmlElement* CreateConfigStringFromReader(const ClassicDICOMSeriesReader* reader) const;
+ tinyxml2::XMLElement* CreateConfigStringFromDICOMDatasetSorter(tinyxml2::XMLDocument& doc, const DICOMTagBasedSorter* sorter) const;
- TiXmlElement* CreateConfigStringFromDICOMDatasetSorter(const DICOMTagBasedSorter* sorter) const;
+ tinyxml2::XMLElement* CreateConfigStringFromDICOMTag(tinyxml2::XMLDocument& doc, const DICOMTag& tag) const;
- TiXmlElement* CreateConfigStringFromDICOMTag(const DICOMTag& tag) const;
+ tinyxml2::XMLElement* CreateDICOMFileReaderTag(tinyxml2::XMLDocument& doc, const DICOMFileReader* reader) const;
- TiXmlElement* CreateDICOMFileReaderTag(const DICOMFileReader* reader) const;
- const char* toString(bool) const;
std::string toHexString(unsigned int i) const;
/** Helper that queries an boolean xml attribute. If the attribute does not exist, the passed default value is used.*/
- bool QueryBooleanAttribute(const TiXmlElement* element, const char* attributeName, bool defaultValue) const;
+ bool QueryBooleanAttribute(const tinyxml2::XMLElement* element, const char* attributeName, bool defaultValue) const;
};
} // namespace
#endif // mitkDICOMReaderConfigurator_h
diff --git a/Modules/DICOM/resource/configurations/3D/classicreader.xml b/Modules/DICOM/resource/configurations/3D/classicreader.xml
index 7ed3332f6a..e5e063d39c 100644
--- a/Modules/DICOM/resource/configurations/3D/classicreader.xml
+++ b/Modules/DICOM/resource/configurations/3D/classicreader.xml
@@ -1,10 +1,10 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="2013 default sorting"
description="Sort images by Image Position, then by Acquisition Number, Acq. Time, Trigger time, group tilted images"
class="ClassicDICOMSeriesReader"
version="2"
group3DnT="false"
fixTiltByShearing="true"
>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3D/imageposition.xml b/Modules/DICOM/resource/configurations/3D/imageposition.xml
index c00d4cd8e2..09b55d3ecf 100644
--- a/Modules/DICOM/resource/configurations/3D/imageposition.xml
+++ b/Modules/DICOM/resource/configurations/3D/imageposition.xml
@@ -1,25 +1,25 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="Image Position"
description="Sort images by Image Position (Patient)"
class="DICOMITKSeriesGDCMReader"
version="2"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="false" expectDistanceOne="false">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesDescription" group="0008" element="103e"/>
<Tag name="ProtocolName" group="0018" element="1030"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
<Tag name="Modality" group="0x0008" element="0x0060"/>
<Tag name="BodyPartExamined" group="0x0018" element="0x0015"/>
<Tag name="SequenceName" group="0x0018" element="0x0024"/>
</Distinguishing>
<Sorting>
<ImagePositionPatient/>
<Tag name="AcquisitionTime" group="0x0008" element="0x0032"/>
<Tag name="TriggerTime" group="0x0018" element="0x1060"/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3D/imageposition_byacquisition.xml b/Modules/DICOM/resource/configurations/3D/imageposition_byacquisition.xml
index 54b9f6377a..d145528099 100644
--- a/Modules/DICOM/resource/configurations/3D/imageposition_byacquisition.xml
+++ b/Modules/DICOM/resource/configurations/3D/imageposition_byacquisition.xml
@@ -1,26 +1,26 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="Image Position by Acquisition"
description="Group images by Acquistion, then sort groups by Image Position (Patient)"
class="DICOMITKSeriesGDCMReader"
version="2"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="false" expectDistanceOne="false">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesDescription" group="0008" element="103e"/>
<Tag name="ProtocolName" group="0018" element="1030"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
<Tag name="AcquisitionNumber" group="0x0020" element="0x0012"/>
<Tag name="Modality" group="0x0008" element="0x0060"/>
<Tag name="BodyPartExamined" group="0x0018" element="0x0015"/>
<Tag name="SequenceName" group="0x0018" element="0x0024"/>
</Distinguishing>
<Sorting>
<ImagePositionPatient/>
<Tag name="AcquisitionTime" group="0x0008" element="0x0032"/>
<Tag name="TriggerTime" group="0x0018" element="0x1060"/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3D/imagetime.xml b/Modules/DICOM/resource/configurations/3D/imagetime.xml
index 83cdb1c1b0..62e97e455f 100644
--- a/Modules/DICOM/resource/configurations/3D/imagetime.xml
+++ b/Modules/DICOM/resource/configurations/3D/imagetime.xml
@@ -1,24 +1,24 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="Image Time"
description="Sort images by Acqusition Time"
class="DICOMITKSeriesGDCMReader"
version="2"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="true" expectDistanceOne="true">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesDescription" group="0008" element="103e"/>
<Tag name="ProtocolName" group="0018" element="1030"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
<Tag name="AcquisitionNumber" group="0x0020" element="0x0012"/>
<Tag name="Modality" group="0x0008" element="0x0060"/>
<Tag name="BodyPartExamined" group="0x0018" element="0x0015"/>
<Tag name="SequenceName" group="0x0018" element="0x0024"/>
</Distinguishing>
<Sorting>
<Tag name="AcquisitionTime" group="0x0008" element="0x0032"/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3D/instancenumber.xml b/Modules/DICOM/resource/configurations/3D/instancenumber.xml
index f83b56e3c8..1fd86e4db6 100644
--- a/Modules/DICOM/resource/configurations/3D/instancenumber.xml
+++ b/Modules/DICOM/resource/configurations/3D/instancenumber.xml
@@ -1,24 +1,24 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="Instance Number, consecutive"
description="Sort images by Instance Number, require equal distances of 1"
class="DICOMITKSeriesGDCMReader"
version="2"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="true" expectDistanceOne="true">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesDescription" group="0008" element="103e"/>
<Tag name="ProtocolName" group="0018" element="1030"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
<Tag name="AcquisitionNumber" group="0x0020" element="0x0012"/>
<Tag name="Modality" group="0x0008" element="0x0060"/>
<Tag name="BodyPartExamined" group="0x0018" element="0x0015"/>
<Tag name="SequenceName" group="0x0018" element="0x0024"/>
</Distinguishing>
<Sorting>
<Tag name="InstanceNumber" group="0x0020" element="0x0013"/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3D/instancenumber_soft.xml b/Modules/DICOM/resource/configurations/3D/instancenumber_soft.xml
index 1c2c660700..9cf61cbfcf 100644
--- a/Modules/DICOM/resource/configurations/3D/instancenumber_soft.xml
+++ b/Modules/DICOM/resource/configurations/3D/instancenumber_soft.xml
@@ -1,24 +1,24 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="Instance Number, non-consecutive"
description="Sort images by Instance Number, do not require consecutive numbers"
class="DICOMITKSeriesGDCMReader"
version="2"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="false" expectDistanceOne="false">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesDescription" group="0008" element="103e"/>
<Tag name="ProtocolName" group="0018" element="1030"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
<Tag name="AcquisitionNumber" group="0x0020" element="0x0012"/>
<Tag name="Modality" group="0x0008" element="0x0060"/>
<Tag name="BodyPartExamined" group="0x0018" element="0x0015"/>
<Tag name="SequenceName" group="0x0018" element="0x0024"/>
</Distinguishing>
<Sorting>
<Tag name="InstanceNumber" group="0x0020" element="0x0013"/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3D/simpleinstancenumber_soft.xml b/Modules/DICOM/resource/configurations/3D/simpleinstancenumber_soft.xml
index 79c636e78b..eba6bbef60 100644
--- a/Modules/DICOM/resource/configurations/3D/simpleinstancenumber_soft.xml
+++ b/Modules/DICOM/resource/configurations/3D/simpleinstancenumber_soft.xml
@@ -1,25 +1,25 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="Instance Number, non-consecutive, simple import"
description="Sort images by Instance Number, do not require consecutive numbers"
class="DICOMITKSeriesGDCMReader"
version="2"
fixTiltByShearing="true"
simpleVolumeImport="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="false" expectDistanceOne="false">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesDescription" group="0008" element="103e"/>
<Tag name="ProtocolName" group="0018" element="1030"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
<Tag name="AcquisitionNumber" group="0x0020" element="0x0012"/>
<Tag name="Modality" group="0x0008" element="0x0060"/>
<Tag name="BodyPartExamined" group="0x0018" element="0x0015"/>
<Tag name="SequenceName" group="0x0018" element="0x0024"/>
</Distinguishing>
<Sorting>
<Tag name="InstanceNumber" group="0x0020" element="0x0013"/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3D/slicelocation.xml b/Modules/DICOM/resource/configurations/3D/slicelocation.xml
index 967bb5af57..7ddb18d2f1 100644
--- a/Modules/DICOM/resource/configurations/3D/slicelocation.xml
+++ b/Modules/DICOM/resource/configurations/3D/slicelocation.xml
@@ -1,24 +1,24 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="Slice Location"
description="Sort images by Slice Location, require equal distance between locations"
class="DICOMITKSeriesGDCMReader"
version="2"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="true" expectDistanceOne="false">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020" element="000e"/>
<Tag name="SeriesDescription" group="0008" element="103e"/>
<Tag name="ProtocolName" group="0018" element="1030"/>
<Tag name="SeriesNumber" group="0020" element="0011"/>
<Tag name="AcquisitionNumber" group="0x0020" element="0x0012"/>
<Tag name="Modality" group="0x0008" element="0x0060"/>
<Tag name="BodyPartExamined" group="0x0018" element="0x0015"/>
<Tag name="SequenceName" group="0x0018" element="0x0024"/>
</Distinguishing>
<Sorting>
<Tag name="SliceLocation" group="0x0020" element="0x1041"/>
<Tag name="SOPInstanceUID" group="0x0008" element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3DnT/classicreader.xml b/Modules/DICOM/resource/configurations/3DnT/classicreader.xml
index 1a0ca7f09a..6d40321c7f 100644
--- a/Modules/DICOM/resource/configurations/3DnT/classicreader.xml
+++ b/Modules/DICOM/resource/configurations/3DnT/classicreader.xml
@@ -1,11 +1,11 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
label="2013 default sorting for 3D+t"
description="ClassicDICOMSeriesReader that is equal to the 2013 implementation for 3D+t images, except it only condenses blocks with same series."
class="ClassicDICOMSeriesReader"
version="2"
group3DnT="true"
fixTiltByShearing="true"
onlyCondenseSameSeries="true"
>
-</DICOMFileReader>
\ No newline at end of file
+</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3DnT/imageposition.xml b/Modules/DICOM/resource/configurations/3DnT/imageposition.xml
index f8e1601952..a44d46cfc9 100644
--- a/Modules/DICOM/resource/configurations/3DnT/imageposition.xml
+++ b/Modules/DICOM/resource/configurations/3DnT/imageposition.xml
@@ -1,21 +1,21 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
class="ThreeDnTDICOMSeriesReader"
version="2"
label="IPP 3D+t"
description="Sort by Image Position (Patient), then group as 3D+t (till 2018/03 this configuration was wrongly stored in the file classicreader.xml (verison 1))"
group3DnT="true"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="true" expectDistanceOne="true">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020," element="000e"/>
</Distinguishing>
<Sorting>
<ImagePositionPatient/>
<Tag name="AcquisitionNumber" group="0x0020," element="0x0012"/>
<Tag name="AcquisitionTime" group="0x0008," element="0x0032"/>
<Tag name="TriggerTime" group="0x0018," element="0x1060"/>
<Tag name="SOPInstanceUID" group="0x0008," element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3DnT/imageposition_byacquisition.xml b/Modules/DICOM/resource/configurations/3DnT/imageposition_byacquisition.xml
index 1a356abfb1..d6815044b6 100644
--- a/Modules/DICOM/resource/configurations/3DnT/imageposition_byacquisition.xml
+++ b/Modules/DICOM/resource/configurations/3DnT/imageposition_byacquisition.xml
@@ -1,19 +1,19 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
class="ThreeDnTDICOMSeriesReader"
version="2"
label="3D+t by AcquisitionNumber" description="Group as 3D+t by AcquisitionTime, then sort by Image Position (Patient)"
group3DnT="true"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="true" expectDistanceOne="true">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020," element="000e"/>
<Tag name="AcquisitionTime" group="0x0008," element="0x0032"/>
</Distinguishing>
<Sorting>
<ImagePositionPatient/>
<Tag name="InstanceNumber" group="0x0020" element="0x0013"/>
<Tag name="SOPInstanceUID" group="0x0008," element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
-</DICOMFileReader>
\ No newline at end of file
+</DICOMFileReader>
diff --git a/Modules/DICOM/resource/configurations/3DnT/imageposition_bytriggertime.xml b/Modules/DICOM/resource/configurations/3DnT/imageposition_bytriggertime.xml
index f8f636255c..1a3f39fae4 100644
--- a/Modules/DICOM/resource/configurations/3DnT/imageposition_bytriggertime.xml
+++ b/Modules/DICOM/resource/configurations/3DnT/imageposition_bytriggertime.xml
@@ -1,19 +1,19 @@
-<?xml version="1.0" standalone=no>
+<?xml version="1.0" standalone="no"?>
<DICOMFileReader
class="ThreeDnTDICOMSeriesReader"
version="2"
label="3D+t by TriggerTime" description="Group as 3D+t by TriggerTime, then sort by Image Position (Patient)"
group3DnT="true"
fixTiltByShearing="true">
<DICOMDatasetSorter class="DICOMTagBasedSorter" strictSorting="true" expectDistanceOne="true">
<Distinguishing>
<Tag name="SeriesInstanceUID" group="0020," element="000e"/>
<Tag name="TriggerTime" group="0x0018," element="0x1060"/>
</Distinguishing>
<Sorting>
<ImagePositionPatient/>
<Tag name="InstanceNumber" group="0x0020" element="0x0013"/>
<Tag name="SOPInstanceUID" group="0x0008," element="0x0018"/>
</Sorting>
</DICOMDatasetSorter>
-</DICOMFileReader>
\ No newline at end of file
+</DICOMFileReader>
diff --git a/Modules/DICOM/src/mitkDICOMReaderConfigurator.cpp b/Modules/DICOM/src/mitkDICOMReaderConfigurator.cpp
index 87e64e6c1c..68f7a4dccb 100644
--- a/Modules/DICOM/src/mitkDICOMReaderConfigurator.cpp
+++ b/Modules/DICOM/src/mitkDICOMReaderConfigurator.cpp
@@ -1,678 +1,673 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkDICOMReaderConfigurator.h"
#include "mitkDICOMSortByTag.h"
#include "mitkSortByImagePositionPatient.h"
+#include <tinyxml2.h>
mitk::DICOMReaderConfigurator
::DICOMReaderConfigurator()
{
}
mitk::DICOMReaderConfigurator
::~DICOMReaderConfigurator()
{
}
mitk::DICOMFileReader::Pointer
mitk::DICOMReaderConfigurator
::CreateFromConfigFile(const std::string& filename) const
{
- TiXmlDocument doc (filename);
- if (doc.LoadFile())
+ tinyxml2::XMLDocument doc;
+ if (tinyxml2::XML_SUCCESS == doc.LoadFile(filename.c_str()))
{
- return this->CreateFromTiXmlDocument( doc );
+ return this->CreateFromXMLDocument( doc );
}
else
{
MITK_ERROR << "Unable to load file at '" << filename <<"'";
return DICOMFileReader::Pointer();
}
}
mitk::DICOMFileReader::Pointer
mitk::DICOMReaderConfigurator
::CreateFromUTF8ConfigString(const std::string& xmlContents) const
{
- TiXmlDocument doc;
- doc.Parse(xmlContents.c_str(), nullptr, TIXML_ENCODING_UTF8);
+ tinyxml2::XMLDocument doc;
+ doc.Parse(xmlContents.c_str());
- return this->CreateFromTiXmlDocument( doc );
+ return this->CreateFromXMLDocument( doc );
}
mitk::DICOMFileReader::Pointer
mitk::DICOMReaderConfigurator
-::CreateFromTiXmlDocument(TiXmlDocument& doc) const
+::CreateFromXMLDocument(tinyxml2::XMLDocument& doc) const
{
- TiXmlHandle root(doc.RootElement());
+ tinyxml2::XMLHandle root(doc.RootElement());
- if (TiXmlElement* rootElement = root.ToElement())
+ if (auto* rootElement = root.ToElement())
{
if (strcmp(rootElement->Value(), "DICOMFileReader")) // :-( no std::string methods
{
MITK_ERROR << "File should contain a <DICOMFileReader> tag at top-level! Found '"
<< (rootElement->Value() ? std::string(rootElement->Value()) : std::string("!nothing!")) << "' instead";
return nullptr;
}
const char* classnameC = rootElement->Attribute("class");
if (!classnameC)
{
MITK_ERROR << "File should name a reader class in the class attribute: <DICOMFileReader class=\"...\">. Found nothing instead";
return nullptr;
}
int version(1);
- if ( rootElement->QueryIntAttribute("version", &version) == TIXML_SUCCESS)
+ if ( rootElement->QueryIntAttribute("version", &version) == tinyxml2::XML_SUCCESS)
{
if (version == 1)
{
MITK_WARN << "Warning the given configuration is for DICOMFileReaders of version 1. "
<< "This old version may be interpreted differently. Reason: "
<< "The default values for the following xml settings have been changed: "
<< "FixTiltByShearing (false -> true); StrictSorting (true -> false); ExpectDistanceOne (true -> false).";
}
else if (version >2)
{
MITK_WARN << "This reader is only capable of creating DICOMFileReaders of version 1 and 2. "
<< "Will not continue, because given configuration is meant for version " << version << ".";
return nullptr;
}
}
else
{
MITK_ERROR << "File should name the version of the reader class in the version attribute: <DICOMFileReader class=\"" << classnameC << "\" version=\"...\">."
<< " Found nothing instead, assuming version 1!";
version = 1;
}
std::string classname(classnameC);
double decimalPlacesForOrientation(mitk::DICOMITKSeriesGDCMReader::GetDefaultDecimalPlacesForOrientation());
bool useDecimalPlacesForOrientation(false);
useDecimalPlacesForOrientation =
- rootElement->QueryDoubleAttribute("decimalPlacesForOrientation", &decimalPlacesForOrientation) == TIXML_SUCCESS; // attribute present and a double value
+ rootElement->QueryDoubleAttribute("decimalPlacesForOrientation", &decimalPlacesForOrientation) == tinyxml2::XML_SUCCESS; // attribute present and a double value
if (classname == "ClassicDICOMSeriesReader")
{
mitk::ClassicDICOMSeriesReader::Pointer reader = mitk::ClassicDICOMSeriesReader::New();
this->ConfigureCommonPropertiesOfDICOMITKSeriesGDCMReader(reader.GetPointer(), rootElement);
this->ConfigureCommonPropertiesOfThreeDnTDICOMSeriesReader(reader.GetPointer(), rootElement);
return reader.GetPointer();
}
if (classname == "ThreeDnTDICOMSeriesReader")
{
mitk::ThreeDnTDICOMSeriesReader::Pointer reader;
if (useDecimalPlacesForOrientation)
reader = mitk::ThreeDnTDICOMSeriesReader::New(decimalPlacesForOrientation);
else
reader = mitk::ThreeDnTDICOMSeriesReader::New();
return ConfigureThreeDnTDICOMSeriesReader(reader, rootElement).GetPointer();
}
else
if (classname == "DICOMITKSeriesGDCMReader")
{
bool simpleVolumeImport = QueryBooleanAttribute(rootElement, "simpleVolumeImport", mitk::DICOMITKSeriesGDCMReader::GetDefaultSimpleVolumeImport());
mitk::DICOMITKSeriesGDCMReader::Pointer reader;
if (useDecimalPlacesForOrientation)
reader = mitk::DICOMITKSeriesGDCMReader::New( decimalPlacesForOrientation, simpleVolumeImport );
else
reader = mitk::DICOMITKSeriesGDCMReader::New( mitk::DICOMITKSeriesGDCMReader::GetDefaultDecimalPlacesForOrientation(), simpleVolumeImport );
// simple volume import that ignores number of frames and inter slice distance
return ConfigureDICOMITKSeriesGDCMReader(reader, rootElement).GetPointer();
}
else
{
MITK_ERROR << "DICOMFileReader tag names unknown class '" << classname << "'";
return nullptr;
}
}
else
{
MITK_ERROR << "Great confusion: no root element in XML document. Expecting a DICOMFileReader tag at top-level.";
return nullptr;
}
}
#define boolStringTrue(s) \
( s == "true" || s == "on" || s == "1" \
|| s == "TRUE" || s == "ON")
bool
mitk::DICOMReaderConfigurator
-::QueryBooleanAttribute(const TiXmlElement* element, const char* attributeName, bool defaultValue) const
+::QueryBooleanAttribute(const tinyxml2::XMLElement* element, const char* attributeName, bool defaultValue) const
{
bool value(defaultValue);
- const char* valueC = element->Attribute(attributeName);
- if (valueC)
+ const auto* valueC = element->Attribute(attributeName);
+
+ if (nullptr != valueC)
{
- std::string valueS(valueC);
+ std::string valueS = valueC;
value = boolStringTrue(valueS);
}
+
return value;
}
void
mitk::DICOMReaderConfigurator
-::ConfigureCommonPropertiesOfThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, TiXmlElement* element) const
+::ConfigureCommonPropertiesOfThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, const tinyxml2::XMLElement* element) const
{
// add the "group3DnT" flag
bool group3DnT = QueryBooleanAttribute(element, "group3DnT", ThreeDnTDICOMSeriesReader::GetDefaultGroup3DandT());
reader->SetGroup3DandT( group3DnT );
// add the "onlyCondenseSameSeries" flag
bool onlyCondenseSameSeries = QueryBooleanAttribute(element, "onlyCondenseSameSeries", ThreeDnTDICOMSeriesReader::GetDefaultOnlyCondenseSameSeries());
reader->SetOnlyCondenseSameSeries(onlyCondenseSameSeries);
}
mitk::ThreeDnTDICOMSeriesReader::Pointer
mitk::DICOMReaderConfigurator
-::ConfigureThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, TiXmlElement* element) const
+::ConfigureThreeDnTDICOMSeriesReader(ThreeDnTDICOMSeriesReader::Pointer reader, const tinyxml2::XMLElement* element) const
{
assert(element);
// use all the base class configuration
if (this->ConfigureDICOMITKSeriesGDCMReader( reader.GetPointer(), element ).IsNull())
{
return nullptr;
}
this->ConfigureCommonPropertiesOfThreeDnTDICOMSeriesReader(reader,element);
return reader;
}
void
mitk::DICOMReaderConfigurator
-::ConfigureCommonPropertiesOfDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, TiXmlElement* element) const
+::ConfigureCommonPropertiesOfDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, const tinyxml2::XMLElement* element) const
{
assert(element);
const char* configLabelC = element->Attribute("label");
if (configLabelC)
{
std::string configLabel(configLabelC);
reader->SetConfigurationLabel(configLabel);
}
const char* configDescriptionC = element->Attribute("description");
if (configDescriptionC)
{
reader->SetConfigurationDescription(configDescriptionC);
}
// "fixTiltByShearing" flag
bool fixTiltByShearing = QueryBooleanAttribute(element, "fixTiltByShearing", DICOMITKSeriesGDCMReader::GetDefaultFixTiltByShearing());
reader->SetFixTiltByShearing( fixTiltByShearing );
}
mitk::DICOMITKSeriesGDCMReader::Pointer
mitk::DICOMReaderConfigurator
-::ConfigureDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, TiXmlElement* element) const
+::ConfigureDICOMITKSeriesGDCMReader(DICOMITKSeriesGDCMReader::Pointer reader, const tinyxml2::XMLElement* element) const
{
assert(element);
this->ConfigureCommonPropertiesOfDICOMITKSeriesGDCMReader(reader, element);
// "acceptTwoSlicesGroups" flag
bool acceptTwoSlicesGroups = QueryBooleanAttribute(element, "acceptTwoSlicesGroups", true);
reader->SetAcceptTwoSlicesGroups( acceptTwoSlicesGroups );
// "toleratedOriginError" attribute (double)
bool toleratedOriginErrorIsAbsolute = QueryBooleanAttribute(element, "toleratedOriginErrorIsAbsolute", false);
double toleratedOriginError(0.3);
- if (element->QueryDoubleAttribute("toleratedOriginError", &toleratedOriginError) == TIXML_SUCCESS) // attribute present and a double value
+ if (element->QueryDoubleAttribute("toleratedOriginError", &toleratedOriginError) == tinyxml2::XML_SUCCESS) // attribute present and a double value
{
if (toleratedOriginErrorIsAbsolute)
{
reader->SetToleratedOriginOffset( toleratedOriginError );
}
else
{
reader->SetToleratedOriginOffsetToAdaptive( toleratedOriginError );
}
}
// DICOMTagBasedSorters are the only thing we create at this point
// TODO for-loop over all child elements of type DICOMTagBasedSorter, BUT actually a single sorter of this type is enough.
- TiXmlElement* dElement = element->FirstChildElement("DICOMDatasetSorter");
+ auto* dElement = element->FirstChildElement("DICOMDatasetSorter");
if (dElement)
{
const char* classnameC = dElement->Attribute("class");
if (!classnameC)
{
MITK_ERROR << "File should name a DICOMDatasetSorter class in the class attribute of <DICOMDatasetSorter class=\"...\">. Found nothing instead";
return nullptr;
}
std::string classname(classnameC);
if (classname == "DICOMTagBasedSorter")
{
DICOMTagBasedSorter::Pointer tagSorter = CreateDICOMTagBasedSorter(dElement);
if (tagSorter.IsNotNull())
{
reader->AddSortingElement( tagSorter );
}
}
else
{
MITK_ERROR << "DICOMDatasetSorter tag names unknown class '" << classname << "'";
return nullptr;
}
}
return reader;
}
mitk::DICOMTagBasedSorter::Pointer
mitk::DICOMReaderConfigurator
-::CreateDICOMTagBasedSorter(TiXmlElement* element) const
+::CreateDICOMTagBasedSorter(const tinyxml2::XMLElement* element) const
{
mitk::DICOMTagBasedSorter::Pointer tagSorter = mitk::DICOMTagBasedSorter::New();
// "strictSorting" parameter!
bool strictSorting = QueryBooleanAttribute(element, "strictSorting", mitk::DICOMTagBasedSorter::GetDefaultStrictSorting());
tagSorter->SetStrictSorting(strictSorting);
// "strictSorting" parameter!
bool expectDistanceOne = QueryBooleanAttribute(element, "expectDistanceOne", mitk::DICOMTagBasedSorter::GetDefaultExpectDistanceOne());
tagSorter->SetExpectDistanceOne(expectDistanceOne);
- TiXmlElement* dElement = element->FirstChildElement("Distinguishing");
+ auto* dElement = element->FirstChildElement("Distinguishing");
if (dElement)
{
- for ( TiXmlElement* tChild = dElement->FirstChildElement();
+ for ( auto* tChild = dElement->FirstChildElement();
tChild != nullptr;
tChild = tChild->NextSiblingElement() )
{
try
{
mitk::DICOMTag tag = tagFromXMLElement(tChild);
int i(5);
- if (tChild->QueryIntAttribute("cutDecimalPlaces", &i) == TIXML_SUCCESS)
+ if (tChild->QueryIntAttribute("cutDecimalPlaces", &i) == tinyxml2::XML_SUCCESS)
{
tagSorter->AddDistinguishingTag( tag, new mitk::DICOMTagBasedSorter::CutDecimalPlaces(i) );
}
else
{
tagSorter->AddDistinguishingTag( tag );
}
}
catch(...)
{
return nullptr;
}
}
}
// "sorting tags"
- TiXmlElement* sElement = element->FirstChildElement("Sorting");
+ auto* sElement = element->FirstChildElement("Sorting");
if (sElement)
{
DICOMSortCriterion::Pointer previousCriterion;
DICOMSortCriterion::Pointer currentCriterion;
- for ( TiXmlNode* tChildNode = sElement->LastChild();
+ for ( auto* tChildNode = sElement->LastChild();
tChildNode != nullptr;
tChildNode = tChildNode->PreviousSibling() )
{
- TiXmlElement* tChild = tChildNode->ToElement();
+ auto* tChild = tChildNode->ToElement();
if (!tChild) continue;
if (!strcmp(tChild->Value(), "Tag"))
{
try
{
currentCriterion = this->CreateDICOMSortByTag(tChild, previousCriterion);
}
catch(...)
{
std::stringstream ss;
- ss << "Could not parse <Tag> element at (input line " << tChild->Row() << ", col. " << tChild->Column() << ")!";
+ ss << "Could not parse <Tag> element at input line " << tChild->GetLineNum() << "!";
MITK_ERROR << ss.str();
return nullptr;
}
}
else
if (!strcmp(tChild->Value(), "ImagePositionPatient"))
{
try
{
currentCriterion = this->CreateSortByImagePositionPatient(tChild, previousCriterion);
}
catch(...)
{
std::stringstream ss;
- ss << "Could not parse <ImagePositionPatient> element at (input line " << tChild->Row() << ", col. " << tChild->Column() << ")!";
+ ss << "Could not parse <ImagePositionPatient> element at input line " << tChild->GetLineNum() << "!";
MITK_ERROR << ss.str();
return nullptr;
}
}
else
{
MITK_ERROR << "File contain unknown tag <" << tChild->Value() << "> tag as child to <Sorting>! Cannot interpret...";
}
previousCriterion = currentCriterion;
}
tagSorter->SetSortCriterion( currentCriterion.GetPointer() );
}
return tagSorter;
}
std::string
mitk::DICOMReaderConfigurator
-::requiredStringAttribute(TiXmlElement* xmlElement, const std::string& key) const
+::requiredStringAttribute(const tinyxml2::XMLElement* xmlElement, const std::string& key) const
{
assert(xmlElement);
const char* gC = xmlElement->Attribute(key.c_str());
if (gC)
{
std::string gS(gC);
return gS;
}
else
{
std::stringstream ss;
- ss << "Expected an attribute '" << key << "' at this position "
- "(input line " << xmlElement->Row() << ", col. " << xmlElement->Column() << ")!";
+ ss << "Expected an attribute '" << key << "' at "
+ "input line " << xmlElement->GetLineNum() << "!";
MITK_ERROR << ss.str();
throw std::invalid_argument( ss.str() );
}
}
unsigned int
mitk::DICOMReaderConfigurator
::hexStringToUInt(const std::string& s) const
{
std::stringstream converter(s);
unsigned int ui;
converter >> std::hex >> ui;
MITK_DEBUG << "Converted string '" << s << "' to unsigned int " << ui;
return ui;
}
mitk::DICOMTag
mitk::DICOMReaderConfigurator
-::tagFromXMLElement(TiXmlElement* xmlElement) const
+::tagFromXMLElement(const tinyxml2::XMLElement* xmlElement) const
{
assert(xmlElement);
if (strcmp(xmlElement->Value(), "Tag")) // :-( no std::string methods
{
std::stringstream ss;
- ss << "Expected a <Tag group=\"..\" element=\"..\"> tag at this position "
- "(input line " << xmlElement->Row() << ", col. " << xmlElement->Column() << ")!";
+ ss << "Expected a <Tag group=\"..\" element=\"..\"> tag at "
+ "input line " << xmlElement->GetLineNum() << "!";
MITK_ERROR << ss.str();
throw std::invalid_argument( ss.str() );
}
std::string groupS = requiredStringAttribute(xmlElement, "group");
std::string elementS = requiredStringAttribute(xmlElement, "element");
try
{
// convert string to int (assuming string is in hex format with leading "0x" like "0x0020")
unsigned int group = hexStringToUInt(groupS);
unsigned int element = hexStringToUInt(elementS);
return DICOMTag(group, element);
}
catch(...)
{
std::stringstream ss;
ss << "Expected group and element values in <Tag group=\"..\" element=\"..\"> to be hexadecimal with leading 0x, e.g. '0x0020'"
- "(input line " << xmlElement->Row() << ", col. " << xmlElement->Column() << ")!";
+ "(input line " << xmlElement->GetLineNum() << ")!";
MITK_ERROR << ss.str();
throw std::invalid_argument( ss.str() );
}
}
mitk::DICOMSortCriterion::Pointer
mitk::DICOMReaderConfigurator
-::CreateDICOMSortByTag(TiXmlElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const
+::CreateDICOMSortByTag(const tinyxml2::XMLElement* xmlElement, DICOMSortCriterion::Pointer secondaryCriterion) const
{
mitk::DICOMTag tag = tagFromXMLElement(xmlElement);
return DICOMSortByTag::New(tag, secondaryCriterion).GetPointer();
}
mitk::DICOMSortCriterion::Pointer
mitk::DICOMReaderConfigurator
-::CreateSortByImagePositionPatient(TiXmlElement*, DICOMSortCriterion::Pointer secondaryCriterion) const
+::CreateSortByImagePositionPatient(const tinyxml2::XMLElement*, DICOMSortCriterion::Pointer secondaryCriterion) const
{
return SortByImagePositionPatient::New(secondaryCriterion).GetPointer();
}
std::string
mitk::DICOMReaderConfigurator
::CreateConfigStringFromReader(DICOMFileReader::ConstPointer reader) const
{
// check possible sub-classes from the most-specific one up to the most generic one
const DICOMFileReader* cPointer = reader;
- TiXmlElement* root;
+ tinyxml2::XMLDocument document;
+ tinyxml2::XMLElement* root = nullptr;
if (const auto* specificReader = dynamic_cast<const ClassicDICOMSeriesReader*>(cPointer))
{
- root = this->CreateConfigStringFromReader(specificReader);
+ root = this->CreateConfigStringFromReader(document, specificReader);
}
else
if (const auto* specificReader = dynamic_cast<const ThreeDnTDICOMSeriesReader*>(cPointer))
{
- root = this->CreateConfigStringFromReader(specificReader);
+ root = this->CreateConfigStringFromReader(document, specificReader);
}
else
if (const auto* specificReader = dynamic_cast<const DICOMITKSeriesGDCMReader*>(cPointer))
{
- root = this->CreateConfigStringFromReader(specificReader);
+ root = this->CreateConfigStringFromReader(document, specificReader);
}
else
{
MITK_WARN << "Unknown reader class passed to DICOMReaderConfigurator::CreateConfigStringFromReader(). Cannot serialize.";
return ""; // no serialization, what a pity
}
- if (root)
+ if (nullptr != root)
{
- TiXmlDocument document;
- document.LinkEndChild( root );
+ document.InsertEndChild( root );
- TiXmlPrinter printer;
- printer.SetIndent( " " );
+ tinyxml2::XMLPrinter printer;
+ document.Print(&printer);
- document.Accept( &printer );
std::string xmltext = printer.CStr();
return xmltext;
}
else
{
MITK_WARN << "DICOMReaderConfigurator::CreateConfigStringFromReader() created empty serialization. Problem?";
return "";
}
}
-TiXmlElement*
+tinyxml2::XMLElement*
mitk::DICOMReaderConfigurator
-::CreateConfigStringFromReader(const DICOMITKSeriesGDCMReader* reader) const
+::CreateConfigStringFromReader(tinyxml2::XMLDocument &doc, const DICOMITKSeriesGDCMReader* reader) const
{
- TiXmlElement* root = this->CreateDICOMFileReaderTag(reader);
+ auto* root = this->CreateDICOMFileReaderTag(doc, reader);
assert(root);
- root->SetAttribute("fixTiltByShearing", toString(reader->GetFixTiltByShearing()));
- root->SetAttribute("acceptTwoSlicesGroups", toString(reader->GetAcceptTwoSlicesGroups()));
- root->SetDoubleAttribute("toleratedOriginError", reader->GetToleratedOriginError());
- root->SetAttribute("toleratedOriginErrorIsAbsolute", toString(reader->IsToleratedOriginOffsetAbsolute()));
- root->SetDoubleAttribute("decimalPlacesForOrientation", reader->GetDecimalPlacesForOrientation());
+ root->SetAttribute("fixTiltByShearing", reader->GetFixTiltByShearing());
+ root->SetAttribute("acceptTwoSlicesGroups", reader->GetAcceptTwoSlicesGroups());
+ root->SetAttribute("toleratedOriginError", reader->GetToleratedOriginError());
+ root->SetAttribute("toleratedOriginErrorIsAbsolute", reader->IsToleratedOriginOffsetAbsolute());
+ root->SetAttribute("decimalPlacesForOrientation", reader->GetDecimalPlacesForOrientation());
// iterate DICOMDatasetSorter objects
DICOMITKSeriesGDCMReader::ConstSorterList sorterList = reader->GetFreelyConfiguredSortingElements();
for(auto sorterIter = sorterList.begin();
sorterIter != sorterList.end();
++sorterIter)
{
const DICOMDatasetSorter* sorter = *sorterIter;
if (const auto* specificSorter = dynamic_cast<const DICOMTagBasedSorter*>(sorter))
{
- TiXmlElement* sorterTag = this->CreateConfigStringFromDICOMDatasetSorter(specificSorter);
- root->LinkEndChild(sorterTag);
+ auto* sorterTag = this->CreateConfigStringFromDICOMDatasetSorter(doc, specificSorter);
+ root->InsertEndChild(sorterTag);
}
else
{
MITK_WARN << "Unknown DICOMDatasetSorter class passed to DICOMReaderConfigurator::CreateConfigStringFromReader(). Cannot serialize.";
return nullptr;
}
}
return root;
}
-TiXmlElement*
+tinyxml2::XMLElement*
mitk::DICOMReaderConfigurator
-::CreateConfigStringFromDICOMDatasetSorter(const DICOMTagBasedSorter* sorter) const
+::CreateConfigStringFromDICOMDatasetSorter(tinyxml2::XMLDocument &doc, const DICOMTagBasedSorter* sorter) const
{
assert(sorter);
- auto sorterTag = new TiXmlElement("DICOMDatasetSorter");
+ auto *sorterTag = doc.NewElement("DICOMDatasetSorter");
sorterTag->SetAttribute("class", sorter->GetNameOfClass());
- sorterTag->SetAttribute("strictSorting", toString(sorter->GetStrictSorting()));
- sorterTag->SetAttribute("expectDistanceOne", toString(sorter->GetExpectDistanceOne()));
+ sorterTag->SetAttribute("strictSorting", sorter->GetStrictSorting());
+ sorterTag->SetAttribute("expectDistanceOne", sorter->GetExpectDistanceOne());
- auto distinguishingTagsElement = new TiXmlElement("Distinguishing");
- sorterTag->LinkEndChild(distinguishingTagsElement);
+ auto *distinguishingTagsElement = doc.NewElement("Distinguishing");
+ sorterTag->InsertEndChild(distinguishingTagsElement);
mitk::DICOMTagList distinguishingTags = sorter->GetDistinguishingTags();
for (auto tagIter = distinguishingTags.begin();
tagIter != distinguishingTags.end();
++tagIter)
{
- TiXmlElement* tag = this->CreateConfigStringFromDICOMTag(*tagIter);
- distinguishingTagsElement->LinkEndChild(tag);
+ auto* tag = this->CreateConfigStringFromDICOMTag(doc, *tagIter);
+ distinguishingTagsElement->InsertEndChild(tag);
const DICOMTagBasedSorter::TagValueProcessor* processor = sorter->GetTagValueProcessorForDistinguishingTag(*tagIter);
if (const auto* specificProcessor = dynamic_cast<const DICOMTagBasedSorter::CutDecimalPlaces*>(processor))
{
- tag->SetDoubleAttribute("cutDecimalPlaces", specificProcessor->GetPrecision());
+ tag->SetAttribute("cutDecimalPlaces", specificProcessor->GetPrecision());
}
}
- auto sortingElement = new TiXmlElement("Sorting");
- sorterTag->LinkEndChild(sortingElement);
+ auto *sortingElement = doc.NewElement("Sorting");
+ sorterTag->InsertEndChild(sortingElement);
mitk::DICOMSortCriterion::ConstPointer sortCriterion = sorter->GetSortCriterion();
while (sortCriterion.IsNotNull())
{
std::string classname = sortCriterion->GetNameOfClass();
if (classname == "SortByImagePositionPatient")
{
- sortingElement->LinkEndChild( new TiXmlElement("ImagePositionPatient") ); // no parameters
+ sortingElement->InsertEndChild( doc.NewElement("ImagePositionPatient") ); // no parameters
}
else
if (classname == "DICOMSortByTag")
{
DICOMTagList pseudoTagList = sortCriterion->GetTagsOfInterest();
if (pseudoTagList.size() == 1)
{
DICOMTag firstTag = pseudoTagList.front();
- TiXmlElement* tagElement = this->CreateConfigStringFromDICOMTag(firstTag);
+ auto* tagElement = this->CreateConfigStringFromDICOMTag(doc, firstTag);
- sortingElement->LinkEndChild( tagElement );
+ sortingElement->InsertEndChild( tagElement );
}
else
{
MITK_ERROR << "Encountered SortByTag class with MULTIPLE tag in CreateConfigStringFromDICOMDatasetSorter. Cannot serialize.";
return nullptr;
}
}
else
{
MITK_ERROR << "Encountered unknown class '" << classname << "' in CreateConfigStringFromDICOMDatasetSorter. Cannot serialize.";
return nullptr;
}
sortCriterion = sortCriterion->GetSecondaryCriterion();
}
return sorterTag;
}
-TiXmlElement*
+tinyxml2::XMLElement*
mitk::DICOMReaderConfigurator
-::CreateConfigStringFromDICOMTag(const DICOMTag& tag) const
+::CreateConfigStringFromDICOMTag(tinyxml2::XMLDocument& doc, const DICOMTag& tag) const
{
- auto tagElement = new TiXmlElement("Tag"); // name group element
+ auto tagElement = doc.NewElement("Tag"); // name group element
tagElement->SetAttribute("name", tag.GetName().c_str());
- tagElement->SetAttribute("group", toHexString(tag.GetGroup()));
- tagElement->SetAttribute("element", toHexString(tag.GetElement()));
+ tagElement->SetAttribute("group", toHexString(tag.GetGroup()).c_str());
+ tagElement->SetAttribute("element", toHexString(tag.GetElement()).c_str());
return tagElement;
}
std::string
mitk::DICOMReaderConfigurator
::toHexString(unsigned int i) const
{
std::stringstream ss;
ss << "0x" << std::setfill ('0') << std::setw(4) << std::hex << i;
return ss.str();
}
-TiXmlElement*
+tinyxml2::XMLElement*
mitk::DICOMReaderConfigurator
-::CreateConfigStringFromReader(const ThreeDnTDICOMSeriesReader* reader) const
+::CreateConfigStringFromReader(tinyxml2::XMLDocument& doc, const ThreeDnTDICOMSeriesReader* reader) const
{
- TiXmlElement* root = this->CreateConfigStringFromReader(static_cast<const DICOMITKSeriesGDCMReader*>(reader));
+ auto* root = this->CreateConfigStringFromReader(doc, static_cast<const DICOMITKSeriesGDCMReader*>(reader));
assert(root);
- root->SetAttribute("group3DnT", toString(reader->GetGroup3DandT()));
+ root->SetAttribute("group3DnT", reader->GetGroup3DandT());
return root;
}
-const char*
-mitk::DICOMReaderConfigurator
-::toString(bool b) const
-{
- return b ? "true" : "false";
-}
-
-TiXmlElement*
+tinyxml2::XMLElement*
mitk::DICOMReaderConfigurator
-::CreateConfigStringFromReader(const ClassicDICOMSeriesReader* reader) const
+::CreateConfigStringFromReader(tinyxml2::XMLDocument& doc, const ClassicDICOMSeriesReader* reader) const
{
- return this->CreateDICOMFileReaderTag(reader);
+ return this->CreateDICOMFileReaderTag(doc, reader);
}
-TiXmlElement*
+tinyxml2::XMLElement*
mitk::DICOMReaderConfigurator
-::CreateDICOMFileReaderTag(const DICOMFileReader* reader) const
+::CreateDICOMFileReaderTag(tinyxml2::XMLDocument& doc, const DICOMFileReader* reader) const
{
- auto readerTag = new TiXmlElement("DICOMFileReader");
+ auto readerTag = doc.NewElement("DICOMFileReader");
readerTag->SetAttribute("class", reader->GetNameOfClass());
readerTag->SetAttribute("label", reader->GetConfigurationLabel().c_str());
readerTag->SetAttribute("description", reader->GetConfigurationDescription().c_str());
readerTag->SetAttribute("version", "1");
return readerTag;
}
diff --git a/Modules/DICOMTesting/CMakeLists.txt b/Modules/DICOMTesting/CMakeLists.txt
index d0d96f0e67..857f5a39a1 100644
--- a/Modules/DICOMTesting/CMakeLists.txt
+++ b/Modules/DICOMTesting/CMakeLists.txt
@@ -1,43 +1,43 @@
if(BUILD_TESTING)
if(GDCM_DIR)
# clear variables from prior files.cmake
# Else CMake would use the content of these variables and would try to create tests (which are not present in DICOMTesting).
set(MODULE_TESTS)
set(MODULE_IMAGE_TESTS)
set(MODULE_SURFACE_TESTS)
set(MODULE_TESTIMAGE)
set(MODULE_TESTSURFACE)
set(MODULE_CUSTOM_TESTS)
set(H_FILES)
set(CPP_FILES)
# now create a new module only for testing purposes
MITK_CREATE_MODULE(
DEPENDS MitkDICOM
PACKAGE_DEPENDS
- PRIVATE GDCM DCMTK ITK|ITKIOGDCM
+ PRIVATE GDCM DCMTK ITK|IOGDCM
)
mitk_check_module_dependencies(MODULES MitkDICOMTesting MISSING_DEPENDENCIES_VAR _missing_deps)
if(_missing_deps)
message(STATUS "mitkDICOMTesting module helper applications won't be built. Missing: ${_missing_deps}")
else(_missing_deps)
# dumps out image information
add_executable(DumpDICOMMitkImage src/DumpDICOMMitkImage.cpp)
mitk_use_modules(TARGET DumpDICOMMitkImage MODULES MitkDICOMTesting)
# compares dumped out image information against reference dump
add_executable(VerifyDICOMMitkImageDump src/VerifyDICOMMitkImageDump.cpp)
mitk_use_modules(TARGET VerifyDICOMMitkImageDump MODULES MitkDICOMTesting)
set_property(TARGET DumpDICOMMitkImage VerifyDICOMMitkImageDump PROPERTY FOLDER
"${MITK_ROOT_FOLDER}/Modules/Tests")
add_subdirectory(test)
endif()
endif()
endif()
diff --git a/Modules/DataTypesExt/CMakeLists.txt b/Modules/DataTypesExt/CMakeLists.txt
index f9af619a57..841888032d 100644
--- a/Modules/DataTypesExt/CMakeLists.txt
+++ b/Modules/DataTypesExt/CMakeLists.txt
@@ -1,14 +1,6 @@
-set(_additional_libs)
-if(USE_ITKZLIB)
- list(APPEND _additional_libs itkzlib)
-else()
- list(APPEND _additional_libs z)
-endif(USE_ITKZLIB)
-
-MITK_CREATE_MODULE(DEPENDS MitkCore
- PACKAGE_DEPENDS PRIVATE ITK|ITKIOImageBase
- ADDITIONAL_LIBS ${_additional_libs}
- )
+mitk_create_module(
+ DEPENDS MitkCore
+ PACKAGE_DEPENDS PRIVATE ITK|ZLIB
+)
add_subdirectory(test)
-
diff --git a/Modules/IGT/CMakeLists.txt b/Modules/IGT/CMakeLists.txt
index 760efba59f..51ae8db7fe 100644
--- a/Modules/IGT/CMakeLists.txt
+++ b/Modules/IGT/CMakeLists.txt
@@ -1,63 +1,61 @@
include(MITKIGTHardware.cmake)
if(MITK_USE_MICRON_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_MICRON_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_MICRON_TRACKER_LIB})
endif(MITK_USE_MICRON_TRACKER)
if(MITK_USE_OPTITRACK_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_OPTITRACK_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_OPTITRACK_TRACKER_LIB})
add_definitions( -DMITK_USE_OPTITRACK_TRACKER )
endif(MITK_USE_OPTITRACK_TRACKER)
if(MITK_USE_MICROBIRD_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_USE_MICROBIRD_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_USE_MICROBIRD_TRACKER_LIB})
endif(MITK_USE_MICROBIRD_TRACKER)
if(MITK_USE_POLHEMUS_TRACKER)
set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_POLHEMUS_TRACKER_INCLUDE_DIR})
set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_POLHEMUS_TRACKER_LIB})
endif(MITK_USE_POLHEMUS_TRACKER)
MITK_CREATE_MODULE(
INCLUDE_DIRS
PUBLIC Algorithms Common DataManagement ExceptionHandling IO Rendering TrackingDevices TestingHelper
PRIVATE ${ADDITIONAL_INCLUDE_DIRS}
DEPENDS PUBLIC MitkImageStatistics MitkSceneSerialization MitkIGTBase MitkOpenIGTLink
- PACKAGE_DEPENDS ITK|ITKRegistrationCommon tinyxml OpenIGTLink
+ PACKAGE_DEPENDS PRIVATE ITK|RegistrationCommon OpenIGTLink tinyxml2
ADDITIONAL_LIBS "${ADDITIONAL_LIBS}"
)
if(MitkIGT_IS_ENABLED)
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/ClaronMicron.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/IntuitiveDaVinci.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAurora.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAurora_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraCompactFG_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraPlanarFG_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraTabletopFG_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraTabletopFG_Prototype_Dome.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisOldModel.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisSpectra.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisSpectraExtendedPyramid.stl )
MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisVicra.stl )
endif()
if(NOT MODULE_IS_ENABLED)
message(STATUS "IGTTutorialStep1 won't be built. Missing: ${_RESULT}")
else()
## create IGT config
configure_file(mitkIGTConfig.h.in ${PROJECT_BINARY_DIR}/mitkIGTConfig.h @ONLY)
-# add test programm for serial communication classADD_EXECUTABLE(SerialCommunicationTest IGTTrackingDevices/mitkSerialCommunicationTest.cpp)target_link_libraries(SerialCommunicationTest mitkIGT Mitk tinyxml PocoXML)
-
add_subdirectory(autoload/DeviceRegistry)
add_subdirectory(Tutorial)
add_subdirectory(Testing)
endif()
diff --git a/Modules/IGT/IO/mitkNavigationDataRecorderDeprecated.cpp b/Modules/IGT/IO/mitkNavigationDataRecorderDeprecated.cpp
index c10728cf92..0f9609216a 100644
--- a/Modules/IGT/IO/mitkNavigationDataRecorderDeprecated.cpp
+++ b/Modules/IGT/IO/mitkNavigationDataRecorderDeprecated.cpp
@@ -1,362 +1,364 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkNavigationDataRecorderDeprecated.h"
#include <fstream>
#include <mitkIGTTimeStamp.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
#include <itksys/SystemTools.hxx>
//headers for exceptions
#include "mitkIGTException.h"
#include "mitkIGTIOException.h"
mitk::NavigationDataRecorderDeprecated::NavigationDataRecorderDeprecated()
{
//set default values
m_NumberOfInputs = 0;
m_RecordingMode = NormalFile;
m_Recording = false;
m_NumberOfRecordedFiles = 0;
m_Stream = nullptr;
m_FileName = "";
m_SystemTimeClock = RealTimeClock::New();
m_OutputFormat = mitk::NavigationDataRecorderDeprecated::xml;
m_RecordCounter = 0;
m_RecordCountLimit = -1;
m_DoNotOverwriteFiles = false;
m_StreamMustBeDeleted = false;
//To get a start time
mitk::IGTTimeStamp::GetInstance()->Start(this);
}
mitk::NavigationDataRecorderDeprecated::~NavigationDataRecorderDeprecated()
{
}
void mitk::NavigationDataRecorderDeprecated::GenerateData()
{
}
void mitk::NavigationDataRecorderDeprecated::AddNavigationData( const NavigationData* nd )
{
// Process object is not const-correct so the const_cast is required here
this->SetNthInput(m_NumberOfInputs,
const_cast< mitk::NavigationData * >( nd ) );
m_NumberOfInputs++;
this->Modified();
}
void mitk::NavigationDataRecorderDeprecated::SetRecordingMode( RecordingMode mode )
{
m_RecordingMode = mode;
this->Modified();
}
void mitk::NavigationDataRecorderDeprecated::Update()
{
if (m_Recording)
{
DataObjectPointerArray inputs = this->GetInputs(); //get all inputs
mitk::NavigationData::TimeStampType timestamp=0.0; // timestamp for mitk time
timestamp = mitk::IGTTimeStamp::GetInstance()->GetElapsed();
mitk::NavigationData::TimeStampType sysTimestamp = 0.0; // timestamp for system time
sysTimestamp = m_SystemTimeClock->GetCurrentStamp();
// cast system time double value to stringstream to avoid low precision rounding
std::ostringstream strs;
strs.precision(15); // rounding precision for system time double value
strs << sysTimestamp;
std::string sysTimeStr = strs.str();
//if csv-mode: write csv header and timestamp at beginning
if (m_OutputFormat == mitk::NavigationDataRecorderDeprecated::csv)
{
//write header only when it's the first line
if (m_firstLine)
{
m_firstLine = false;
*m_Stream << "TimeStamp";
for (unsigned int index = 0; index < inputs.size(); index++){ *m_Stream << ";Valid_Tool" << index <<
";X_Tool" << index <<
";Y_Tool" << index <<
";Z_Tool" << index <<
";QX_Tool" << index <<
";QY_Tool" << index <<
";QZ_Tool" << index <<
";QR_Tool" << index;}
*m_Stream << "\n";
}
//write timestamp (always)
*m_Stream << timestamp;
}
//write tool data for every tool
for (unsigned int index = 0; index < inputs.size(); index++)
{
mitk::NavigationData* nd = dynamic_cast<mitk::NavigationData*>(inputs[index].GetPointer());
nd->Update(); // call update to propagate update to previous filters
mitk::NavigationData::PositionType position;
mitk::NavigationData::OrientationType orientation(0.0, 0.0, 0.0, 0.0);
mitk::NavigationData::CovarianceMatrixType matrix;
bool hasPosition = true;
bool hasOrientation = true;
bool dataValid = false;
position.Fill(0.0);
matrix.SetIdentity();
position = nd->GetPosition();
orientation = nd->GetOrientation();
matrix = nd->GetCovErrorMatrix();
hasPosition = nd->GetHasPosition();
hasOrientation = nd->GetHasOrientation();
dataValid = nd->IsDataValid();
//use this one if you want the timestamps of the source
//timestamp = nd->GetIGTTimeStamp();
//a timestamp is never < 0! this case happens only if you are using the timestamp of the nd object instead of getting a new one
if (timestamp >= 0)
{
if (this->m_OutputFormat == mitk::NavigationDataRecorderDeprecated::xml)
- {
- auto elem = new TiXmlElement("NavigationData");
-
- elem->SetDoubleAttribute("Time", timestamp);
- elem->SetAttribute("SystemTime", sysTimeStr); // tag for system time
- elem->SetDoubleAttribute("Tool", index);
- elem->SetDoubleAttribute("X", position[0]);
- elem->SetDoubleAttribute("Y", position[1]);
- elem->SetDoubleAttribute("Z", position[2]);
-
- elem->SetDoubleAttribute("QX", orientation[0]);
- elem->SetDoubleAttribute("QY", orientation[1]);
- elem->SetDoubleAttribute("QZ", orientation[2]);
- elem->SetDoubleAttribute("QR", orientation[3]);
-
- elem->SetDoubleAttribute("C00", matrix[0][0]);
- elem->SetDoubleAttribute("C01", matrix[0][1]);
- elem->SetDoubleAttribute("C02", matrix[0][2]);
- elem->SetDoubleAttribute("C03", matrix[0][3]);
- elem->SetDoubleAttribute("C04", matrix[0][4]);
- elem->SetDoubleAttribute("C05", matrix[0][5]);
- elem->SetDoubleAttribute("C10", matrix[1][0]);
- elem->SetDoubleAttribute("C11", matrix[1][1]);
- elem->SetDoubleAttribute("C12", matrix[1][2]);
- elem->SetDoubleAttribute("C13", matrix[1][3]);
- elem->SetDoubleAttribute("C14", matrix[1][4]);
- elem->SetDoubleAttribute("C15", matrix[1][5]);
+ {
+ tinyxml2::XMLDocument doc;
+ auto *elem = doc.NewElement("NavigationData");
+
+ elem->SetAttribute("Time", timestamp);
+ elem->SetAttribute("SystemTime", sysTimeStr.c_str()); // tag for system time
+ elem->SetAttribute("Tool", index);
+ elem->SetAttribute("X", position[0]);
+ elem->SetAttribute("Y", position[1]);
+ elem->SetAttribute("Z", position[2]);
+
+ elem->SetAttribute("QX", orientation[0]);
+ elem->SetAttribute("QY", orientation[1]);
+ elem->SetAttribute("QZ", orientation[2]);
+ elem->SetAttribute("QR", orientation[3]);
+
+ elem->SetAttribute("C00", matrix[0][0]);
+ elem->SetAttribute("C01", matrix[0][1]);
+ elem->SetAttribute("C02", matrix[0][2]);
+ elem->SetAttribute("C03", matrix[0][3]);
+ elem->SetAttribute("C04", matrix[0][4]);
+ elem->SetAttribute("C05", matrix[0][5]);
+ elem->SetAttribute("C10", matrix[1][0]);
+ elem->SetAttribute("C11", matrix[1][1]);
+ elem->SetAttribute("C12", matrix[1][2]);
+ elem->SetAttribute("C13", matrix[1][3]);
+ elem->SetAttribute("C14", matrix[1][4]);
+ elem->SetAttribute("C15", matrix[1][5]);
if (dataValid)
elem->SetAttribute("Valid",1);
else
elem->SetAttribute("Valid",0);
if (hasOrientation)
elem->SetAttribute("hO",1);
else
elem->SetAttribute("hO",0);
if (hasPosition)
elem->SetAttribute("hP",1);
else
elem->SetAttribute("hP",0);
// set additional attribute?
auto
it = m_AdditionalAttributes.find( nd );
if( it != m_AdditionalAttributes.end() )
{
- elem->SetAttribute(it->second.first, it->second.second);
+ elem->SetAttribute(it->second.first.c_str(), it->second.second.c_str());
}
- *m_Stream << " " << *elem << std::endl;
+ tinyxml2::XMLPrinter printer;
+ doc.Print(&printer);
- delete elem;
+ *m_Stream << " " << printer.CStr() << std::endl;
}
else if (this->m_OutputFormat == mitk::NavigationDataRecorderDeprecated::csv)
{
*m_Stream << ";" << dataValid << ";" << position[0] << ";" << position[1] << ";" << position[2] << ";" << orientation[0] << ";" << orientation[1] << ";" << orientation[2] << ";" << orientation[3];
}
}
}
if (this->m_OutputFormat == mitk::NavigationDataRecorderDeprecated::csv)
{
*m_Stream << "\n";
}
}
m_RecordCounter++;
if ((m_RecordCountLimit<=m_RecordCounter)&&(m_RecordCountLimit != -1)) {StopRecording();}
}
void mitk::NavigationDataRecorderDeprecated::SetAdditionalAttribute(const NavigationData* nd,
const std::string& attributeName
, const std::string& attributeValue )
{
auto
it = m_AdditionalAttributes.find( nd );
if( it == m_AdditionalAttributes.end() )
m_AdditionalAttributes[nd] = std::pair<std::string, std::string>(attributeName, attributeValue);
else
{
it->second.first = attributeName;
it->second.second = attributeValue;
}
}
void mitk::NavigationDataRecorderDeprecated::RemoveAdditionalAttribute( const NavigationData* nd )
{
auto
it = m_AdditionalAttributes.find( nd );
if( it != m_AdditionalAttributes.end() )
m_AdditionalAttributes.erase(it);
}
void mitk::NavigationDataRecorderDeprecated::StartRecording()
{
if(!m_Recording)
{
if (m_Stream == nullptr)
{
std::stringstream ss;
std::ostream* stream;
//An existing extension will be cut and replaced with .xml
std::string tmpPath = itksys::SystemTools::GetFilenamePath(m_FileName);
m_FileName = itksys::SystemTools::GetFilenameWithoutExtension(m_FileName);
std::string extension = ".xml";
if (m_OutputFormat == mitk::NavigationDataRecorderDeprecated::csv)
extension = ".csv";
ss << tmpPath << "/" << m_FileName << "-" << m_NumberOfRecordedFiles << extension;
if( m_DoNotOverwriteFiles )
{
unsigned int index = m_NumberOfRecordedFiles+1;
while( itksys::SystemTools::FileExists( ss.str().c_str() ) )
{
ss.str("");
ss << tmpPath << "/" << m_FileName << "-" << index << extension;
index++;
}
}
switch(m_RecordingMode)
{
case Console:
stream = &std::cout;
break;
case NormalFile:
if (m_FileName == "") //Check if there is a file name and path
{
std::string message = "No file name or file path set.";
MITK_ERROR << message;
mitkThrowException(mitk::IGTException) << message;
}
else
{
stream = new std::ofstream(ss.str().c_str());
}
break;
case ZipFile:
stream = &std::cout;
MITK_WARN << "Sorry no ZipFile support yet";
break;
default:
stream = &std::cout;
break;
}
m_Stream = stream;
m_StreamMustBeDeleted = true;
m_firstLine = true;
m_RecordCounter = 0;
StartRecording(stream);
}
}
else if (m_Recording)
{
MITK_WARN << "Already recording please stop before start new recording session";
return;
}
}
void mitk::NavigationDataRecorderDeprecated::StartRecording(std::ostream* stream)
{
if (m_Recording)
{
MITK_WARN << "Already recording please stop before start new recording session";
return;
}
m_Stream = stream;
m_Stream->precision(10);
//TODO store date and GMT time
//cheking if the stream is good
if (m_Stream->good())
{
if (m_OutputFormat == mitk::NavigationDataRecorderDeprecated::xml)
{
*m_Stream << "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>" << std::endl;
/**m_Stream << "<Version Ver=\"1\" />" << std::endl;*/
// should be a generic version, meaning a member variable, which has the actual version
*m_Stream << " " << "<Data ToolCount=\"" << (m_NumberOfInputs) << "\" version=\"1.0\">" << std::endl;
}
m_Recording = true;
}
else
{
m_Recording = false;
mitkThrowException(mitk::IGTException)<<"The stream is not good";
}
}
void mitk::NavigationDataRecorderDeprecated::StopRecording()
{
if (!m_Recording)
{
std::cout << "You have to start a recording first" << std::endl;
return;
}
if ((m_Stream) && (m_OutputFormat == mitk::NavigationDataRecorderDeprecated::xml))
{
*m_Stream << "</Data>" << std::endl;
}
m_NumberOfRecordedFiles++;
m_Recording = false;
m_Stream->flush();
if (m_StreamMustBeDeleted) //stream must only be deleted if it was created inside this class
{
m_StreamMustBeDeleted = false;
delete m_Stream;
}
m_Stream = nullptr;
}
diff --git a/Modules/IGTBase/autoload/IO/CMakeLists.txt b/Modules/IGTBase/autoload/IO/CMakeLists.txt
index e6e391249c..cdda327e30 100644
--- a/Modules/IGTBase/autoload/IO/CMakeLists.txt
+++ b/Modules/IGTBase/autoload/IO/CMakeLists.txt
@@ -1,5 +1,5 @@
MITK_CREATE_MODULE(IGTIO
DEPENDS MitkIGTBase
- PACKAGE_DEPENDS tinyxml
+ PACKAGE_DEPENDS tinyxml2
AUTOLOAD_WITH MitkCore
)
diff --git a/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.cpp b/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.cpp
index 24551b7f0a..7195fd995e 100644
--- a/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.cpp
+++ b/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.cpp
@@ -1,364 +1,214 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include "mitkNavigationDataReaderXML.h"
#include <mitkIGTMimeTypes.h>
#include <mitkLocaleSwitch.h>
// Third Party
#include <itksys/SystemTools.hxx>
#include <fstream>
-#include <tinyxml.h>
+#include <tinyxml2.h>
-
-mitk::NavigationDataReaderXML::NavigationDataReaderXML() : AbstractFileReader(
- mitk::IGTMimeTypes::NAVIGATIONDATASETXML_MIMETYPE(),
- "MITK NavigationData Reader (XML)"), m_parentElement(nullptr), m_currentNode(nullptr)
+namespace
{
- RegisterService();
-}
+ mitk::NavigationData::Pointer ReadNavigationData(const tinyxml2::XMLElement* ndElem)
+ {
+ if (nullptr == ndElem)
+ return nullptr;
-mitk::NavigationDataReaderXML::~NavigationDataReaderXML()
-{
-}
+ mitk::NavigationData::TimeStampType timeStamp = -1;
-mitk::NavigationDataReaderXML::NavigationDataReaderXML(const mitk::NavigationDataReaderXML& other) : AbstractFileReader(other), m_parentElement(nullptr), m_currentNode(nullptr)
-{
-}
+ ndElem->QueryDoubleAttribute("Time", &timeStamp);
-mitk::NavigationDataReaderXML* mitk::NavigationDataReaderXML::Clone() const
-{
- return new NavigationDataReaderXML(*this);
-}
+ if (-1 == timeStamp)
+ return nullptr;
+ mitk::NavigationData::PositionType position;
+ position.Fill(0.0);
-std::vector<itk::SmartPointer<mitk::BaseData>> mitk::NavigationDataReaderXML::DoRead()
-{
- mitk::NavigationDataSet::Pointer dataset;
- std::istream* in = GetInputStream();
- if (in == nullptr)
- {
- dataset = Read(GetInputLocation());
- } else {
- dataset = Read(in);
- }
- std::vector<mitk::BaseData::Pointer> result;
- mitk::BaseData::Pointer base = dataset.GetPointer();
- result.push_back(base);
- return result;
-}
+ ndElem->QueryDoubleAttribute("X", &position[0]);
+ ndElem->QueryDoubleAttribute("Y", &position[1]);
+ ndElem->QueryDoubleAttribute("Z", &position[2]);
+ mitk::NavigationData::OrientationType orientation;
+ ndElem->QueryDoubleAttribute("QX", &orientation[0]);
+ ndElem->QueryDoubleAttribute("QY", &orientation[1]);
+ ndElem->QueryDoubleAttribute("QZ", &orientation[2]);
+ ndElem->QueryDoubleAttribute("QR", &orientation[3]);
-mitk::NavigationDataSet::Pointer mitk::NavigationDataReaderXML::Read(std::string fileName)
-{
- //define own locale
- mitk::LocaleSwitch localeSwitch("C");
+ mitk::NavigationData::CovarianceMatrixType matrix;
+ matrix.SetIdentity();
- m_FileName = fileName;
+ ndElem->QueryDoubleAttribute("C00", &matrix[0][0]);
+ ndElem->QueryDoubleAttribute("C01", &matrix[0][1]);
+ ndElem->QueryDoubleAttribute("C02", &matrix[0][2]);
+ ndElem->QueryDoubleAttribute("C03", &matrix[0][3]);
+ ndElem->QueryDoubleAttribute("C04", &matrix[0][4]);
+ ndElem->QueryDoubleAttribute("C05", &matrix[0][5]);
+ ndElem->QueryDoubleAttribute("C10", &matrix[1][0]);
+ ndElem->QueryDoubleAttribute("C11", &matrix[1][1]);
+ ndElem->QueryDoubleAttribute("C12", &matrix[1][2]);
+ ndElem->QueryDoubleAttribute("C13", &matrix[1][3]);
+ ndElem->QueryDoubleAttribute("C14", &matrix[1][4]);
+ ndElem->QueryDoubleAttribute("C15", &matrix[1][5]);
- TiXmlDocument document;
- if (!document.LoadFile(fileName))
- {
- mitkThrowException(mitk::IGTIOException) << "File '" << fileName << "' could not be loaded.";
- }
+ int attrib = 0;
+ ndElem->QueryIntAttribute("Valid", &attrib);
+ bool isValid = 0 != attrib;
- TiXmlElement* m_DataElem = document.FirstChildElement("Version");
- if (!m_DataElem)
- {
- // for backwards compatibility of version tag
- m_DataElem = document.FirstChildElement("Data");
- if (!m_DataElem)
- {
- mitkThrowException(mitk::IGTIOException) << "Data element not found.";
- }
+ attrib = 0;
+ ndElem->QueryIntAttribute("hP", &attrib);
+ bool hasPosition = 0 != attrib;
- }
+ attrib = 0;
+ ndElem->QueryIntAttribute("hO", &attrib);
+ bool hasOrientation = 0 != attrib;
- if (m_DataElem->QueryIntAttribute("Ver", &m_FileVersion) != TIXML_SUCCESS)
- {
- if (m_DataElem->QueryIntAttribute("version", &m_FileVersion) != TIXML_SUCCESS)
- {
- mitkThrowException(mitk::IGTIOException) << "Version not specified in XML file.";
- }
- }
+ auto navData = mitk::NavigationData::New();
- if (m_FileVersion != 1)
- {
- mitkThrowException(mitk::IGTIOException) << "File format version " << m_FileVersion << " is not supported.";
- }
+ navData->SetIGTTimeStamp(timeStamp);
+ navData->SetPosition(position);
+ navData->SetOrientation(orientation);
+ navData->SetCovErrorMatrix(matrix);
+ navData->SetDataValid(isValid);
+ navData->SetHasPosition(hasPosition);
+ navData->SetHasOrientation(hasOrientation);
- m_parentElement = document.FirstChildElement("Data");
- if (!m_parentElement)
- {
- mitkThrowException(mitk::IGTIOException) << "Data element not found.";
+ return navData;
}
-
- m_parentElement->QueryIntAttribute("ToolCount", &m_NumberOfOutputs);
-
- mitk::NavigationDataSet::Pointer navigationDataSet = this->ReadNavigationDataSet();
-
- return navigationDataSet;
}
-mitk::NavigationDataSet::Pointer mitk::NavigationDataReaderXML::Read(std::istream* stream)
+mitk::NavigationDataReaderXML::NavigationDataReaderXML()
+ : AbstractFileReader(IGTMimeTypes::NAVIGATIONDATASETXML_MIMETYPE(), "MITK NavigationData Reader (XML)")
{
- //define own locale
- mitk::LocaleSwitch localeSwitch("C");
-
- // first get the file version
- m_FileVersion = this->GetFileVersion(stream);
-
- // check if we have a valid version: m_FileVersion has to be always bigger than 1 for playing
- if (m_FileVersion < 1)
- {
- StreamInvalid("Playing not possible. Invalid file version!");
- return nullptr;
- }
+ this->RegisterService();
+}
- m_NumberOfOutputs = this->GetNumberOfNavigationDatas(stream);
- if (m_NumberOfOutputs == 0) { return nullptr; }
+mitk::NavigationDataReaderXML::~NavigationDataReaderXML()
+{
+}
- mitk::NavigationDataSet::Pointer dataSet = this->ReadNavigationDataSet();
+mitk::NavigationDataReaderXML::NavigationDataReaderXML(const mitk::NavigationDataReaderXML& other)
+ : AbstractFileReader(other)
+{
+}
- return dataSet;
+mitk::NavigationDataReaderXML* mitk::NavigationDataReaderXML::Clone() const
+{
+ return new NavigationDataReaderXML(*this);
}
-mitk::NavigationDataSet::Pointer mitk::NavigationDataReaderXML::ReadNavigationDataSet()
+std::vector<itk::SmartPointer<mitk::BaseData>> mitk::NavigationDataReaderXML::DoRead()
{
- mitk::NavigationDataSet::Pointer navigationDataSet = mitk::NavigationDataSet::New(m_NumberOfOutputs);
- mitk::NavigationData::Pointer curNavigationData;
+ mitk::NavigationDataSet::Pointer dataset = nullptr == this->GetInputStream()
+ ? this->Read(this->GetInputLocation())
+ : this->Read(*this->GetInputStream());
- do
- {
- std::vector<mitk::NavigationData::Pointer> navDatas(m_NumberOfOutputs);
- for (int n = 0; n < m_NumberOfOutputs; ++n)
- {
- curNavigationData = this->ReadVersion1();
+ std::vector<mitk::BaseData::Pointer> result;
+ result.emplace_back(dataset.GetPointer());
- if (curNavigationData.IsNull())
- {
- if (n != 0)
- {
- MITK_WARN("mitkNavigationDataReaderXML")
- << "Different number of NavigationData objects for different tools. Ignoring last ones.";
- }
- break;
- }
- navDatas.at(n) = curNavigationData;
- }
+ return result;
+}
- if (curNavigationData.IsNotNull())
- {
- navigationDataSet->AddNavigationDatas(navDatas);
- }
- }
- while (curNavigationData.IsNotNull());
+mitk::NavigationDataSet::Pointer mitk::NavigationDataReaderXML::Read(const std::string& fileName)
+{
+ std::ifstream stream(fileName);
+ stream.imbue(std::locale::classic());
- return navigationDataSet;
+ return this->Read(stream);
}
-mitk::NavigationData::Pointer mitk::NavigationDataReaderXML::ReadVersion1()
+mitk::NavigationDataSet::Pointer mitk::NavigationDataReaderXML::Read(std::istream& stream)
{
- if ( !m_parentElement )
- {
- mitkThrowException(mitk::IGTIOException) << "Reading XML is not possible. Parent element is not set.";
- }
+ std::string string(std::istreambuf_iterator<char>(stream), {});
+ tinyxml2::XMLDocument doc;
+
+ if (tinyxml2::XML_SUCCESS != doc.Parse(string.c_str()))
+ mitkThrowException(IGTIOException) << "Could not parse stream.";
+
+ const auto* rootElem = doc.RootElement();
+ decltype(rootElem) dataElem = nullptr;
- TiXmlElement* elem;
- m_currentNode = m_parentElement->IterateChildren(m_currentNode);
+ if (nullptr == rootElem)
+ return nullptr;
- bool delElem;
+ int version = 0;
+ auto err = tinyxml2::XML_SUCCESS;
+
+ std::string rootElemVal = rootElem->Value();
- if(m_currentNode)
+ if ("Version" == rootElemVal)
{
- elem = m_currentNode->ToElement();
- if(elem==nullptr)
- {
- mitkThrowException(mitk::IGTException) << "Cannot find element: Is this file damaged?";
- }
- delElem = false;
+ err = rootElem->QueryIntAttribute("Ver", &version);
+ dataElem = rootElem->NextSiblingElement("Data");
}
-
- else
+ else if ("Data" == rootElemVal)
{
- elem = new TiXmlElement("");
- delElem = true;
+ err = rootElem->QueryIntAttribute("version", &version);
+ dataElem = rootElem;
}
+ if (err != tinyxml2::XML_SUCCESS)
+ mitkThrowException(IGTIOException) << "Could not parse file format version.";
- mitk::NavigationData::Pointer nd = this->ReadNavigationData(elem);
+ if (version != 1)
+ mitkThrowException(IGTIOException) << "File format version " << version << " is not supported.";
- if(delElem) { delete elem; }
+ if (nullptr == dataElem)
+ mitkThrowException(IGTIOException) << "Data element not found.";
- return nd;
-}
+ int toolCount = 0;
-mitk::NavigationData::Pointer mitk::NavigationDataReaderXML::ReadNavigationData(TiXmlElement* elem)
-{
- if (elem == nullptr) {mitkThrow() << "Error: Element is nullptr!";}
-
- mitk::NavigationData::Pointer nd = mitk::NavigationData::New();
+ if (tinyxml2::XML_SUCCESS != dataElem->QueryIntAttribute("ToolCount", &toolCount))
+ mitkThrowException(IGTIOException) << "ToolCount attribute missing from Data element.";
- mitk::NavigationData::PositionType position;
- mitk::NavigationData::OrientationType orientation(0.0,0.0,0.0,0.0);
- mitk::NavigationData::TimeStampType timestamp = -1;
- mitk::NavigationData::CovarianceMatrixType matrix;
+ if (0 >= toolCount)
+ mitkThrowException(IGTIOException) << "Invalid ToolCount: " << toolCount << ".";
- bool hasPosition = true;
- bool hasOrientation = true;
- bool dataValid = false;
+ auto navDataSet = NavigationDataSet::New(static_cast<unsigned int>(toolCount));
+ NavigationData::Pointer navData;
- position.Fill(0.0);
- matrix.SetIdentity();
+ const auto* ndElem = dataElem->FirstChildElement();
- elem->QueryDoubleAttribute("Time",×tamp);
- if (timestamp == -1)
+ if (nullptr != ndElem)
{
- return nullptr; //the calling method should check the return value if it is valid/not nullptr
- }
-
- elem->QueryDoubleAttribute("X", &position[0]);
- elem->QueryDoubleAttribute("Y", &position[1]);
- elem->QueryDoubleAttribute("Z", &position[2]);
-
- elem->QueryDoubleAttribute("QX", &orientation[0]);
- elem->QueryDoubleAttribute("QY", &orientation[1]);
- elem->QueryDoubleAttribute("QZ", &orientation[2]);
- elem->QueryDoubleAttribute("QR", &orientation[3]);
-
- elem->QueryDoubleAttribute("C00", &matrix[0][0]);
- elem->QueryDoubleAttribute("C01", &matrix[0][1]);
- elem->QueryDoubleAttribute("C02", &matrix[0][2]);
- elem->QueryDoubleAttribute("C03", &matrix[0][3]);
- elem->QueryDoubleAttribute("C04", &matrix[0][4]);
- elem->QueryDoubleAttribute("C05", &matrix[0][5]);
- elem->QueryDoubleAttribute("C10", &matrix[1][0]);
- elem->QueryDoubleAttribute("C11", &matrix[1][1]);
- elem->QueryDoubleAttribute("C12", &matrix[1][2]);
- elem->QueryDoubleAttribute("C13", &matrix[1][3]);
- elem->QueryDoubleAttribute("C14", &matrix[1][4]);
- elem->QueryDoubleAttribute("C15", &matrix[1][5]);
-
- int tmpval = 0;
- elem->QueryIntAttribute("Valid", &tmpval);
- if (tmpval == 0)
- dataValid = false;
- else
- dataValid = true;
-
- tmpval = 0;
- elem->QueryIntAttribute("hO", &tmpval);
- if (tmpval == 0)
- hasOrientation = false;
- else
- hasOrientation = true;
-
- tmpval = 0;
- elem->QueryIntAttribute("hP", &tmpval);
- if (tmpval == 0)
- hasPosition = false;
- else
- hasPosition = true;
-
- nd->SetIGTTimeStamp(timestamp);
- nd->SetPosition(position);
- nd->SetOrientation(orientation);
- nd->SetCovErrorMatrix(matrix);
- nd->SetDataValid(dataValid);
- nd->SetHasOrientation(hasOrientation);
- nd->SetHasPosition(hasPosition);
-
-
- return nd;
-}
+ do
+ {
+ std::vector<NavigationData::Pointer> navDatas(toolCount);
-// -- deprecated | begin
-unsigned int mitk::NavigationDataReaderXML::GetFileVersion(std::istream* stream)
-{
- if (stream==nullptr)
- {
- MITK_ERROR << "No input stream set!";
- mitkThrowException(mitk::IGTIOException)<<"No input stream set!";
- }
- if (!stream->good())
- {
- MITK_ERROR << "Stream is not good!";
- mitkThrowException(mitk::IGTIOException)<<"Stream is not good!";
- }
- int version = 1;
+ for (decltype(toolCount) i = 0; i < toolCount; ++i)
+ {
+ navData = ReadNavigationData(ndElem);
- auto dec = new TiXmlDeclaration();
- *stream >> *dec;
- if(strcmp(dec->Version(),"") == 0)
- {
- MITK_ERROR << "The input stream seems to have XML incompatible format";
- mitkThrowException(mitk::IGTIOException) << "The input stream seems to have XML incompatible format";
- }
+ if (navData.IsNull())
+ {
+ if (0 != i)
+ MITK_WARN("mitkNavigationDataReaderXML") << "Different number of NavigationData objects for different tools. Ignoring last ones.";
- m_parentElement = new TiXmlElement("");
- *stream >> *m_parentElement; //2nd line this is the file version
+ break;
+ }
- std::string tempValue = m_parentElement->Value();
- if(tempValue != "Version")
- {
- if(tempValue == "Data"){
- m_parentElement->QueryIntAttribute("version",&version);
+ navDatas[i] = navData;
+ ndElem = ndElem->NextSiblingElement();
}
- }
- else
- {
- m_parentElement->QueryIntAttribute("Ver",&version);
- }
- if (version > 0) { return version; }
- else { return 0; }
-}
+ if (navData.IsNotNull())
+ navDataSet->AddNavigationDatas(navDatas);
-unsigned int mitk::NavigationDataReaderXML::GetNumberOfNavigationDatas(std::istream* stream)
-{
- if (stream == nullptr)
- {
- MITK_ERROR << "No input stream set!";
- mitkThrowException(mitk::IGTException)<<"No input stream set!";
- }
- if (!stream->good())
- {
- MITK_ERROR << "Stream not good!";
- mitkThrowException(mitk::IGTException)<<"Stream not good!";
- }
-
- //If something has changed in a future version of the XML definition e.g. navigationcount or addional parameters
- //catch this here with a select case block (see GenerateData() method)
-
- int numberOfTools = 0;
-
- std::string tempValue = m_parentElement->Value();
- if(tempValue == "Version"){
- *stream >> *m_parentElement;
+ } while (nullptr != ndElem && navData.IsNotNull());
}
- m_parentElement->QueryIntAttribute("ToolCount",&numberOfTools);
-
- if (numberOfTools > 0) { return numberOfTools; }
- return 0;
-}
-
-void mitk::NavigationDataReaderXML::StreamInvalid(std::string message)
-{
- m_StreamEnd = true;
- m_ErrorMessage = message;
- m_StreamValid = false;
- mitkThrowException(mitk::IGTIOException) << "Invalid stream!";
+ return navDataSet;
}
-// -- deprecated | end
diff --git a/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.h b/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.h
index 8c6dc89b47..2209f661e6 100644
--- a/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.h
+++ b/Modules/IGTBase/autoload/IO/mitkNavigationDataReaderXML.h
@@ -1,106 +1,50 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKNavigationDataReaderXML_H_HEADER_INCLUDED_
#define MITKNavigationDataReaderXML_H_HEADER_INCLUDED_
#include <MitkIGTIOExports.h>
#include <mitkAbstractFileReader.h>
#include <mitkNavigationDataSet.h>
// includes for exceptions
#include <mitkIGTException.h>
#include <mitkIGTIOException.h>
-class TiXmlElement;
-class TiXmlNode;
-
namespace mitk {
class MITKIGTIO_EXPORT NavigationDataReaderXML : public AbstractFileReader
{
public:
NavigationDataReaderXML();
~NavigationDataReaderXML() override;
using AbstractFileReader::Read;
protected:
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
NavigationDataReaderXML(const NavigationDataReaderXML& other);
mitk::NavigationDataReaderXML* Clone() const override;
- NavigationDataSet::Pointer ReadNavigationDataSet();
-
- /**
- * \brief This method reads one line of the XML document and returns the data as a NavigationData object
- * If there is a new file version another method must be added which reads this data.
- * @throw mitk::IGTException Throws an exceptions if file is damaged.
- */
- mitk::NavigationData::Pointer ReadVersion1();
- mitk::NavigationData::Pointer ReadNavigationData(TiXmlElement* elem);
-
std::string m_FileName;
- TiXmlElement* m_parentElement;
- TiXmlNode* m_currentNode;
-
- int m_FileVersion; ///< indicates which XML encoding is used
- int m_NumberOfOutputs; ///< stores the number of outputs known from the XML document
-
- // -- deprecated | begin
- //std::istream* m_Stream; ///< stores a pointer to the input stream
- bool m_StreamEnd; ///< stores if the input stream arrived at end
- bool m_StreamValid; ///< stores if the input stream is valid or not
- std::string m_ErrorMessage; ///< stores the error message if the stream is invalid
-
- /**
- * \brief Creates a stream out of the filename given by the variable m_FileName.
- * The stream is then set to m_Stream.
- *
- * @throw mitk::IGTIOException Throws an exception if file does not exist
- * @throw mitk::IGTException Throws an exception if the stream is nullptr
- */
- //void CreateStreamFromFilename();
-
- /**
- * \brief Returns the file version out of the XML document.
- * @throw mitk::IGTException Throws an mitk::IGTException an exception if stream is nullptr or not good.
- * @throw mitk::IGTIOException Throws an mitk::IGTIOException if the stream has an incompatible XML format.
- */
- unsigned int GetFileVersion(std::istream* stream);
-
- /**
- * \brief Returns the number of tracked tools out of the XML document.
- * @throw Throws an exception if stream is nullptr.
- * @throw Throws an exception if the input stream has an XML incompatible format.
- */
- unsigned int GetNumberOfNavigationDatas(std::istream* stream);
-
- /**
- * @brief This is a helping method which gives an error message and throws an exception with the given message.
- * It can be used if a stream is found to be invalid.
- *
- * @throw mitk::IGTIOException Always throws an exception.
- */
- void StreamInvalid(std::string message); ///< help method which sets the stream invalid and displays an error
- // -- deprecated | end
private:
- NavigationDataSet::Pointer Read(std::istream* stream);
- NavigationDataSet::Pointer Read(std::string fileName);
+ NavigationDataSet::Pointer Read(std::istream& stream);
+ NavigationDataSet::Pointer Read(const std::string& fileName);
};
} // namespace mitk
#endif // MITKNavigationDataReaderXML_H_HEADER_INCLUDED_
diff --git a/Modules/IGTBase/autoload/IO/mitkNavigationDataSetWriterXML.cpp b/Modules/IGTBase/autoload/IO/mitkNavigationDataSetWriterXML.cpp
index 8816d1ab38..1256f4f8f0 100644
--- a/Modules/IGTBase/autoload/IO/mitkNavigationDataSetWriterXML.cpp
+++ b/Modules/IGTBase/autoload/IO/mitkNavigationDataSetWriterXML.cpp
@@ -1,139 +1,141 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include "mitkNavigationDataSetWriterXML.h"
#include <mitkIGTMimeTypes.h>
#include <mitkLocaleSwitch.h>
// Third Party
-#include <tinyxml.h>
+#include <tinyxml2.h>
#include <itksys/SystemTools.hxx>
#include <fstream>
#include <iostream>
mitk::NavigationDataSetWriterXML::NavigationDataSetWriterXML() : AbstractFileWriter(NavigationDataSet::GetStaticNameOfClass(),
mitk::IGTMimeTypes::NAVIGATIONDATASETXML_MIMETYPE(),
"MITK NavigationDataSet Writer (XML)")
{
RegisterService();
}
mitk::NavigationDataSetWriterXML::NavigationDataSetWriterXML(const mitk::NavigationDataSetWriterXML& other) : AbstractFileWriter(other)
{
}
mitk::NavigationDataSetWriterXML::~NavigationDataSetWriterXML()
{
}
mitk::NavigationDataSetWriterXML* mitk::NavigationDataSetWriterXML::Clone() const
{
return new NavigationDataSetWriterXML(*this);
}
void mitk::NavigationDataSetWriterXML::Write()
{
std::ostream* out = GetOutputStream();
if (out == nullptr)
{
out = new std::ofstream( GetOutputLocation().c_str() );
}
mitk::NavigationDataSet::ConstPointer data = dynamic_cast<const NavigationDataSet*> (this->GetInput());
mitk::LocaleSwitch localeSwitch("C");
StreamHeader(out, data);
StreamData(out, data);
StreamFooter(out);
// Cleanup
out->flush();
delete out;
}
void mitk::NavigationDataSetWriterXML::StreamHeader (std::ostream* stream, mitk::NavigationDataSet::ConstPointer data)
{
stream->precision(10);
//TODO store date and GMT time
//checking if the stream is good
if (stream->good())
{
*stream << "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>" << std::endl;
/**m_Stream << "<Version Ver=\"1\" />" << std::endl;*/
// should be a generic version, meaning a member variable, which has the actual version
*stream << " " << "<Data ToolCount=\"" << data->GetNumberOfTools() << "\" version=\"1.0\">" << std::endl;
}
}
void mitk::NavigationDataSetWriterXML::StreamData (std::ostream* stream, mitk::NavigationDataSet::ConstPointer data)
{
// For each time step in the Dataset
for (auto it = data->Begin(); it != data->End(); it++)
{
for (std::size_t toolIndex = 0; toolIndex < it->size(); toolIndex++)
{
mitk::NavigationData::Pointer nd = it->at(toolIndex);
- auto elem = new TiXmlElement("ND");
+ tinyxml2::XMLDocument doc;
+ auto *elem = doc.NewElement("ND");
- elem->SetDoubleAttribute("Time", nd->GetIGTTimeStamp());
+ elem->SetAttribute("Time", nd->GetIGTTimeStamp());
// elem->SetAttribute("SystemTime", sysTimeStr); // tag for system time
- elem->SetDoubleAttribute("Tool", toolIndex);
- elem->SetDoubleAttribute("X", nd->GetPosition()[0]);
- elem->SetDoubleAttribute("Y", nd->GetPosition()[1]);
- elem->SetDoubleAttribute("Z", nd->GetPosition()[2]);
-
- elem->SetDoubleAttribute("QX", nd->GetOrientation()[0]);
- elem->SetDoubleAttribute("QY", nd->GetOrientation()[1]);
- elem->SetDoubleAttribute("QZ", nd->GetOrientation()[2]);
- elem->SetDoubleAttribute("QR", nd->GetOrientation()[3]);
-
- elem->SetDoubleAttribute("C00", nd->GetCovErrorMatrix()[0][0]);
- elem->SetDoubleAttribute("C01", nd->GetCovErrorMatrix()[0][1]);
- elem->SetDoubleAttribute("C02", nd->GetCovErrorMatrix()[0][2]);
- elem->SetDoubleAttribute("C03", nd->GetCovErrorMatrix()[0][3]);
- elem->SetDoubleAttribute("C04", nd->GetCovErrorMatrix()[0][4]);
- elem->SetDoubleAttribute("C05", nd->GetCovErrorMatrix()[0][5]);
- elem->SetDoubleAttribute("C10", nd->GetCovErrorMatrix()[1][0]);
- elem->SetDoubleAttribute("C11", nd->GetCovErrorMatrix()[1][1]);
- elem->SetDoubleAttribute("C12", nd->GetCovErrorMatrix()[1][2]);
- elem->SetDoubleAttribute("C13", nd->GetCovErrorMatrix()[1][3]);
- elem->SetDoubleAttribute("C14", nd->GetCovErrorMatrix()[1][4]);
- elem->SetDoubleAttribute("C15", nd->GetCovErrorMatrix()[1][5]);
+ elem->SetAttribute("Tool", static_cast<int>(toolIndex));
+ elem->SetAttribute("X", nd->GetPosition()[0]);
+ elem->SetAttribute("Y", nd->GetPosition()[1]);
+ elem->SetAttribute("Z", nd->GetPosition()[2]);
+
+ elem->SetAttribute("QX", nd->GetOrientation()[0]);
+ elem->SetAttribute("QY", nd->GetOrientation()[1]);
+ elem->SetAttribute("QZ", nd->GetOrientation()[2]);
+ elem->SetAttribute("QR", nd->GetOrientation()[3]);
+
+ elem->SetAttribute("C00", nd->GetCovErrorMatrix()[0][0]);
+ elem->SetAttribute("C01", nd->GetCovErrorMatrix()[0][1]);
+ elem->SetAttribute("C02", nd->GetCovErrorMatrix()[0][2]);
+ elem->SetAttribute("C03", nd->GetCovErrorMatrix()[0][3]);
+ elem->SetAttribute("C04", nd->GetCovErrorMatrix()[0][4]);
+ elem->SetAttribute("C05", nd->GetCovErrorMatrix()[0][5]);
+ elem->SetAttribute("C10", nd->GetCovErrorMatrix()[1][0]);
+ elem->SetAttribute("C11", nd->GetCovErrorMatrix()[1][1]);
+ elem->SetAttribute("C12", nd->GetCovErrorMatrix()[1][2]);
+ elem->SetAttribute("C13", nd->GetCovErrorMatrix()[1][3]);
+ elem->SetAttribute("C14", nd->GetCovErrorMatrix()[1][4]);
+ elem->SetAttribute("C15", nd->GetCovErrorMatrix()[1][5]);
if (nd->IsDataValid())
elem->SetAttribute("Valid",1);
else
elem->SetAttribute("Valid",0);
if (nd->GetHasOrientation())
elem->SetAttribute("hO",1);
else
elem->SetAttribute("hO",0);
if (nd->GetHasPosition())
elem->SetAttribute("hP",1);
else
elem->SetAttribute("hP",0);
- *stream << " " << *elem << std::endl;
+ tinyxml2::XMLPrinter printer;
+ doc.Print(&printer);
- delete elem;
+ *stream << " " << printer.CStr() << std::endl;
}
}
}
void mitk::NavigationDataSetWriterXML::StreamFooter (std::ostream* stream)
{
*stream << "</Data>" << std::endl;
}
diff --git a/Modules/IOExt/CMakeLists.txt b/Modules/IOExt/CMakeLists.txt
index 61b51b291e..7084badf96 100644
--- a/Modules/IOExt/CMakeLists.txt
+++ b/Modules/IOExt/CMakeLists.txt
@@ -1,4 +1,4 @@
MITK_CREATE_MODULE(DEPENDS MitkDataTypesExt MitkMapperExt MitkSceneSerialization MitkLegacyIO
- PACKAGE_DEPENDS PRIVATE ITK|ITKIOImageBase VTK|IOPLY+IOExport+IOParallelXML
+ PACKAGE_DEPENDS PRIVATE VTK|IOPLY+IOExport+IOParallelXML
AUTOLOAD_WITH MitkCore
)
diff --git a/Modules/ImageExtraction/CMakeLists.txt b/Modules/ImageExtraction/CMakeLists.txt
index ad9d099dda..f522d94f78 100644
--- a/Modules/ImageExtraction/CMakeLists.txt
+++ b/Modules/ImageExtraction/CMakeLists.txt
@@ -1,10 +1,9 @@
MITK_CREATE_MODULE(
DEPENDS MitkAlgorithmsExt
- PACKAGE_DEPENDS PRIVATE ITK|ITKIOImageBase
)
if(BUILD_TESTING)
add_subdirectory(Testing)
endif(BUILD_TESTING)
diff --git a/Modules/ImageStatistics/CMakeLists.txt b/Modules/ImageStatistics/CMakeLists.txt
index 532b38bdf4..1cf692bc6f 100644
--- a/Modules/ImageStatistics/CMakeLists.txt
+++ b/Modules/ImageStatistics/CMakeLists.txt
@@ -1,10 +1,8 @@
-MITK_CREATE_MODULE(
+mitk_create_module(
DEPENDS MitkImageExtraction MitkPlanarFigure MitkMultilabel
- PACKAGE_DEPENDS
- PUBLIC ITK|ITKIOXML
- PRIVATE ITK|ITKVTK+ITKConvolution VTK|IOImage
+ PACKAGE_DEPENDS PRIVATE ITK|VTK VTK|IOImage
)
if(BUILD_TESTING)
add_subdirectory(Testing)
endif()
diff --git a/Modules/ImageStatistics/Testing/CMakeLists.txt b/Modules/ImageStatistics/Testing/CMakeLists.txt
index 5eca89a43e..834d6d6592 100644
--- a/Modules/ImageStatistics/Testing/CMakeLists.txt
+++ b/Modules/ImageStatistics/Testing/CMakeLists.txt
@@ -1,34 +1,38 @@
MITK_CREATE_MODULE_TESTS()
+if(TARGET ${TESTDRIVER})
+ mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK|IOXML)
+endif()
+
# mitkAddCustomModuleTest(mitkRoiMeasurementsTests mitkRoiMeasurementsTest ${MITK_DATA_DIR}/ImageStatisticsTestData/)
file(GLOB allHotSpotTests RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}/Data/Hotspot" "${CMAKE_CURRENT_SOURCE_DIR}/Data/Hotspot/*.xml")
foreach(testcase ${allHotSpotTests})
string(REGEX REPLACE "[^a-zA-Z0-9_]" "_" testcaseName ${testcase})
mitkAddCustomModuleTest(mitkImageStatisticsHotspotTest_${testcaseName} mitkImageStatisticsHotspotTest ${CMAKE_CURRENT_SOURCE_DIR}/Data/Hotspot/${testcase})
endforeach()
#
# The following lines may be activated to generate new test cases for mitkImageStatisticsHotspotTest.
# Test cases are generated by mitkMultiGaussianTest. All .xml files in Data/TestGeneration/Input will
# be processed and transformed into new .xml files containing statistics in Data/TestGeneration/Output.
#
if (false)
set(testInputDir ${CMAKE_CURRENT_SOURCE_DIR}/Data/TestGeneration/Input)
set(testOutputDir ${CMAKE_CURRENT_SOURCE_DIR}/Data/TestGeneration/Output)
file(GLOB testcasesToGenerate RELATIVE "${testInputDir}" "${testInputDir}/*.xml")
if (NOT EXISTS ${testOutputDir})
file(MAKE_DIRECTORY ${testOutputDir})
endif()
foreach(testinput ${testcasesToGenerate})
string(REGEX REPLACE "[^a-zA-Z0-9_]\\+" "_" testcaseName ${testinput})
string(REGEX REPLACE "\\.xml" "" testoutput ${testinput})
message("Generate hotspot test case '${testinput}'. Output in '${testoutput}.xml' and '${testoutput}.nrrd'")
mitkAddCustomModuleTest(mitkMultiGaussianTest_${testcaseName}
mitkMultiGaussianTest
${testOutputDir}/${testoutput}
${testInputDir}/${testinput})
endforeach()
endif()
diff --git a/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h b/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h
index c724cd6e81..0e61304fef 100644
--- a/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h
+++ b/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h
@@ -1,149 +1,145 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKPLANARFIGUREMASKGENERATOR
#define MITKPLANARFIGUREMASKGENERATOR
#include <MitkImageStatisticsExports.h>
#include <itkImage.h>
-#include <itkVTKImageExport.h>
-#include <itkVTKImageImport.h>
#include <mitkImage.h>
#include <mitkMaskGenerator.h>
#include <mitkPlanarFigure.h>
-#include <vtkImageExport.h>
-#include <vtkImageImport.h>
#include <vtkSmartPointer.h>
namespace mitk
{
/**
* \class PlanarFigureMaskGenerator
* \brief Derived from MaskGenerator. This class is used to convert a mitk::PlanarFigure into a binary image mask
*/
class MITKIMAGESTATISTICS_EXPORT PlanarFigureMaskGenerator : public MaskGenerator
{
public:
/** Standard Self typedef */
typedef PlanarFigureMaskGenerator Self;
typedef MaskGenerator Superclass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self); /** Runtime information support. */
itkTypeMacro(PlanarFigureMaskGenerator, MaskGenerator);
/**
* @brief GetMask Computes and returns the mask
* @return mitk::Image::Pointer of the generated mask
*/
mitk::Image::Pointer GetMask() override;
void SetPlanarFigure(mitk::PlanarFigure::Pointer planarFigure);
mitk::Image::ConstPointer GetReferenceImage() override;
/**
* @brief SetTimeStep is used to set the time step for which the mask is to be generated
* @param timeStep
*/
void SetTimeStep(unsigned int timeStep) override;
itkGetConstMacro(PlanarFigureAxis, unsigned int);
itkGetConstMacro(PlanarFigureSlice, unsigned int);
/** Helper function that indicates if a passed planar geometry is tilted regarding a given geometry and its main axis.
*@pre If either planarGeometry or geometry is nullptr it will return false.*/
static bool CheckPlanarFigureIsNotTilted(const PlaneGeometry* planarGeometry, const BaseGeometry *geometry);
protected:
PlanarFigureMaskGenerator()
: Superclass(),
m_ReferenceImage(nullptr),
m_PlanarFigureAxis(0),
m_InternalMaskUpdateTime(0),
m_PlanarFigureSlice(0)
{
m_InternalMask = mitk::Image::New();
}
private:
void CalculateMask();
template <typename TPixel, unsigned int VImageDimension>
void InternalCalculateMaskFromPlanarFigure(const itk::Image<TPixel, VImageDimension> *image, unsigned int axis);
template <typename TPixel, unsigned int VImageDimension>
void InternalCalculateMaskFromOpenPlanarFigure(const itk::Image<TPixel, VImageDimension> *image, unsigned int axis);
mitk::Image::ConstPointer extract2DImageSlice(unsigned int axis, unsigned int slice);
/** Helper function that deduces if the passed vector is equal to one of the primary axis of the geometry.*/
static bool GetPrincipalAxis(const BaseGeometry *geometry, Vector3D vector, unsigned int &axis);
/** Connection from ITK to VTK */
template <typename ITK_Exporter, typename VTK_Importer>
void ConnectPipelines(ITK_Exporter exporter, vtkSmartPointer<VTK_Importer> importer)
{
importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
importer->SetSpacingCallback(exporter->GetSpacingCallback());
importer->SetOriginCallback(exporter->GetOriginCallback());
importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
importer->SetCallbackUserData(exporter->GetCallbackUserData());
}
/** Connection from VTK to ITK */
template <typename VTK_Exporter, typename ITK_Importer>
void ConnectPipelines(vtkSmartPointer<VTK_Exporter> exporter, ITK_Importer importer)
{
importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
importer->SetSpacingCallback(exporter->GetSpacingCallback());
importer->SetOriginCallback(exporter->GetOriginCallback());
importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
importer->SetCallbackUserData(exporter->GetCallbackUserData());
}
bool IsUpdateRequired() const;
mitk::PlanarFigure::Pointer m_PlanarFigure;
itk::Image<unsigned short, 2>::Pointer m_InternalITKImageMask2D;
mitk::Image::ConstPointer m_InternalTimeSliceImage;
mitk::Image::ConstPointer m_ReferenceImage;
unsigned int m_PlanarFigureAxis;
unsigned long m_InternalMaskUpdateTime;
unsigned int m_PlanarFigureSlice;
};
} // namespace mitk
#endif // MITKPLANARFIGUREMASKGENERATOR
diff --git a/Modules/LegacyIO/CMakeLists.txt b/Modules/LegacyIO/CMakeLists.txt
index d9debfbd64..6a2376d3af 100644
--- a/Modules/LegacyIO/CMakeLists.txt
+++ b/Modules/LegacyIO/CMakeLists.txt
@@ -1,8 +1,8 @@
mitkFunctionCheckCompilerFlags("/wd4996" CMAKE_CXX_FLAGS)
mitkFunctionCheckCompilerFlags("-Wno-deprecated-declarations" CMAKE_CXX_FLAGS)
MITK_CREATE_MODULE(
DEPENDS MitkCore
- PACKAGE_DEPENDS PRIVATE ITK|ITKIOGDCM+ITKIORAW tinyxml
+ PACKAGE_DEPENDS tinyxml2
DEPRECATED_SINCE 2014.10
)
diff --git a/Modules/LegacyIO/mitkPointSetReader.cpp b/Modules/LegacyIO/mitkPointSetReader.cpp
index 7222c061e5..f33d2cc3f8 100644
--- a/Modules/LegacyIO/mitkPointSetReader.cpp
+++ b/Modules/LegacyIO/mitkPointSetReader.cpp
@@ -1,195 +1,195 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPointSetReader.h"
#include <fstream>
#include <iostream>
#include <mitkLocaleSwitch.h>
+#include <tinyxml2.h>
mitk::PointSetReader::PointSetReader()
{
m_Success = false;
}
mitk::PointSetReader::~PointSetReader()
{
}
void mitk::PointSetReader::GenerateData()
{
// Switch the current locale to "C"
LocaleSwitch localeSwitch("C");
m_Success = false;
if (m_FileName == "")
{
itkWarningMacro(<< "Sorry, filename has not been set!");
return;
}
if (!this->CanReadFile(m_FileName.c_str()))
{
itkWarningMacro(<< "Sorry, can't read file " << m_FileName << "!");
return;
}
try
{
- TiXmlDocument doc(m_FileName.c_str());
- bool loadOkay = doc.LoadFile();
- if (loadOkay)
+ tinyxml2::XMLDocument doc;
+ if (tinyxml2::XML_SUCCESS == doc.LoadFile(m_FileName.c_str()))
{
- TiXmlHandle docHandle(&doc);
+ tinyxml2::XMLHandle docHandle(&doc);
unsigned int pointSetCounter(0);
- for (TiXmlElement *currentPointSetElement =
+ for (auto *currentPointSetElement =
docHandle.FirstChildElement("point_set_file").FirstChildElement("point_set").ToElement();
currentPointSetElement != nullptr;
currentPointSetElement = currentPointSetElement->NextSiblingElement())
{
mitk::PointSet::Pointer newPointSet = mitk::PointSet::New();
if (currentPointSetElement->FirstChildElement("time_series") != nullptr)
{
- for (TiXmlElement *currentTimeSeries = currentPointSetElement->FirstChildElement("time_series")->ToElement();
+ for (auto *currentTimeSeries = currentPointSetElement->FirstChildElement("time_series");
currentTimeSeries != nullptr;
currentTimeSeries = currentTimeSeries->NextSiblingElement())
{
unsigned int currentTimeStep(0);
- TiXmlElement *currentTimeSeriesID = currentTimeSeries->FirstChildElement("time_series_id");
+ auto *currentTimeSeriesID = currentTimeSeries->FirstChildElement("time_series_id");
currentTimeStep = atoi(currentTimeSeriesID->GetText());
newPointSet = this->ReadPoint(newPointSet, currentTimeSeries, currentTimeStep);
}
}
else
{
newPointSet = this->ReadPoint(newPointSet, currentPointSetElement, 0);
}
this->SetNthOutput(pointSetCounter, newPointSet);
pointSetCounter++;
}
}
else
{
MITK_WARN << "XML parser error!";
}
}
catch (...)
{
MITK_ERROR << "Cannot read point set.";
m_Success = false;
}
m_Success = true;
}
mitk::PointSet::Pointer mitk::PointSetReader::ReadPoint(mitk::PointSet::Pointer newPointSet,
- TiXmlElement *currentTimeSeries,
+ const tinyxml2::XMLElement *currentTimeSeries,
unsigned int currentTimeStep)
{
if (currentTimeSeries->FirstChildElement("point") != nullptr)
{
- for (TiXmlElement *currentPoint = currentTimeSeries->FirstChildElement("point")->ToElement();
+ for (auto *currentPoint = currentTimeSeries->FirstChildElement("point");
currentPoint != nullptr;
currentPoint = currentPoint->NextSiblingElement())
{
unsigned int id(0);
mitk::PointSpecificationType spec((mitk::PointSpecificationType)0);
double x(0.0);
double y(0.0);
double z(0.0);
id = atoi(currentPoint->FirstChildElement("id")->GetText());
if (currentPoint->FirstChildElement("specification") != nullptr)
{
spec = (mitk::PointSpecificationType)atoi(currentPoint->FirstChildElement("specification")->GetText());
}
x = atof(currentPoint->FirstChildElement("x")->GetText());
y = atof(currentPoint->FirstChildElement("y")->GetText());
z = atof(currentPoint->FirstChildElement("z")->GetText());
mitk::Point3D point;
mitk::FillVector3D(point, x, y, z);
newPointSet->SetPoint(id, point, spec, currentTimeStep);
}
}
else
{
if (currentTimeStep != newPointSet->GetTimeSteps() + 1)
{
newPointSet->Expand(currentTimeStep + 1); // expand time step series with empty time step
}
}
return newPointSet;
}
void mitk::PointSetReader::GenerateOutputInformation()
{
}
int mitk::PointSetReader::CanReadFile(const char *name)
{
std::ifstream in(name);
bool isGood = in.good();
in.close();
return isGood;
}
bool mitk::PointSetReader::CanReadFile(const std::string filename,
const std::string filePrefix,
const std::string filePattern)
{
// First check the extension
if (filename == "")
{
// MITK_INFO<<"No filename specified."<<std::endl;
return false;
}
// check if image is serie
if (filePattern != "" && filePrefix != "")
return false;
bool extensionFound = false;
std::string::size_type MPSPos = filename.rfind(".mps");
if ((MPSPos != std::string::npos) && (MPSPos == filename.length() - 4))
{
extensionFound = true;
}
MPSPos = filename.rfind(".MPS");
if ((MPSPos != std::string::npos) && (MPSPos == filename.length() - 4))
{
extensionFound = true;
}
if (!extensionFound)
{
// MITK_INFO<<"The filename extension is not recognized."<<std::endl;
return false;
}
return true;
}
void mitk::PointSetReader::ResizeOutputs(const unsigned int &num)
{
unsigned int prevNum = this->GetNumberOfOutputs();
this->SetNumberOfIndexedOutputs(num);
for (unsigned int i = prevNum; i < num; ++i)
{
this->SetNthOutput(i, this->MakeOutput(i).GetPointer());
}
}
bool mitk::PointSetReader::GetSuccess() const
{
return m_Success;
}
diff --git a/Modules/LegacyIO/mitkPointSetReader.h b/Modules/LegacyIO/mitkPointSetReader.h
index eb4cc27c51..9ea21cd980 100644
--- a/Modules/LegacyIO/mitkPointSetReader.h
+++ b/Modules/LegacyIO/mitkPointSetReader.h
@@ -1,141 +1,145 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef _MITK_POINT_SET_READER__H_
#define _MITK_POINT_SET_READER__H_
#include <MitkLegacyIOExports.h>
#include <mitkFileReader.h>
#include <mitkPointSetSource.h>
#include <stack>
#include <string>
-#include <tinyxml.h>
#include <vtkXMLParser.h>
+namespace tinyxml2
+{
+ class XMLElement;
+}
+
namespace mitk
{
/**
* @brief reads xml representations of mitk::PointSets from a file
*
* Reader for xml files containing one or multiple xml represenations of
* mitk::PointSets. If multiple mitk::PointSets are stored in one file,
* these are assigned to multiple outputs of the filter. The number of point
* sets which have be read can be retrieven by a call to GetNumberOfOutputs()
* after the pipeline update().
* The reader is able to read the old 3D Pointsets without the "specification" and "timeseries" tags and the new 4D
* Pointsets.
* @note loading point sets from multiple files according to a given file pattern
* is not yet supported!
*
* @ingroup MitkLegacyIOModule
*
* @deprecatedSince{2014_10} Use mitk::IOUtils or mitk::FileReaderRegistry instead.
*/
class MITKLEGACYIO_EXPORT PointSetReader : public PointSetSource, public FileReader
{
public:
mitkClassMacro(PointSetReader, FileReader);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
/**
* @brief Sets the filename of the file to be read
* @param _arg the filename of the point set xml-file
*/
itkSetStringMacro(FileName);
/**
* @brief Returns the filename of the point set xml-file.
* @returns the filename of the point set xml-file.
*/
itkGetStringMacro(FileName);
/**
* @warning multiple load not (yet) supported
*/
itkSetStringMacro(FilePrefix);
/**
* @warning multiple load not (yet) supported
*/
itkGetStringMacro(FilePrefix);
/**
* @warning multiple load not (yet) supported
*/
itkSetStringMacro(FilePattern);
/**
* @warning multiple load not (yet) supported
*/
itkGetStringMacro(FilePattern);
static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern);
/**
* @returns whether the last read attempt was successful or not.
*/
bool GetSuccess() const;
protected:
/**
* Constructor
*/
PointSetReader();
/**
* Virtual destructor
*/
~PointSetReader() override;
/**
* Actually reads the point sets from the given file
*/
void GenerateData() override;
virtual mitk::PointSet::Pointer ReadPoint(mitk::PointSet::Pointer newPointSet,
- TiXmlElement *currentTimeSeries,
+ const tinyxml2::XMLElement *currentTimeSeries,
unsigned int currentTimeStep);
/**
* Does nothing in the current implementation
*/
void GenerateOutputInformation() override;
/**
* Resizes the output-objects according to the given number.
* @param num the new number of output objects.
*/
virtual void ResizeOutputs(const unsigned int &num);
/**
* Checks if the given file has appropriate
* read access.
* @returns true if the file exists and may be read
* or false otherwise.
*/
virtual int CanReadFile(const char *name);
std::string m_FileName;
std::string m_FilePrefix;
std::string m_FilePattern;
bool m_Success;
};
}
#endif
diff --git a/Modules/MapperExt/CMakeLists.txt b/Modules/MapperExt/CMakeLists.txt
index ca202f89be..e437f52956 100644
--- a/Modules/MapperExt/CMakeLists.txt
+++ b/Modules/MapperExt/CMakeLists.txt
@@ -1,14 +1,10 @@
mitk_create_module(
DEPENDS MitkDataTypesExt MitkLegacyGL
- PACKAGE_DEPENDS PRIVATE VTK|CommonComputationalGeometry+CommonSystem+RenderingVolumeOpenGL2
+ PACKAGE_DEPENDS PUBLIC OpenMP PRIVATE VTK|CommonComputationalGeometry+CommonSystem+RenderingVolumeOpenGL2
)
if(TARGET ${MODULE_TARGET})
- if(MITK_USE_OpenMP)
- target_link_libraries(${MODULE_TARGET} PUBLIC OpenMP::OpenMP_CXX)
- endif()
-
if(BUILD_TESTING)
add_subdirectory(test)
endif()
endif()
diff --git a/Modules/MatchPointRegistration/autoload/IO/CMakeLists.txt b/Modules/MatchPointRegistration/autoload/IO/CMakeLists.txt
index 0881f2493b..4df0d899e9 100644
--- a/Modules/MatchPointRegistration/autoload/IO/CMakeLists.txt
+++ b/Modules/MatchPointRegistration/autoload/IO/CMakeLists.txt
@@ -1,7 +1,7 @@
-MITK_CREATE_MODULE(MatchPointRegistrationIO
+mitk_create_module(MatchPointRegistrationIO
DEPENDS
PUBLIC MitkMatchPointRegistration MitkSceneSerializationBase
PACKAGE_DEPENDS
- PRIVATE ITK MatchPoint
+ PRIVATE MatchPoint
AUTOLOAD_WITH MitkCore
)
diff --git a/Modules/MatchPointRegistration/cmdapps/CMakeLists.txt b/Modules/MatchPointRegistration/cmdapps/CMakeLists.txt
index f02ab70bc2..272923372e 100644
--- a/Modules/MatchPointRegistration/cmdapps/CMakeLists.txt
+++ b/Modules/MatchPointRegistration/cmdapps/CMakeLists.txt
@@ -1,33 +1,32 @@
option(BUILD_MatchPointCmdApps "Build commandline tools for the MatchPoint module" OFF)
if(BUILD_MatchPointCmdApps OR MITK_BUILD_ALL_APPS)
# needed include directories
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
# list of CmdApps
# if an app requires additional dependencies
# they are added after a "^^" and separated by "_"
set( cmdapps
StitchImagesMiniApp^^
)
foreach(cmdapp ${cmdapps})
# extract cmd name and dependencies
string(REPLACE "^^" "\\;" cmdapp_info ${cmdapp})
set(cmdapp_info_list ${cmdapp_info})
list(GET cmdapp_info_list 0 appname)
list(GET cmdapp_info_list 1 raw_dependencies)
string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
set(dependencies_list ${dependencies})
mitkFunctionCreateCommandLineApp(
NAME ${appname}
DEPENDS MitkCore MitkMatchPointRegistration ${dependencies_list}
- PACKAGE_DEPENDS ITK
)
endforeach()
endif(BUILD_MatchPointCmdApps OR MITK_BUILD_ALL_APPS)
diff --git a/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp b/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp
index 1ec8334ada..5e8e7529c9 100644
--- a/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp
+++ b/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp
@@ -1,639 +1,639 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef itkStitchImageFilter_hxx
#define itkStitchImageFilter_hxx
#include "itkStitchImageFilter.h"
#include "itkObjectFactory.h"
#include "itkIdentityTransform.h"
#include "itkProgressReporter.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkImageScanlineIterator.h"
#include "itkSpecialCoordinatesImage.h"
#include "itkDefaultConvertPixelTraits.h"
#include "itkSimpleDataObjectDecorator.h"
#include <numeric>
namespace itk
{
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::StitchImageFilter() :
m_OutputSpacing( 1.0 ),
m_OutputOrigin( 0.0 ),
m_UseReferenceImage( false ),
m_StitchStrategy(StitchStrategy::Mean)
{
m_Size.Fill( 0 );
m_OutputStartIndex.Fill( 0 );
m_OutputDirection.SetIdentity();
// Pipeline input configuration
// implicit input index set:
// #1 "ReferenceImage" optional
Self::AddOptionalInputName("ReferenceImage");
m_DefaultPixelValue
= NumericTraits<PixelType>::ZeroValue( m_DefaultPixelValue );
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetInput(const InputImageType* image)
{
this->SetInput(0, image, itk::IdentityTransform< TTransformPrecisionType, ImageDimension>::New().GetPointer(), LinearInterpolatorType::New().GetPointer());
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetInput(unsigned int index, const InputImageType* image)
{
this->SetInput(index, image, itk::IdentityTransform< TTransformPrecisionType, ImageDimension>::New().GetPointer(), LinearInterpolatorType::New().GetPointer());
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetInput(unsigned int index, const InputImageType* image, const TransformType* transform)
{
this->SetInput(index, image, transform, LinearInterpolatorType::New().GetPointer());
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetInput(unsigned int index, const InputImageType* image, const TransformType* transform, InterpolatorType* interpolator)
{
Superclass::SetInput(index, image);
m_Interpolators[image] = interpolator;
this->SetTransform(index, transform);
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetTransform(unsigned int index, const TransformType* transform)
{
const auto transformName = this->GetTransformInputName(index);
typedef SimpleDataObjectDecorator< TransformPointerType > DecoratorType;
const DecoratorType* oldInput = itkDynamicCastInDebugMode< const DecoratorType* >(this->ProcessObject::GetInput(transformName));
if (!oldInput || oldInput->Get() != transform)
{
typename DecoratorType::Pointer newInput = DecoratorType::New();
// Process object is not const-correct so the const_cast is required here
newInput->Set(const_cast<TransformType*>(transform));
this->ProcessObject::SetInput(transformName, newInput);
}
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
const typename StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >::TransformType*
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::GetTransform(unsigned int index) const
{
typedef SimpleDataObjectDecorator< TransformPointerType > DecoratorType;
const DecoratorType* input = itkDynamicCastInDebugMode< const DecoratorType* >(this->ProcessObject::GetInput(this->GetTransformInputName(index)));
if (nullptr != input)
{
return input->Get();
}
return nullptr;
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
const typename StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >::InterpolatorType*
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::GetInterpolator(unsigned int index) const
{
auto input = this->GetInput(index);
if (m_Interpolators.find(input) != std::end(m_Interpolators))
{
return m_Interpolators[input];
}
return nullptr;
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetOutputSpacing(const double *spacing)
{
SpacingType s;
for(unsigned int i = 0; i < TOutputImage::ImageDimension; ++i)
{
s[i] = static_cast< typename SpacingType::ValueType >(spacing[i]);
}
this->SetOutputSpacing(s);
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetOutputOrigin(const double *origin)
{
OriginPointType p(origin);
this->SetOutputOrigin(p);
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::SetOutputParametersFromImage(const ImageBaseType *image)
{
this->SetOutputOrigin ( image->GetOrigin() );
this->SetOutputSpacing ( image->GetSpacing() );
this->SetOutputDirection ( image->GetDirection() );
this->SetOutputStartIndex ( image->GetLargestPossibleRegion().GetIndex() );
this->SetSize ( image->GetLargestPossibleRegion().GetSize() );
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::BeforeThreadedGenerateData()
{
this->EnsureInterpolators();
this->EnsureTransforms();
for (const auto& interpolator : m_Interpolators)
{
interpolator.second->SetInputImage(interpolator.first);
}
unsigned int nComponents
= DefaultConvertPixelTraits<PixelType>::GetNumberOfComponents(
m_DefaultPixelValue );
if (nComponents == 0)
{
PixelComponentType zeroComponent
- = NumericTraits<PixelComponentType>::ZeroValue( zeroComponent );
+ = NumericTraits<PixelComponentType>::ZeroValue();
nComponents = this->GetInput()->GetNumberOfComponentsPerPixel();
NumericTraits<PixelType>::SetLength(m_DefaultPixelValue, nComponents );
for (unsigned int n=0; n<nComponents; n++)
{
PixelConvertType::SetNthComponent( n, m_DefaultPixelValue,
zeroComponent );
}
}
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::AfterThreadedGenerateData()
{
// Disconnect input image from the interpolator
for (auto& interpolator : m_Interpolators)
{
interpolator.second->SetInputImage(ITK_NULLPTR);
}
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread,
ThreadIdType threadId)
{
if( outputRegionForThread.GetNumberOfPixels() == 0 )
{
return;
}
// Get the output pointers
OutputImageType* outputPtr = this->GetOutput();
// Get this input pointers
InputImageVectorType inputs = this->GetInputs();
TransformMapType transforms = this->GetTransforms();
std::map<const InputImageType*, typename InputImageType::IndexType> lowerIndices;
std::map<const InputImageType*, typename InputImageType::IndexType> upperIndices;
for (const auto& input : inputs)
{
const auto largestRegion = input->GetLargestPossibleRegion();
lowerIndices[input] = largestRegion.GetIndex();
upperIndices[input] = largestRegion.GetUpperIndex();
}
// Create an iterator that will walk the output region for this thread.
typedef ImageRegionIteratorWithIndex< OutputImageType > OutputIterator;
OutputIterator outIt(outputPtr, outputRegionForThread);
// Define a few indices that will be used to translate from an input pixel
// to an output pixel
PointType outputPoint; // Coordinates of current output pixel
PointType inputPoint; // Coordinates of current input pixel
ContinuousInputIndexType inputIndex;
// Support for progress methods/callbacks
ProgressReporter progress(this,
threadId,
outputRegionForThread.GetNumberOfPixels());
// Min/max values of the output pixel type AND these values
// represented as the output type of the interpolator
const PixelComponentType minValue = NumericTraits< PixelComponentType >::NonpositiveMin();
const PixelComponentType maxValue = NumericTraits< PixelComponentType >::max();
typedef typename InterpolatorType::OutputType OutputType;
const ComponentType minOutputValue = static_cast<ComponentType>(minValue);
const ComponentType maxOutputValue = static_cast<ComponentType>(maxValue);
// Walk the output region
outIt.GoToBegin();
while (!outIt.IsAtEnd())
{
// Determine the index of the current output pixel
outputPtr->TransformIndexToPhysicalPoint(outIt.GetIndex(), outputPoint);
std::vector<PixelType> pixvals;
std::vector<double> pixDistance;
for (const auto& input : inputs)
{
// Compute corresponding input pixel position
inputPoint = transforms[input]->TransformPoint(outputPoint);
const bool isInsideInput = input->TransformPhysicalPointToContinuousIndex(inputPoint, inputIndex);
// Evaluate input at right position and copy to the output
if (m_Interpolators[input]->IsInsideBuffer(inputIndex) && isInsideInput)
{
OutputType value = m_Interpolators[input]->EvaluateAtContinuousIndex(inputIndex);
pixvals.emplace_back(this->CastPixelWithBoundsChecking(value, minOutputValue, maxOutputValue));
ContinuousInputIndexType indexDistance;
const auto spacing = input->GetSpacing();
double minBorderDistance = std::numeric_limits<double>::max();
for (unsigned int i = 0; i < ImageDimension; ++i)
{
minBorderDistance = std::min(minBorderDistance, std::min(std::abs(lowerIndices[input][i] - inputIndex[i]) * spacing[i], std::abs(upperIndices[input][i] - inputIndex[i]) * spacing[i]));
}
pixDistance.emplace_back(minBorderDistance);
}
}
if (!pixvals.empty())
{ //at least one input provided a value
if (StitchStrategy::Mean == m_StitchStrategy)
{
double sum = std::accumulate(pixvals.begin(), pixvals.end(), 0.0);
outIt.Set(sum / pixvals.size());
}
else
{
auto finding = std::max_element(pixDistance.begin(), pixDistance.end());
outIt.Set(pixvals[std::distance(pixDistance.begin(), finding)]);
}
}
else
{
outIt.Set(m_DefaultPixelValue); // default background value
}
progress.CompletedPixel();
++outIt;
}
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
typename StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::PixelType
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::CastPixelWithBoundsChecking(const InterpolatorOutputType value,
const ComponentType minComponent,
const ComponentType maxComponent ) const
{
const unsigned int nComponents = InterpolatorConvertType::GetNumberOfComponents(value);
PixelType outputValue;
NumericTraits<PixelType>::SetLength( outputValue, nComponents );
for (unsigned int n = 0; n < nComponents; n++)
{
ComponentType component = InterpolatorConvertType::GetNthComponent( n, value );
if ( component < minComponent )
{
PixelConvertType::SetNthComponent( n, outputValue, static_cast<PixelComponentType>( minComponent ) );
}
else if ( component > maxComponent )
{
PixelConvertType::SetNthComponent( n, outputValue, static_cast<PixelComponentType>( maxComponent ) );
}
else
{
PixelConvertType::SetNthComponent(n, outputValue,
static_cast<PixelComponentType>( component ) );
}
}
return outputValue;
}
template<typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType>
typename StitchImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::InputImageVectorType
StitchImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>
::GetInputs()
{
InputImageVectorType inputs;
for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); ++i)
{
auto input = this->GetInput(i);
if (nullptr != input)
{
inputs.push_back(input);
}
}
return inputs;
}
template<typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType>
typename StitchImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>::TransformMapType
StitchImageFilter<TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType>
::GetTransforms()
{
TransformMapType transforms;
for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); ++i)
{
auto input = this->GetInput(i);
auto transform = this->GetTransform(i);
transforms[input] = transform;
}
return transforms;
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::GenerateInputRequestedRegion()
{
// Call the superclass' implementation of this method
Superclass::GenerateInputRequestedRegion();
if ( !this->GetInput() )
{
return;
}
// Get pointers to the input
auto inputs = this->GetInputs();
for (auto& input : inputs)
{
InputImagePointer inputPtr =
const_cast<TInputImage*>(input);
// Determining the actual input region is non-trivial, especially
// when we cannot assume anything about the transform being used.
// So we do the easy thing and request the entire input image.
//
inputPtr->SetRequestedRegionToLargestPossibleRegion();
}
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::GenerateOutputInformation()
{
// Call the superclass' implementation of this method
Superclass::GenerateOutputInformation();
// Get pointers to the input and output
OutputImageType *outputPtr = this->GetOutput();
if ( !outputPtr )
{
return;
}
const ReferenceImageBaseType *referenceImage = this->GetReferenceImage();
// Set the size of the output region
if ( m_UseReferenceImage && referenceImage )
{
outputPtr->SetLargestPossibleRegion(
referenceImage->GetLargestPossibleRegion() );
}
else
{
typename TOutputImage::RegionType outputLargestPossibleRegion;
outputLargestPossibleRegion.SetSize(m_Size);
outputLargestPossibleRegion.SetIndex(m_OutputStartIndex);
outputPtr->SetLargestPossibleRegion(outputLargestPossibleRegion);
}
// Set spacing and origin
if ( m_UseReferenceImage && referenceImage )
{
outputPtr->SetSpacing( referenceImage->GetSpacing() );
outputPtr->SetOrigin( referenceImage->GetOrigin() );
outputPtr->SetDirection( referenceImage->GetDirection() );
}
else
{
outputPtr->SetSpacing(m_OutputSpacing);
outputPtr->SetOrigin(m_OutputOrigin);
outputPtr->SetDirection(m_OutputDirection);
}
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
ModifiedTimeType
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::GetMTime(void) const
{
ModifiedTimeType latestTime = Object::GetMTime();
for (const auto& interpolator : m_Interpolators)
{
if (interpolator.second.GetPointer())
{
if (latestTime < interpolator.second->GetMTime())
{
latestTime = interpolator.second->GetMTime();
}
}
}
return latestTime;
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::PrintSelf(std::ostream & os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "DefaultPixelValue: "
<< static_cast< typename NumericTraits< PixelType >::PrintType >
( m_DefaultPixelValue )
<< std::endl;
os << indent << "Size: " << m_Size << std::endl;
os << indent << "OutputStartIndex: " << m_OutputStartIndex << std::endl;
os << indent << "OutputSpacing: " << m_OutputSpacing << std::endl;
os << indent << "OutputOrigin: " << m_OutputOrigin << std::endl;
os << indent << "OutputDirection: " << m_OutputDirection << std::endl;
for (const auto& interpolator : m_Interpolators)
{
os << indent << "Interpolator: " << interpolator.second.GetPointer() << std::endl;
}
os << indent << "UseReferenceImage: " << ( m_UseReferenceImage ? "On" : "Off" )
<< std::endl;
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::EnsureTransforms()
{
const auto inputCount = this->GetNumberOfIndexedInputs();
for (unsigned int i = 0; i < inputCount; ++i)
{
auto input = this->GetInput(i);
if (nullptr == input)
{
itkExceptionMacro(<< "Nth input image is not set (n: " << i << ").");
}
auto transform = this->GetTransform(i);
if (nullptr == transform)
{
this->SetTransform(i, itk::IdentityTransform< TTransformPrecisionType, ImageDimension>::New().GetPointer());
}
}
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
void
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::EnsureInterpolators()
{
const auto inputCount = this->GetNumberOfIndexedInputs();
InterpolatorMapType newInterpolatorMap;
for (unsigned int i = 0; i < inputCount; ++i)
{
auto input = this->GetInput(i);
if (nullptr == input)
{
itkExceptionMacro(<< "Nth input image is not set (n: " << i << ").");
}
if (m_Interpolators[input].IsNull())
{
newInterpolatorMap[input] = LinearInterpolatorType::New().GetPointer();
}
else
{
newInterpolatorMap[input] = m_Interpolators[input];
}
}
m_Interpolators = newInterpolatorMap;
}
template< typename TInputImage,
typename TOutputImage,
typename TInterpolatorPrecisionType,
typename TTransformPrecisionType >
std::string
StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >
::GetTransformInputName(unsigned int index)
{
return "transform_" + std::to_string(index);
}
} // end namespace itk
#endif
diff --git a/Modules/ModelFit/CMakeLists.txt b/Modules/ModelFit/CMakeLists.txt
index 6ddd33235a..673e5e128c 100644
--- a/Modules/ModelFit/CMakeLists.txt
+++ b/Modules/ModelFit/CMakeLists.txt
@@ -1,19 +1,18 @@
-MITK_CREATE_MODULE(ModelFit
+mitk_create_module(ModelFit
INCLUDE_DIRS
PUBLIC ${MITK_BINARY_DIR}
PRIVATE src/Common src/Functors src/Models src/TestingHelper
DEPENDS
PUBLIC MitkCore MitkSceneSerializationBase
PRIVATE MitkMultilabel
PACKAGE_DEPENDS
- PUBLIC ITK|ITKOptimizers
- PRIVATE Boost
+ PUBLIC ITK|Optimizers
)
if(BUILD_TESTING)
- ADD_SUBDIRECTORY(test)
-endif(BUILD_TESTING)
+ add_subdirectory(test)
+endif()
-ADD_SUBDIRECTORY(autoload/IO)
-ADD_SUBDIRECTORY(autoload/Models)
-ADD_SUBDIRECTORY(cmdapps)
+add_subdirectory(autoload/IO)
+add_subdirectory(autoload/Models)
+add_subdirectory(cmdapps)
diff --git a/Modules/ModelFit/cmdapps/CMakeLists.txt b/Modules/ModelFit/cmdapps/CMakeLists.txt
index cda6e31973..9ba9628919 100644
--- a/Modules/ModelFit/cmdapps/CMakeLists.txt
+++ b/Modules/ModelFit/cmdapps/CMakeLists.txt
@@ -1,35 +1,34 @@
option(BUILD_ModelFitMiniApps "Build commandline tools for the ModelFit module" OFF)
if(BUILD_ModelFitMiniApps OR MITK_BUILD_ALL_APPS)
# needed include directories
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
# list of miniapps
# if an app requires additional dependencies
# they are added after a "^^" and separated by "_"
set( miniapps
GenericFittingMiniApp^^
PixelDumpMiniApp^^
Fuse3Dto4DImageMiniApp^^
)
foreach(miniapp ${miniapps})
# extract mini app name and dependencies
string(REPLACE "^^" "\\;" miniapp_info ${miniapp})
set(miniapp_info_list ${miniapp_info})
list(GET miniapp_info_list 0 appname)
list(GET miniapp_info_list 1 raw_dependencies)
string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
set(dependencies_list ${dependencies})
mitkFunctionCreateCommandLineApp(
NAME ${appname}
DEPENDS MitkCore MitkModelFit ${dependencies_list}
- PACKAGE_DEPENDS ITK
)
endforeach()
endif(BUILD_ModelFitMiniApps OR MITK_BUILD_ALL_APPS)
diff --git a/Modules/ModelFit/include/mitkScalarListLookupTablePropertySerializer.h b/Modules/ModelFit/include/mitkScalarListLookupTablePropertySerializer.h
index b3db0deccc..d26f60e0d1 100644
--- a/Modules/ModelFit/include/mitkScalarListLookupTablePropertySerializer.h
+++ b/Modules/ModelFit/include/mitkScalarListLookupTablePropertySerializer.h
@@ -1,55 +1,55 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkScalarListLookupTablePropertySerializer_h
#define mitkScalarListLookupTablePropertySerializer_h
#include "mitkBasePropertySerializer.h"
#include "mitkBaseProperty.h"
#include "MitkModelFitExports.h"
namespace mitk
{
/**
* @brief Serializer for the ScalarListLookupTableProperty so it can be written and read from
* file.
*/
class ScalarListLookupTablePropertySerializer : public BasePropertySerializer
{
public:
mitkClassMacro(ScalarListLookupTablePropertySerializer, BasePropertySerializer);
itkNewMacro(Self);
- TiXmlElement* Serialize() override;
- BaseProperty::Pointer Deserialize(TiXmlElement* element) override;
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override;
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement* element) override;
protected:
ScalarListLookupTablePropertySerializer() {}
~ScalarListLookupTablePropertySerializer() override {}
};
namespace PropertyPersistenceSerialization
{
/** Serialization of a ScalarListLookupTableProperty into a XML string.*/
MITKMODELFIT_EXPORT ::std::string serializeScalarListLookupTablePropertyToXML(const mitk::BaseProperty *prop);
}
namespace PropertyPersistenceDeserialization
{
/**Deserialize a passed XML string into a ScalarListLookupTableProperty.*/
MITKMODELFIT_EXPORT mitk::BaseProperty::Pointer deserializeXMLToScalarListLookupTableProperty(const std::string &value);
}
}
#endif // mitkScalarListLookupTablePropertySerializer_h
diff --git a/Modules/ModelFit/src/Common/mitkScalarListLookupTablePropertySerializer.cpp b/Modules/ModelFit/src/Common/mitkScalarListLookupTablePropertySerializer.cpp
index 751a407cce..e54b48d683 100644
--- a/Modules/ModelFit/src/Common/mitkScalarListLookupTablePropertySerializer.cpp
+++ b/Modules/ModelFit/src/Common/mitkScalarListLookupTablePropertySerializer.cpp
@@ -1,127 +1,129 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkScalarListLookupTableProperty.h"
#include "mitkScalarListLookupTablePropertySerializer.h"
+#include <tinyxml2.h>
-
-TiXmlElement* mitk::ScalarListLookupTablePropertySerializer::Serialize()
+tinyxml2::XMLElement* mitk::ScalarListLookupTablePropertySerializer::Serialize(tinyxml2::XMLDocument& doc)
{
- const ScalarListLookupTableProperty* prop =
- dynamic_cast<const ScalarListLookupTableProperty*>(m_Property.GetPointer());
-
- if (prop == nullptr)
- {
- MITK_ERROR << "Serialization: Property is NULL";
- return nullptr;
- }
-
- ScalarListLookupTable lut = prop->GetValue();
- const ScalarListLookupTable::LookupTableType& map = lut.GetLookupTable();
-
- TiXmlElement* mapElement = new TiXmlElement("ScalarListLookupTable");
-
- for (ScalarListLookupTable::LookupTableType::const_iterator mapIter = map.begin();
- mapIter != map.end(); ++mapIter)
- {
- const ScalarListLookupTable::ValueType& list = mapIter->second;
- TiXmlElement* listElement = new TiXmlElement("List");
- listElement->SetAttribute("name", mapIter->first);
-
- for (ScalarListLookupTable::ValueType::const_iterator listIter = list.begin();
- listIter != list.end(); ++listIter)
- {
- TiXmlElement* valueElement = new TiXmlElement("Element");
- valueElement->SetDoubleAttribute("value", *listIter);
- listElement->LinkEndChild(valueElement);
- }
-
- mapElement->LinkEndChild(listElement);
- }
-
- return mapElement;
+ const ScalarListLookupTableProperty* prop =
+ dynamic_cast<const ScalarListLookupTableProperty*>(m_Property.GetPointer());
+
+ if (prop == nullptr)
+ {
+ MITK_ERROR << "Serialization: Property is NULL";
+ return nullptr;
+ }
+
+ ScalarListLookupTable lut = prop->GetValue();
+ const ScalarListLookupTable::LookupTableType& map = lut.GetLookupTable();
+
+ auto* mapElement = doc.NewElement("ScalarListLookupTable");
+
+ for (ScalarListLookupTable::LookupTableType::const_iterator mapIter = map.begin();
+ mapIter != map.end(); ++mapIter)
+ {
+ const ScalarListLookupTable::ValueType& list = mapIter->second;
+ auto* listElement = doc.NewElement("List");
+ listElement->SetAttribute("name", mapIter->first.c_str());
+
+ for (ScalarListLookupTable::ValueType::const_iterator listIter = list.begin();
+ listIter != list.end(); ++listIter)
+ {
+ auto* valueElement = doc.NewElement("Element");
+ valueElement->SetAttribute("value", *listIter);
+ listElement->InsertEndChild(valueElement);
+ }
+
+ mapElement->InsertEndChild(listElement);
+ }
+
+ return mapElement;
}
mitk::BaseProperty::Pointer
-mitk::ScalarListLookupTablePropertySerializer::Deserialize(TiXmlElement* element)
+mitk::ScalarListLookupTablePropertySerializer::Deserialize(const tinyxml2::XMLElement* element)
{
- if (!element)
- {
- MITK_ERROR << "Deserialization: Element is NULL";
- return nullptr;
- }
-
- ScalarListLookupTable lut;
-
- for (TiXmlElement* listElement = element->FirstChildElement("List");
- listElement != nullptr; listElement = listElement->NextSiblingElement("List"))
- {
- std::string name;
-
- if (listElement->Attribute("name") != nullptr)
- {
- name = listElement->Attribute("name");
- }
- else
- {
- MITK_ERROR << "Deserialization: No element with attribute 'name' found";
- return nullptr;
- }
-
- ScalarListLookupTable::ValueType list;
-
- for (TiXmlElement* valueElement = listElement->FirstChildElement("Element");
- valueElement != nullptr;
- valueElement = valueElement->NextSiblingElement("Element"))
- {
- double value;
-
- if (valueElement->QueryDoubleAttribute("value", &value) == TIXML_WRONG_TYPE)
- {
- MITK_ERROR << "Deserialization: No element with attribute 'value' found";
- return nullptr;
- }
-
- list.push_back(value);
- }
-
- lut.SetTableValue(name, list);
- }
-
- return ScalarListLookupTableProperty::New(lut).GetPointer();
+ if (!element)
+ {
+ MITK_ERROR << "Deserialization: Element is NULL";
+ return nullptr;
+ }
+
+ ScalarListLookupTable lut;
+
+ for (auto* listElement = element->FirstChildElement("List");
+ listElement != nullptr; listElement = listElement->NextSiblingElement("List"))
+ {
+ std::string name;
+
+ if (listElement->Attribute("name") != nullptr)
+ {
+ name = listElement->Attribute("name");
+ }
+ else
+ {
+ MITK_ERROR << "Deserialization: No element with attribute 'name' found";
+ return nullptr;
+ }
+
+ ScalarListLookupTable::ValueType list;
+
+ for (auto* valueElement = listElement->FirstChildElement("Element");
+ valueElement != nullptr;
+ valueElement = valueElement->NextSiblingElement("Element"))
+ {
+ double value;
+
+ if (valueElement->QueryDoubleAttribute("value", &value) != tinyxml2::XML_SUCCESS)
+ {
+ MITK_ERROR << "Deserialization: No element with attribute 'value' found";
+ return nullptr;
+ }
+
+ list.push_back(value);
+ }
+
+ lut.SetTableValue(name, list);
+ }
+
+ return ScalarListLookupTableProperty::New(lut).GetPointer();
}
MITK_REGISTER_SERIALIZER(ScalarListLookupTablePropertySerializer);
::std::string mitk::PropertyPersistenceSerialization::serializeScalarListLookupTablePropertyToXML(
const mitk::BaseProperty *prop)
{
mitk::ScalarListLookupTablePropertySerializer::Pointer lutSerializer = mitk::ScalarListLookupTablePropertySerializer::New();
lutSerializer->SetProperty(prop);
- auto xmlLut = lutSerializer->Serialize();
- TiXmlPrinter printer;
- xmlLut->Accept(&printer);
- printer.SetStreamPrinting();
- return printer.Str();
+ tinyxml2::XMLDocument doc;
+ lutSerializer->Serialize(doc);
+
+ tinyxml2::XMLPrinter printer;
+ doc.Print(&printer);
+
+ return printer.CStr();
}
mitk::BaseProperty::Pointer mitk::PropertyPersistenceDeserialization::deserializeXMLToScalarListLookupTableProperty(
const std::string &value)
{
mitk::ScalarListLookupTablePropertySerializer::Pointer lutSerializer = mitk::ScalarListLookupTablePropertySerializer::New();
- TiXmlDocument doc;
+ tinyxml2::XMLDocument doc;
doc.Parse(value.c_str());
return lutSerializer->Deserialize(doc.RootElement());
}
diff --git a/Modules/ModelFitUI/CMakeLists.txt b/Modules/ModelFitUI/CMakeLists.txt
index 0e03ef28e4..a5c118715b 100644
--- a/Modules/ModelFitUI/CMakeLists.txt
+++ b/Modules/ModelFitUI/CMakeLists.txt
@@ -1,5 +1,5 @@
MITK_CREATE_MODULE(ModelFitUI
INCLUDE_DIRS Common Qmitk
DEPENDS MitkModelFit MitkQtWidgets MitkQtWidgetsExt
- PACKAGE_DEPENDS Qt5|Core CTK|CTKWidgets Boost
+ PACKAGE_DEPENDS CTK|CTKWidgets
)
diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake
index e9a5d07801..c36c213269 100644
--- a/Modules/ModuleList.cmake
+++ b/Modules/ModuleList.cmake
@@ -1,85 +1,81 @@
# The entries in the mitk_modules list must be
# ordered according to their dependencies.
set(MITK_MODULES
Core
CommandLine
CoreCmdApps
AppUtil
LegacyIO
DataTypesExt
Annotation
LegacyGL
AlgorithmsExt
MapperExt
DICOM
DICOMQI
DICOMTesting
SceneSerializationBase
PlanarFigure
ImageDenoising
ImageExtraction
SceneSerialization
Gizmo
GraphAlgorithms
Multilabel
Chart
ImageStatistics
ContourModel
SurfaceInterpolation
Segmentation
QtWidgets
QtWidgetsExt
ImageStatisticsUI
SegmentationUI
MatchPointRegistration
MatchPointRegistrationUI
Classification
OpenIGTLink
IGTBase
IGT
CameraCalibration
OpenCL
OpenCVVideoSupport
QtOverlays
ToFHardware
ToFProcessing
ToFUI
- PhotoacousticsHardware
- PhotoacousticsAlgorithms
- PhotoacousticsLib
US
USUI
DICOMUI
Remeshing
Python
QtPython
Persistence
OpenIGTLinkUI
IGTUI
RT
RTUI
IOExt
XNAT
TubeGraph
- BiophotonicsHardware
BoundingShape
RenderWindowManager
RenderWindowManagerUI
SemanticRelations
SemanticRelationsUI
CEST
BasicImageProcessing
ModelFit
ModelFitUI
Pharmacokinetics
PharmacokineticsUI
DICOMPM
REST
RESTService
DICOMweb
)
if(MITK_ENABLE_PIC_READER)
list(APPEND MITK_MODULES IpPicSupportIO)
endif()
diff --git a/Modules/Multilabel/CMakeLists.txt b/Modules/Multilabel/CMakeLists.txt
index 24ed1c1596..51a2a06fd3 100644
--- a/Modules/Multilabel/CMakeLists.txt
+++ b/Modules/Multilabel/CMakeLists.txt
@@ -1,10 +1,10 @@
-MITK_CREATE_MODULE(
+mitk_create_module(
DEPENDS MitkCore MitkAlgorithmsExt MitkSceneSerializationBase MitkDICOMQI
- PACKAGE_DEPENDS PRIVATE ITK|ITKQuadEdgeMesh+ITKAntiAlias+ITKIONRRD
)
add_subdirectory(autoload/IO)
add_subdirectory(autoload/DICOMSegIO)
+
if(BUILD_TESTING)
add_subdirectory(Testing)
endif()
diff --git a/Modules/Multilabel/autoload/IO/CMakeLists.txt b/Modules/Multilabel/autoload/IO/CMakeLists.txt
index 9a0856eff7..a61aebf0db 100644
--- a/Modules/Multilabel/autoload/IO/CMakeLists.txt
+++ b/Modules/Multilabel/autoload/IO/CMakeLists.txt
@@ -1,6 +1,5 @@
-MITK_CREATE_MODULE( MultilabelIO
+mitk_create_module(MultilabelIO
DEPENDS PUBLIC MitkMultilabel MitkSceneSerialization
- PACKAGE_DEPENDS
- PRIVATE ITK|ITKQuadEdgeMesh+ITKAntiAlias+ITKIONRRD
+ PACKAGE_DEPENDS PRIVATE ITK|IONRRD
AUTOLOAD_WITH MitkCore
)
diff --git a/Modules/Multilabel/autoload/IO/mitkLabelSetImageIO.cpp b/Modules/Multilabel/autoload/IO/mitkLabelSetImageIO.cpp
index 0e041818c9..981ea9cf30 100644
--- a/Modules/Multilabel/autoload/IO/mitkLabelSetImageIO.cpp
+++ b/Modules/Multilabel/autoload/IO/mitkLabelSetImageIO.cpp
@@ -1,652 +1,648 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef __mitkLabelSetImageWriter__cpp
#define __mitkLabelSetImageWriter__cpp
#include "mitkLabelSetImageIO.h"
#include "mitkBasePropertySerializer.h"
#include "mitkIOMimeTypes.h"
#include "mitkImageAccessByItk.h"
#include "mitkLabelSetIOHelper.h"
#include "mitkLabelSetImageConverter.h"
#include <mitkLocaleSwitch.h>
#include <mitkArbitraryTimeGeometry.h>
#include <mitkIPropertyPersistence.h>
#include <mitkCoreServices.h>
#include <mitkItkImageIO.h>
#include <mitkUIDManipulator.h>
// itk
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkMetaDataDictionary.h"
#include "itkMetaDataObject.h"
#include "itkNrrdImageIO.h"
+#include <tinyxml2.h>
+
namespace mitk
{
const char* const PROPERTY_NAME_TIMEGEOMETRY_TYPE = "org.mitk.timegeometry.type";
const char* const PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS = "org.mitk.timegeometry.timepoints";
const char* const PROPERTY_KEY_TIMEGEOMETRY_TYPE = "org_mitk_timegeometry_type";
const char* const PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS = "org_mitk_timegeometry_timepoints";
const char* const PROPERTY_KEY_UID = "org_mitk_uid";
LabelSetImageIO::LabelSetImageIO()
: AbstractFileIO(LabelSetImage::GetStaticNameOfClass(), IOMimeTypes::NRRD_MIMETYPE(), "MITK Multilabel Image")
{
AbstractFileWriter::SetRanking(10);
AbstractFileReader::SetRanking(10);
this->RegisterService();
}
IFileIO::ConfidenceLevel LabelSetImageIO::GetWriterConfidenceLevel() const
{
if (AbstractFileIO::GetWriterConfidenceLevel() == Unsupported)
return Unsupported;
const auto *input = static_cast<const LabelSetImage *>(this->GetInput());
if (input)
return Supported;
else
return Unsupported;
}
void LabelSetImageIO::Write()
{
ValidateOutputLocation();
auto input = dynamic_cast<const LabelSetImage *>(this->GetInput());
mitk::LocaleSwitch localeSwitch("C");
mitk::Image::Pointer inputVector = mitk::ConvertLabelSetImageToImage(input);
// image write
if (inputVector.IsNull())
{
mitkThrow() << "Cannot write non-image data";
}
itk::NrrdImageIO::Pointer nrrdImageIo = itk::NrrdImageIO::New();
// Clone the image geometry, because we might have to change it
// for writing purposes
BaseGeometry::Pointer geometry = inputVector->GetGeometry()->Clone();
// Check if geometry information will be lost
if (inputVector->GetDimension() == 2 && !geometry->Is2DConvertable())
{
MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might "
"consider using Convert2Dto3DImageFilter before saving.";
// set matrix to identity
mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
affTrans->SetIdentity();
mitk::Vector3D spacing = geometry->GetSpacing();
mitk::Point3D origin = geometry->GetOrigin();
geometry->SetIndexToWorldTransform(affTrans);
geometry->SetSpacing(spacing);
geometry->SetOrigin(origin);
}
LocalFile localFile(this);
const std::string path = localFile.GetFileName();
MITK_INFO << "Writing image: " << path << std::endl;
try
{
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
const unsigned int dimension = inputVector->GetDimension();
const unsigned int *const dimensions = inputVector->GetDimensions();
const mitk::PixelType pixelType = inputVector->GetPixelType();
const mitk::Vector3D mitkSpacing = geometry->GetSpacing();
const mitk::Point3D mitkOrigin = geometry->GetOrigin();
// Due to templating in itk, we are forced to save a 4D spacing and 4D Origin,
// though they are not supported in MITK
itk::Vector<double, 4u> spacing4D;
spacing4D[0] = mitkSpacing[0];
spacing4D[1] = mitkSpacing[1];
spacing4D[2] = mitkSpacing[2];
spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here
itk::Vector<double, 4u> origin4D;
origin4D[0] = mitkOrigin[0];
origin4D[1] = mitkOrigin[1];
origin4D[2] = mitkOrigin[2];
origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here
// Set the necessary information for imageIO
nrrdImageIo->SetNumberOfDimensions(dimension);
nrrdImageIo->SetPixelType(pixelType.GetPixelType());
nrrdImageIo->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
nrrdImageIo->SetNumberOfComponents(pixelType.GetNumberOfComponents());
itk::ImageIORegion ioRegion(dimension);
for (unsigned int i = 0; i < dimension; i++)
{
nrrdImageIo->SetDimensions(i, dimensions[i]);
nrrdImageIo->SetSpacing(i, spacing4D[i]);
nrrdImageIo->SetOrigin(i, origin4D[i]);
mitk::Vector3D mitkDirection;
mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
itk::Vector<double, 4u> direction4D;
direction4D[0] = mitkDirection[0];
direction4D[1] = mitkDirection[1];
direction4D[2] = mitkDirection[2];
// MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
// save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
if (i == 3)
{
direction4D[3] = 1; // homogenous component
}
else
{
direction4D[3] = 0;
}
vnl_vector<double> axisDirection(dimension);
for (unsigned int j = 0; j < dimension; j++)
{
axisDirection[j] = direction4D[j] / spacing4D[i];
}
nrrdImageIo->SetDirection(i, axisDirection);
ioRegion.SetSize(i, inputVector->GetLargestPossibleRegion().GetSize(i));
ioRegion.SetIndex(i, inputVector->GetLargestPossibleRegion().GetIndex(i));
}
// use compression if available
nrrdImageIo->UseCompressionOn();
nrrdImageIo->SetIORegion(ioRegion);
nrrdImageIo->SetFileName(path);
// label set specific meta data
char keybuffer[512];
char valbuffer[512];
sprintf(keybuffer, "modality");
sprintf(valbuffer, "org.mitk.image.multilabel");
itk::EncapsulateMetaData<std::string>(
nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
sprintf(keybuffer, "layers");
sprintf(valbuffer, "%1d", input->GetNumberOfLayers());
itk::EncapsulateMetaData<std::string>(
nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
for (unsigned int layerIdx = 0; layerIdx < input->GetNumberOfLayers(); layerIdx++)
{
sprintf(keybuffer, "layer_%03u", layerIdx); // layer idx
sprintf(valbuffer, "%1u", input->GetNumberOfLabels(layerIdx)); // number of labels for the layer
itk::EncapsulateMetaData<std::string>(
nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), std::string(valbuffer));
auto iter = input->GetLabelSet(layerIdx)->IteratorConstBegin();
unsigned int count(0);
while (iter != input->GetLabelSet(layerIdx)->IteratorConstEnd())
{
- std::unique_ptr<TiXmlDocument> document;
- document.reset(new TiXmlDocument());
-
- auto *decl = new TiXmlDeclaration("1.0", "", ""); // TODO what to write here? encoding? etc....
- document->LinkEndChild(decl);
- TiXmlElement *labelElem = mitk::LabelSetIOHelper::GetLabelAsTiXmlElement(iter->second);
- document->LinkEndChild(labelElem);
- TiXmlPrinter printer;
- printer.SetIndent("");
- printer.SetLineBreak("");
-
- document->Accept(&printer);
+ tinyxml2::XMLDocument document;
+ document.InsertEndChild(document.NewDeclaration());
+ auto *labelElem = mitk::LabelSetIOHelper::GetLabelAsXMLElement(document, iter->second);
+ document.InsertEndChild(labelElem);
+ tinyxml2::XMLPrinter printer;
+ document.Print(&printer);
sprintf(keybuffer, "org.mitk.label_%03u_%05u", layerIdx, count);
itk::EncapsulateMetaData<std::string>(
- nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), printer.Str());
+ nrrdImageIo->GetMetaDataDictionary(), std::string(keybuffer), printer.CStr());
++iter;
++count;
}
}
// end label set specific meta data
// Handle time geometry
const auto* arbitraryTG = dynamic_cast<const ArbitraryTimeGeometry*>(input->GetTimeGeometry());
if (arbitraryTG)
{
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(),
PROPERTY_KEY_TIMEGEOMETRY_TYPE,
ArbitraryTimeGeometry::GetStaticNameOfClass());
auto metaTimePoints = ConvertTimePointListToMetaDataObject(arbitraryTG);
nrrdImageIo->GetMetaDataDictionary().Set(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS, metaTimePoints);
}
// Handle properties
mitk::PropertyList::Pointer imagePropertyList = input->GetPropertyList();
for (const auto& property : *imagePropertyList->GetMap())
{
mitk::CoreServicePointer<IPropertyPersistence> propPersistenceService(mitk::CoreServices::GetPropertyPersistence());
IPropertyPersistence::InfoResultType infoList = propPersistenceService->GetInfo(property.first, GetMimeType()->GetName(), true);
if (infoList.empty())
{
continue;
}
std::string value = infoList.front()->GetSerializationFunction()(property.second);
if (value == mitk::BaseProperty::VALUE_CANNOT_BE_CONVERTED_TO_STRING)
{
continue;
}
std::string key = infoList.front()->GetKey();
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), key, value);
}
// Handle UID
itk::EncapsulateMetaData<std::string>(nrrdImageIo->GetMetaDataDictionary(), PROPERTY_KEY_UID, input->GetUID());
ImageReadAccessor imageAccess(inputVector);
nrrdImageIo->Write(imageAccess.GetData());
}
catch (const std::exception &e)
{
mitkThrow() << e.what();
}
// end image write
}
IFileIO::ConfidenceLevel LabelSetImageIO::GetReaderConfidenceLevel() const
{
if (AbstractFileIO::GetReaderConfidenceLevel() == Unsupported)
return Unsupported;
const std::string fileName = this->GetLocalFileName();
itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New();
io->SetFileName(fileName);
io->ReadImageInformation();
itk::MetaDataDictionary imgMetaDataDictionary = io->GetMetaDataDictionary();
std::string value("");
itk::ExposeMetaData<std::string>(imgMetaDataDictionary, "modality", value);
if (value.compare("org.mitk.image.multilabel") == 0)
{
return Supported;
}
else
return Unsupported;
}
std::vector<BaseData::Pointer> LabelSetImageIO::DoRead()
{
mitk::LocaleSwitch localeSwitch("C");
// begin regular image loading, adapted from mitkItkImageIO
itk::NrrdImageIO::Pointer nrrdImageIO = itk::NrrdImageIO::New();
Image::Pointer image = Image::New();
const unsigned int MINDIM = 2;
const unsigned int MAXDIM = 4;
const std::string path = this->GetLocalFileName();
MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;
// Check to see if we can read the file given the name or prefix
if (path.empty())
{
mitkThrow() << "Empty filename in mitk::ItkImageIO ";
}
// Got to allocate space for the image. Determine the characteristics of
// the image.
nrrdImageIO->SetFileName(path);
nrrdImageIO->ReadImageInformation();
unsigned int ndim = nrrdImageIO->GetNumberOfDimensions();
if (ndim < MINDIM || ndim > MAXDIM)
{
MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim
<< " dimensions! Reading as 4D.";
ndim = MAXDIM;
}
itk::ImageIORegion ioRegion(ndim);
itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();
unsigned int dimensions[MAXDIM];
dimensions[0] = 0;
dimensions[1] = 0;
dimensions[2] = 0;
dimensions[3] = 0;
ScalarType spacing[MAXDIM];
spacing[0] = 1.0f;
spacing[1] = 1.0f;
spacing[2] = 1.0f;
spacing[3] = 1.0f;
Point3D origin;
origin.Fill(0);
unsigned int i;
for (i = 0; i < ndim; ++i)
{
ioStart[i] = 0;
ioSize[i] = nrrdImageIO->GetDimensions(i);
if (i < MAXDIM)
{
dimensions[i] = nrrdImageIO->GetDimensions(i);
spacing[i] = nrrdImageIO->GetSpacing(i);
if (spacing[i] <= 0)
spacing[i] = 1.0f;
}
if (i < 3)
{
origin[i] = nrrdImageIO->GetOrigin(i);
}
}
ioRegion.SetSize(ioSize);
ioRegion.SetIndex(ioStart);
MITK_INFO << "ioRegion: " << ioRegion << std::endl;
nrrdImageIO->SetIORegion(ioRegion);
void *buffer = new unsigned char[nrrdImageIO->GetImageSizeInBytes()];
nrrdImageIO->Read(buffer);
image->Initialize(MakePixelType(nrrdImageIO), ndim, dimensions);
image->SetImportChannel(buffer, 0, Image::ManageMemory);
// access direction of itk::Image and include spacing
mitk::Matrix3D matrix;
matrix.SetIdentity();
unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim);
for (i = 0; i < itkDimMax3; ++i)
for (j = 0; j < itkDimMax3; ++j)
matrix[i][j] = nrrdImageIO->GetDirection(j)[i];
// re-initialize PlaneGeometry with origin and direction
PlaneGeometry *planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
planeGeometry->SetOrigin(origin);
planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);
// re-initialize SlicedGeometry3D
SlicedGeometry3D *slicedGeometry = image->GetSlicedGeometry(0);
slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
slicedGeometry->SetSpacing(spacing);
MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false);
MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true);
// re-initialize TimeGeometry
const itk::MetaDataDictionary& dictionary = nrrdImageIO->GetMetaDataDictionary();
TimeGeometry::Pointer timeGeometry;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE) || dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TYPE))
{ // also check for the name because of backwards compatibility. Past code version stored with the name and not with
// the key
itk::MetaDataObject<std::string>::ConstPointer timeGeometryTypeData;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE))
{
timeGeometryTypeData =
dynamic_cast<const itk::MetaDataObject<std::string>*>(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TYPE));
}
else
{
timeGeometryTypeData =
dynamic_cast<const itk::MetaDataObject<std::string>*>(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TYPE));
}
if (timeGeometryTypeData->GetMetaDataObjectValue() == ArbitraryTimeGeometry::GetStaticNameOfClass())
{
MITK_INFO << "used time geometry: " << ArbitraryTimeGeometry::GetStaticNameOfClass();
typedef std::vector<TimePointType> TimePointVector;
TimePointVector timePoints;
if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS))
{
timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS));
}
else if (dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS))
{
timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS));
}
if (timePoints.empty())
{
MITK_ERROR << "Stored timepoints are empty. Meta information seems to bee invalid. Switch to ProportionalTimeGeometry fallback";
}
else if (timePoints.size() - 1 != image->GetDimension(3))
{
MITK_ERROR << "Stored timepoints (" << timePoints.size() - 1 << ") and size of image time dimension ("
<< image->GetDimension(3) << ") do not match. Switch to ProportionalTimeGeometry fallback";
}
else
{
ArbitraryTimeGeometry::Pointer arbitraryTimeGeometry = ArbitraryTimeGeometry::New();
TimePointVector::const_iterator pos = timePoints.begin();
auto prePos = pos++;
for (; pos != timePoints.end(); ++prePos, ++pos)
{
arbitraryTimeGeometry->AppendNewTimeStepClone(slicedGeometry, *prePos, *pos);
}
timeGeometry = arbitraryTimeGeometry;
}
}
}
if (timeGeometry.IsNull())
{ // Fallback. If no other valid time geometry has been created, create a ProportionalTimeGeometry
MITK_INFO << "used time geometry: " << ProportionalTimeGeometry::GetStaticNameOfClass();
ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New();
propTimeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
timeGeometry = propTimeGeometry;
}
image->SetTimeGeometry(timeGeometry);
buffer = nullptr;
MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents();
// end regular image loading
LabelSetImage::Pointer output = ConvertImageToLabelSetImage(image);
// get labels and add them as properties to the image
char keybuffer[256];
unsigned int numberOfLayers = GetIntByKey(dictionary, "layers");
std::string _xmlStr;
mitk::Label::Pointer label;
for (unsigned int layerIdx = 0; layerIdx < numberOfLayers; layerIdx++)
{
sprintf(keybuffer, "layer_%03u", layerIdx);
int numberOfLabels = GetIntByKey(dictionary, keybuffer);
mitk::LabelSet::Pointer labelSet = mitk::LabelSet::New();
for (int labelIdx = 0; labelIdx < numberOfLabels; labelIdx++)
{
- TiXmlDocument doc;
+ tinyxml2::XMLDocument doc;
sprintf(keybuffer, "label_%03u_%05d", layerIdx, labelIdx);
_xmlStr = GetStringByKey(dictionary, keybuffer);
- doc.Parse(_xmlStr.c_str());
+ doc.Parse(_xmlStr.c_str(), _xmlStr.size());
- TiXmlElement *labelElem = doc.FirstChildElement("Label");
+ auto *labelElem = doc.FirstChildElement("Label");
if (labelElem == nullptr)
mitkThrow() << "Error parsing NRRD header for mitk::LabelSetImage IO";
- label = mitk::LabelSetIOHelper::LoadLabelFromTiXmlDocument(labelElem);
+ label = mitk::LabelSetIOHelper::LoadLabelFromXMLDocument(labelElem);
if (label->GetValue() == 0) // set exterior label is needed to hold exterior information
output->SetExteriorLabel(label);
labelSet->AddLabel(label);
labelSet->SetLayer(layerIdx);
}
output->AddLabelSetToLayer(layerIdx, labelSet);
}
for (auto iter = dictionary.Begin(), iterEnd = dictionary.End(); iter != iterEnd;
++iter)
{
if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
{
const std::string& key = iter->first;
std::string assumedPropertyName = key;
std::replace(assumedPropertyName.begin(), assumedPropertyName.end(), '_', '.');
std::string mimeTypeName = GetMimeType()->GetName();
// Check if there is already a info for the key and our mime type.
mitk::CoreServicePointer<IPropertyPersistence> propPersistenceService(mitk::CoreServices::GetPropertyPersistence());
IPropertyPersistence::InfoResultType infoList = propPersistenceService->GetInfoByKey(key);
auto predicate = [&mimeTypeName](const PropertyPersistenceInfo::ConstPointer& x) {
return x.IsNotNull() && x->GetMimeTypeName() == mimeTypeName;
};
auto finding = std::find_if(infoList.begin(), infoList.end(), predicate);
if (finding == infoList.end())
{
auto predicateWild = [](const PropertyPersistenceInfo::ConstPointer& x) {
return x.IsNotNull() && x->GetMimeTypeName() == PropertyPersistenceInfo::ANY_MIMETYPE_NAME();
};
finding = std::find_if(infoList.begin(), infoList.end(), predicateWild);
}
PropertyPersistenceInfo::ConstPointer info;
if (finding != infoList.end())
{
assumedPropertyName = (*finding)->GetName();
info = *finding;
}
else
{ // we have not found anything suitable so we generate our own info
auto newInfo = PropertyPersistenceInfo::New();
newInfo->SetNameAndKey(assumedPropertyName, key);
newInfo->SetMimeTypeName(PropertyPersistenceInfo::ANY_MIMETYPE_NAME());
info = newInfo;
}
std::string value =
dynamic_cast<itk::MetaDataObject<std::string>*>(iter->second.GetPointer())->GetMetaDataObjectValue();
mitk::BaseProperty::Pointer loadedProp = info->GetDeserializationFunction()(value);
output->SetProperty(assumedPropertyName.c_str(), loadedProp);
// Read properties should be persisted unless they are default properties
// which are written anyway
bool isDefaultKey = false;
for (const auto& defaultKey : m_DefaultMetaDataKeys)
{
if (defaultKey.length() <= assumedPropertyName.length())
{
// does the start match the default key
if (assumedPropertyName.substr(0, defaultKey.length()).find(defaultKey) != std::string::npos)
{
isDefaultKey = true;
break;
}
}
}
if (!isDefaultKey)
{
propPersistenceService->AddInfo(info);
}
}
}
// Handle UID
if (dictionary.HasKey(PROPERTY_KEY_UID))
{
itk::MetaDataObject<std::string>::ConstPointer uidData = dynamic_cast<const itk::MetaDataObject<std::string>*>(dictionary.Get(PROPERTY_KEY_UID));
if (uidData.IsNotNull())
{
mitk::UIDManipulator uidManipulator(output);
uidManipulator.SetUID(uidData->GetMetaDataObjectValue());
}
}
MITK_INFO << "...finished!";
std::vector<BaseData::Pointer> result;
result.push_back(output.GetPointer());
return result;
}
int LabelSetImageIO::GetIntByKey(const itk::MetaDataDictionary &dic, const std::string &str)
{
std::vector<std::string> imgMetaKeys = dic.GetKeys();
std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
std::string metaString("");
for (; itKey != imgMetaKeys.end(); itKey++)
{
itk::ExposeMetaData<std::string>(dic, *itKey, metaString);
if (itKey->find(str.c_str()) != std::string::npos)
{
return atoi(metaString.c_str());
}
}
return 0;
}
std::string LabelSetImageIO::GetStringByKey(const itk::MetaDataDictionary &dic, const std::string &str)
{
std::vector<std::string> imgMetaKeys = dic.GetKeys();
std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
std::string metaString("");
for (; itKey != imgMetaKeys.end(); itKey++)
{
itk::ExposeMetaData<std::string>(dic, *itKey, metaString);
if (itKey->find(str.c_str()) != std::string::npos)
{
return metaString;
}
}
return metaString;
}
LabelSetImageIO *LabelSetImageIO::IOClone() const { return new LabelSetImageIO(*this); }
void LabelSetImageIO::InitializeDefaultMetaDataKeys()
{
this->m_DefaultMetaDataKeys.push_back("NRRD.space");
this->m_DefaultMetaDataKeys.push_back("NRRD.kinds");
this->m_DefaultMetaDataKeys.push_back(PROPERTY_NAME_TIMEGEOMETRY_TYPE);
this->m_DefaultMetaDataKeys.push_back(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS);
this->m_DefaultMetaDataKeys.push_back("ITK.InputFilterName");
this->m_DefaultMetaDataKeys.push_back("label_");
this->m_DefaultMetaDataKeys.push_back("layer_");
}
} // namespace
#endif //__mitkLabelSetImageWriter__cpp
diff --git a/Modules/Multilabel/mitkLabel.cpp b/Modules/Multilabel/mitkLabel.cpp
index b7952a6ef9..f2b6df44c5 100644
--- a/Modules/Multilabel/mitkLabel.cpp
+++ b/Modules/Multilabel/mitkLabel.cpp
@@ -1,299 +1,298 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkLabel.h"
#include "itkProcessObject.h"
-#include "tinyxml.h"
#include <itkCommand.h>
#include <mitkProperties.h>
#include <mitkDICOMSegmentationPropertyHelper.h>
#include <mitkStringProperty.h>
const mitk::Label::PixelType mitk::Label::MAX_LABEL_VALUE = std::numeric_limits<mitk::Label::PixelType>::max();
mitk::Label::Label() : PropertyList()
{
if (GetProperty("locked") == nullptr)
SetLocked(true);
if (GetProperty("visible") == nullptr)
SetVisible(true);
if (GetProperty("opacity") == nullptr)
SetOpacity(0.6);
if (GetProperty("center.coordinates") == nullptr)
{
mitk::Point3D pnt;
pnt.SetElement(0, 0);
pnt.SetElement(1, 0);
pnt.SetElement(2, 0);
SetCenterOfMassCoordinates(pnt);
}
if (GetProperty("center.index") == nullptr)
{
mitk::Point3D pnt;
pnt.SetElement(0, 0);
pnt.SetElement(1, 0);
pnt.SetElement(2, 0);
SetCenterOfMassIndex(pnt);
}
if (GetProperty("color") == nullptr)
{
mitk::Color col;
col.Set(0, 0, 0);
SetColor(col);
}
if (GetProperty("name") == nullptr)
SetName("noName!");
if (GetProperty("value") == nullptr)
SetValue(0);
if (GetProperty("layer") == nullptr)
SetLayer(0);
DICOMSegmentationPropertyHelper::SetDICOMSegmentProperties(this);
}
mitk::Label::Label(const Label &other) : PropertyList(other)
// copyconstructer of property List handles the coping action
{
auto *map = this->GetMap();
auto it = map->begin();
auto end = map->end();
for (; it != end; ++it)
{
itk::SimpleMemberCommand<Label>::Pointer command = itk::SimpleMemberCommand<Label>::New();
command->SetCallbackFunction(this, &Label::Modified);
it->second->AddObserver(itk::ModifiedEvent(), command);
}
}
mitk::Label::~Label()
{
}
void mitk::Label::SetProperty(const std::string &propertyKey, BaseProperty *property, const std::string &contextName, bool fallBackOnDefaultContext)
{
itk::SimpleMemberCommand<Label>::Pointer command = itk::SimpleMemberCommand<Label>::New();
command->SetCallbackFunction(this, &Label::Modified);
property->AddObserver(itk::ModifiedEvent(), command);
Superclass::SetProperty(propertyKey, property, contextName, fallBackOnDefaultContext);
}
void mitk::Label::SetLocked(bool locked)
{
mitk::BoolProperty *property = dynamic_cast<mitk::BoolProperty *>(GetProperty("locked"));
if (property != nullptr)
// Update Property
property->SetValue(locked);
else
// Create new Property
SetBoolProperty("locked", locked);
}
bool mitk::Label::GetLocked() const
{
bool locked;
GetBoolProperty("locked", locked);
return locked;
}
void mitk::Label::SetVisible(bool visible)
{
mitk::BoolProperty *property = dynamic_cast<mitk::BoolProperty *>(GetProperty("visible"));
if (property != nullptr)
// Update Property
property->SetValue(visible);
else
// Create new Property
SetBoolProperty("visible", visible);
}
bool mitk::Label::GetVisible() const
{
bool visible;
GetBoolProperty("visible", visible);
return visible;
}
void mitk::Label::SetOpacity(float opacity)
{
mitk::FloatProperty *property = dynamic_cast<mitk::FloatProperty *>(GetProperty("opacity"));
if (property != nullptr)
// Update Property
property->SetValue(opacity);
else
// Create new Property
SetFloatProperty("opacity", opacity);
}
float mitk::Label::GetOpacity() const
{
float opacity;
GetFloatProperty("opacity", opacity);
return opacity;
}
void mitk::Label::SetName(const std::string &name)
{
SetStringProperty("name", name.c_str());
}
std::string mitk::Label::GetName() const
{
std::string name;
GetStringProperty("name", name);
return name;
}
void mitk::Label::SetValue(PixelType pixelValue)
{
mitk::UShortProperty *property = dynamic_cast<mitk::UShortProperty *>(GetProperty("value"));
if (property != nullptr)
// Update Property
property->SetValue(pixelValue);
else
// Create new Property
SetProperty("value", mitk::UShortProperty::New(pixelValue));
}
mitk::Label::PixelType mitk::Label::GetValue() const
{
PixelType pixelValue;
mitk::UShortProperty *property = dynamic_cast<UShortProperty *>(GetProperty("value"));
assert(property);
pixelValue = property->GetValue();
return pixelValue;
}
void mitk::Label::SetLayer(unsigned int layer)
{
mitk::UIntProperty *property = dynamic_cast<mitk::UIntProperty *>(GetProperty("layer"));
if (property != nullptr)
// Update Property
property->SetValue(layer);
else
// Create new Property
SetProperty("layer", mitk::UIntProperty::New(layer));
}
unsigned int mitk::Label::GetLayer() const
{
unsigned int layer;
mitk::UIntProperty *prop = dynamic_cast<mitk::UIntProperty *>(GetProperty("layer"));
layer = prop->GetValue();
return layer;
}
const mitk::Color &mitk::Label::GetColor() const
{
mitk::ColorProperty *colorProp = dynamic_cast<mitk::ColorProperty *>(GetProperty("color"));
return colorProp->GetColor();
}
void mitk::Label::SetColor(const mitk::Color &_color)
{
mitk::ColorProperty *colorProp = dynamic_cast<mitk::ColorProperty *>(GetProperty("color"));
if (colorProp != nullptr)
// Update Property
colorProp->SetColor(_color);
else
// Create new Property
SetProperty("color", mitk::ColorProperty::New(_color));
}
void mitk::Label::SetCenterOfMassIndex(const mitk::Point3D ¢er)
{
mitk::Point3dProperty *property = dynamic_cast<mitk::Point3dProperty *>(GetProperty("center.index"));
if (property != nullptr)
// Update Property
property->SetValue(center);
else
// Create new Property
SetProperty("center.index", mitk::Point3dProperty::New(center));
}
mitk::Point3D mitk::Label::GetCenterOfMassIndex() const
{
mitk::Point3dProperty *property = dynamic_cast<mitk::Point3dProperty *>(GetProperty("center.index"));
return property->GetValue();
}
void mitk::Label::SetCenterOfMassCoordinates(const mitk::Point3D ¢er)
{
mitk::Point3dProperty *property = dynamic_cast<mitk::Point3dProperty *>(GetProperty("center.coordinates"));
if (property != nullptr)
// Update Property
property->SetValue(center);
else
// Create new Property
SetProperty("center.coordinates", mitk::Point3dProperty::New(center));
}
mitk::Point3D mitk::Label::GetCenterOfMassCoordinates() const
{
mitk::Point3dProperty *property = dynamic_cast<mitk::Point3dProperty *>(GetProperty("center.coordinates"));
return property->GetValue();
}
itk::LightObject::Pointer mitk::Label::InternalClone() const
{
itk::LightObject::Pointer result(new Self(*this));
result->UnRegister();
return result;
}
void mitk::Label::PrintSelf(std::ostream & /*os*/, itk::Indent /*indent*/) const
{
// todo
}
bool mitk::Equal(const mitk::Label &leftHandSide, const mitk::Label &rightHandSide, ScalarType /*eps*/, bool verbose)
{
MITK_INFO(verbose) << "--- Label Equal ---";
bool returnValue = true;
// have to be replaced until a PropertyList Equal was implemented :
// returnValue = mitk::Equal((const mitk::PropertyList &)leftHandSide,(const mitk::PropertyList
// &)rightHandSide,eps,verbose);
const mitk::PropertyList::PropertyMap *lhsmap = leftHandSide.GetMap();
const mitk::PropertyList::PropertyMap *rhsmap = rightHandSide.GetMap();
returnValue = lhsmap->size() == rhsmap->size();
if (!returnValue)
{
MITK_INFO(verbose) << "Labels in label container are not equal.";
return returnValue;
}
auto lhsmapIt = lhsmap->begin();
auto lhsmapItEnd = lhsmap->end();
for (; lhsmapIt != lhsmapItEnd; ++lhsmapIt)
{
if (rhsmap->find(lhsmapIt->first) == rhsmap->end())
{
returnValue = false;
break;
}
}
if (!returnValue)
{
MITK_INFO(verbose) << "Labels in label container are not equal.";
return returnValue;
}
return returnValue;
}
diff --git a/Modules/Multilabel/mitkLabel.h b/Modules/Multilabel/mitkLabel.h
index 2cf6e84fed..c4e8bdeafc 100644
--- a/Modules/Multilabel/mitkLabel.h
+++ b/Modules/Multilabel/mitkLabel.h
@@ -1,107 +1,104 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef __mitkLabel_H_
#define __mitkLabel_H_
#include "MitkMultilabelExports.h"
#include <mitkColorProperty.h>
#include <mitkPropertyList.h>
#include <mitkVector.h>
-class TiXmlDocument;
-class TiXmlElement;
-
namespace mitk
{
//##
//##Documentation
//## @brief A data structure describing a label.
//## @ingroup Data
//##
class MITKMULTILABEL_EXPORT Label : public PropertyList
{
public:
mitkClassMacro(Label, mitk::PropertyList);
itkNewMacro(Self);
typedef unsigned short PixelType;
/// The maximum value a label can get: Since the value is of type unsigned short MAX_LABEL_VALUE = 65535
static const PixelType MAX_LABEL_VALUE;
void SetLocked(bool locked);
bool GetLocked() const;
void SetVisible(bool visible);
bool GetVisible() const;
void SetOpacity(float opacity);
float GetOpacity() const;
void SetName(const std::string &name);
std::string GetName() const;
void SetCenterOfMassIndex(const mitk::Point3D ¢er);
mitk::Point3D GetCenterOfMassIndex() const;
void SetCenterOfMassCoordinates(const mitk::Point3D ¢er);
mitk::Point3D GetCenterOfMassCoordinates() const;
void SetColor(const mitk::Color &);
const mitk::Color &GetColor() const;
void SetValue(PixelType pixelValue);
PixelType GetValue() const;
void SetLayer(unsigned int layer);
unsigned int GetLayer() const;
void SetProperty(const std::string &propertyKey, BaseProperty *property, const std::string &contextName = "", bool fallBackOnDefaultContext = false) override;
using itk::Object::Modified;
void Modified() { Superclass::Modified(); }
Label();
~Label() override;
protected:
void PrintSelf(std::ostream &os, itk::Indent indent) const override;
Label(const Label &other);
private:
itk::LightObject::Pointer InternalClone() const override;
};
/**
* @brief Equal A function comparing two labels for beeing equal in data
*
* @ingroup MITKTestingAPI
*
* Following aspects are tested for equality:
* - Lebel equality via Equal-PropetyList
*
* @param rightHandSide An image to be compared
* @param leftHandSide An image to be compared
* @param eps Tolarence for comparison. You can use mitk::eps in most cases.
* @param verbose Flag indicating if the user wants detailed console output or not.
* @return true, if all subsequent comparisons are true, false otherwise
*/
MITKMULTILABEL_EXPORT bool Equal(const mitk::Label &leftHandSide,
const mitk::Label &rightHandSide,
ScalarType eps,
bool verbose);
} // namespace mitk
#endif // __mitkLabel_H_
diff --git a/Modules/Multilabel/mitkLabelSetIOHelper.cpp b/Modules/Multilabel/mitkLabelSetIOHelper.cpp
index 1149e997f0..70d5e47426 100644
--- a/Modules/Multilabel/mitkLabelSetIOHelper.cpp
+++ b/Modules/Multilabel/mitkLabelSetIOHelper.cpp
@@ -1,264 +1,271 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkLabelSetIOHelper.h"
#include "mitkLabelSetImage.h"
#include <mitkBasePropertySerializer.h>
-#include <tinyxml.h>
+
+#include <tinyxml2.h>
namespace
{
std::string EnsureExtension(const std::string& filename)
{
const std::string extension = ".lsetp";
if (filename.size() < extension.size() || std::string::npos == filename.find(extension, filename.size() - extension.size()))
return filename + extension;
return filename;
}
}
bool mitk::LabelSetIOHelper::SaveLabelSetImagePreset(const std::string &presetFilename,
mitk::LabelSetImage::Pointer &inputImage)
{
const auto filename = EnsureExtension(presetFilename);
- TiXmlDocument xmlDocument;
- xmlDocument.LinkEndChild(new TiXmlDeclaration("1.0", "", ""));
+ tinyxml2::XMLDocument xmlDocument;
+ xmlDocument.InsertEndChild(xmlDocument.NewDeclaration());
- auto *rootElement = new TiXmlElement("LabelSetImagePreset");
+ auto *rootElement = xmlDocument.NewElement("LabelSetImagePreset");
rootElement->SetAttribute("layers", inputImage->GetNumberOfLayers());
- xmlDocument.LinkEndChild(rootElement);
+ xmlDocument.InsertEndChild(rootElement);
for (unsigned int layerIndex = 0; layerIndex < inputImage->GetNumberOfLayers(); layerIndex++)
{
- auto *layerElement = new TiXmlElement("Layer");
+ auto *layerElement = xmlDocument.NewElement("Layer");
layerElement->SetAttribute("index", layerIndex);
layerElement->SetAttribute("labels", inputImage->GetNumberOfLabels(layerIndex));
- rootElement->LinkEndChild(layerElement);
+ rootElement->InsertEndChild(layerElement);
for (unsigned int labelIndex = 0; labelIndex < inputImage->GetNumberOfLabels(layerIndex); labelIndex++)
- layerElement->LinkEndChild(LabelSetIOHelper::GetLabelAsTiXmlElement(inputImage->GetLabel(labelIndex, layerIndex)));
+ layerElement->InsertEndChild(LabelSetIOHelper::GetLabelAsXMLElement(xmlDocument, inputImage->GetLabel(labelIndex, layerIndex)));
}
- return xmlDocument.SaveFile(filename);
+ return tinyxml2::XML_SUCCESS == xmlDocument.SaveFile(filename.c_str());
}
void mitk::LabelSetIOHelper::LoadLabelSetImagePreset(const std::string &presetFilename,
mitk::LabelSetImage::Pointer &inputImage)
{
if (inputImage.IsNull())
return;
const auto filename = EnsureExtension(presetFilename);
- TiXmlDocument xmlDocument;
+ tinyxml2::XMLDocument xmlDocument;
- if(!xmlDocument.LoadFile(filename))
+ if(tinyxml2::XML_SUCCESS != xmlDocument.LoadFile(filename.c_str()))
return;
auto *rootElement = xmlDocument.FirstChildElement("LabelSetImagePreset");
if (nullptr == rootElement)
{
MITK_WARN << "Not a valid LabelSet preset";
return;
}
auto activeLayerBackup = inputImage->GetActiveLayer();
int numberOfLayers = 0;
rootElement->QueryIntAttribute("layers", &numberOfLayers);
auto* layerElement = rootElement->FirstChildElement("Layer");
if (nullptr == layerElement)
{
MITK_WARN << "LabelSet preset does not contain any layers";
return;
}
for (int layerIndex = 0; layerIndex < numberOfLayers; layerIndex++)
{
int numberOfLabels = 0;
layerElement->QueryIntAttribute("labels", &numberOfLabels);
if (nullptr == inputImage->GetLabelSet(layerIndex))
{
inputImage->AddLayer();
}
else
{
inputImage->SetActiveLayer(layerIndex);
}
auto *labelElement = layerElement->FirstChildElement("Label");
if (nullptr == labelElement)
continue;
for (int labelIndex = 0; labelIndex < numberOfLabels; labelIndex++)
{
- auto label = mitk::LabelSetIOHelper::LoadLabelFromTiXmlDocument(labelElement);
+ auto label = mitk::LabelSetIOHelper::LoadLabelFromXMLDocument(labelElement);
const auto labelValue = label->GetValue();
if (0 != labelValue)
{
auto* labelSet = inputImage->GetLabelSet(layerIndex);
auto* alreadyExistingLabel = labelSet->GetLabel(labelValue);
if (nullptr != alreadyExistingLabel)
{
// Override existing label with label from preset
alreadyExistingLabel->ConcatenatePropertyList(label);
labelSet->UpdateLookupTable(labelValue);
}
else
{
labelSet->AddLabel(label);
}
}
labelElement = labelElement->NextSiblingElement("Label");
if (nullptr == labelElement)
continue;
}
layerElement = layerElement->NextSiblingElement("Layer");
if (nullptr == layerElement)
continue;
}
inputImage->SetActiveLayer(activeLayerBackup);
}
-TiXmlElement *mitk::LabelSetIOHelper::GetLabelAsTiXmlElement(Label *label)
+tinyxml2::XMLElement *mitk::LabelSetIOHelper::GetLabelAsXMLElement(tinyxml2::XMLDocument &doc, Label *label)
{
- auto *labelElem = new TiXmlElement("Label");
+ auto *labelElem = doc.NewElement("Label");
// add XML contents
const PropertyList::PropertyMap *propmap = label->GetMap();
for (auto iter = propmap->begin(); iter != propmap->end(); ++iter)
{
std::string key = iter->first;
const BaseProperty *property = iter->second;
- TiXmlElement *element = PropertyToXmlElem(key, property);
+ auto *element = PropertyToXMLElement(doc, key, property);
if (element)
- labelElem->LinkEndChild(element);
+ labelElem->InsertEndChild(element);
}
return labelElem;
}
-mitk::Label::Pointer mitk::LabelSetIOHelper::LoadLabelFromTiXmlDocument(TiXmlElement *labelElem)
+mitk::Label::Pointer mitk::LabelSetIOHelper::LoadLabelFromXMLDocument(const tinyxml2::XMLElement *labelElem)
{
// reread
- TiXmlElement *propElem = labelElem->FirstChildElement("property");
+ auto *propElem = labelElem->FirstChildElement("property");
std::string name;
mitk::BaseProperty::Pointer prop;
mitk::Label::Pointer label = mitk::Label::New();
while (propElem)
{
- LabelSetIOHelper::PropertyFromXmlElem(name, prop, propElem);
+ LabelSetIOHelper::PropertyFromXMLElement(name, prop, propElem);
label->SetProperty(name, prop);
propElem = propElem->NextSiblingElement("property");
}
return label.GetPointer();
}
-TiXmlElement *mitk::LabelSetIOHelper::PropertyToXmlElem(const std::string &key, const BaseProperty *property)
+tinyxml2::XMLElement *mitk::LabelSetIOHelper::PropertyToXMLElement(tinyxml2::XMLDocument &doc, const std::string &key, const BaseProperty *property)
{
- auto *keyelement = new TiXmlElement("property");
- keyelement->SetAttribute("key", key);
+ auto *keyelement = doc.NewElement("property");
+ keyelement->SetAttribute("key", key.c_str());
keyelement->SetAttribute("type", property->GetNameOfClass());
// construct name of serializer class
std::string serializername(property->GetNameOfClass());
serializername += "Serializer";
std::list<itk::LightObject::Pointer> allSerializers =
itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str());
if (allSerializers.size() < 1)
MITK_ERROR << "No serializer found for " << property->GetNameOfClass() << ". Skipping object";
if (allSerializers.size() > 1)
MITK_WARN << "Multiple serializers found for " << property->GetNameOfClass() << "Using arbitrarily the first one.";
for (auto iter = allSerializers.begin(); iter != allSerializers.end();
++iter)
{
if (auto *serializer = dynamic_cast<BasePropertySerializer *>(iter->GetPointer()))
{
serializer->SetProperty(property);
try
{
- TiXmlElement *valueelement = serializer->Serialize();
+ auto *valueelement = serializer->Serialize(doc);
if (valueelement)
- keyelement->LinkEndChild(valueelement);
+ keyelement->InsertEndChild(valueelement);
}
catch (std::exception &e)
{
MITK_ERROR << "Serializer " << serializer->GetNameOfClass() << " failed: " << e.what();
}
break;
}
}
return keyelement;
}
-bool mitk::LabelSetIOHelper::PropertyFromXmlElem(std::string &key,
- mitk::BaseProperty::Pointer &prop,
- TiXmlElement *elem)
+bool mitk::LabelSetIOHelper::PropertyFromXMLElement(std::string &key,
+ mitk::BaseProperty::Pointer &prop,
+ const tinyxml2::XMLElement *elem)
{
- std::string type;
- elem->QueryStringAttribute("type", &type);
- elem->QueryStringAttribute("key", &key);
+ const char* typeC = elem->Attribute("type");
+ std::string type = nullptr != typeC
+ ? typeC
+ : "";
+
+ const char* keyC = elem->Attribute("key");
+ key = nullptr != keyC
+ ? keyC
+ : "";
// construct name of serializer class
std::string serializername(type);
serializername += "Serializer";
std::list<itk::LightObject::Pointer> allSerializers =
itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str());
if (allSerializers.size() < 1)
MITK_ERROR << "No serializer found for " << type << ". Skipping object";
if (allSerializers.size() > 1)
MITK_WARN << "Multiple deserializers found for " << type << "Using arbitrarily the first one.";
for (auto iter = allSerializers.begin(); iter != allSerializers.end();
++iter)
{
if (auto *serializer = dynamic_cast<BasePropertySerializer *>(iter->GetPointer()))
{
try
{
prop = serializer->Deserialize(elem->FirstChildElement());
}
catch (std::exception &e)
{
MITK_ERROR << "Deserializer " << serializer->GetNameOfClass() << " failed: " << e.what();
return false;
}
break;
}
}
if (prop.IsNull())
return false;
return true;
}
diff --git a/Modules/Multilabel/mitkLabelSetIOHelper.h b/Modules/Multilabel/mitkLabelSetIOHelper.h
index 3800fda33a..a43c16c686 100644
--- a/Modules/Multilabel/mitkLabelSetIOHelper.h
+++ b/Modules/Multilabel/mitkLabelSetIOHelper.h
@@ -1,91 +1,97 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef __mitkLabelSetIOHelper_h
#define __mitkLabelSetIOHelper_h
#include <MitkMultilabelExports.h>
#include <itkSmartPointer.h>
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
class BaseProperty;
class LabelSetImage;
class Label;
/**
* @brief The LabelSetIOHelper is a static helper class that supports serialization of mitk::LabelSetImage
*
* This class provides static functions for converting mitk::Label into XML and also allows the serialization
* of mitk::LabelSet as presets
*/
class MITKMULTILABEL_EXPORT LabelSetIOHelper
{
public:
/**
* @brief Saves the mitk::LabelSet configuration of inputImage to presetFilename.
* The preset is stored as "*.lsetp"
* @param presetFilename the filename including the filesystem path
* @param inputImage the input image from which the preset should be generated
* @return true if the serialization was successful and false otherwise
*/
static bool SaveLabelSetImagePreset(const std::string &presetFilename,
itk::SmartPointer<mitk::LabelSetImage> &inputImage);
/**
* @brief Loads an existing preset for a mitk::LabelSetImage from presetFilename and applies it to inputImage
* @param presetFilename the filename of the preset including the filesystem path
* @param inputImage the image to which the loaded preset will be applied
*/
static void LoadLabelSetImagePreset(const std::string &presetFilename,
itk::SmartPointer<mitk::LabelSetImage> &inputImage);
/**
- * @brief Creates a mitk::Label from a TiXmlElement
+ * @brief Creates a mitk::Label from an XML element
* @param labelElem the xml element from which a mitk::Label will be created
* @return the created mitk::Label
*/
- static itk::SmartPointer<mitk::Label> LoadLabelFromTiXmlDocument(TiXmlElement *labelElem);
+ static itk::SmartPointer<mitk::Label> LoadLabelFromXMLDocument(const tinyxml2::XMLElement *labelElem);
/**
- * @brief Creates a TiXmlElement from a mitk::Label
+ * @brief Creates an XML element from a mitk::Label
+ * @param doc
* @param label the mitk::Label from which the xml element will be created
- * @return the created TiXmlElement
+ * @return the created XML element
*/
- static TiXmlElement *GetLabelAsTiXmlElement(Label *label);
+ static tinyxml2::XMLElement *GetLabelAsXMLElement(tinyxml2::XMLDocument &doc, Label *label);
/**
* @brief Since a mitk::Label is basically a mitk::PropertyList this function coverts the label's properties into
* XML
+ * @param doc
* @param key the property's key which will be used in the XML element
* @param property the mitk::BaseProperty that should be converted
- * @return the created TiXmlElement
+ * @return the created XML element
*/
- static TiXmlElement *PropertyToXmlElem(const std::string &key, const BaseProperty *property);
+ static tinyxml2::XMLElement *PropertyToXMLElement(tinyxml2::XMLDocument& doc, const std::string &key, const BaseProperty *property);
/**
* @brief Since a mitk::Label is basically a mitk::PropertyList this function coverts a XML element into a property
* @param key the property's key
* @param prop the mitk::BaseProperty that will be created
* @param elem the XML elem from which the property will be created
* @return true if the conversion was successful and false otherwise
*/
- static bool PropertyFromXmlElem(std::string &key, itk::SmartPointer<mitk::BaseProperty> &prop, TiXmlElement *elem);
+ static bool PropertyFromXMLElement(std::string &key, itk::SmartPointer<mitk::BaseProperty> &prop, const tinyxml2::XMLElement *elem);
private:
LabelSetIOHelper();
};
}
#endif // __mitkLabelSetIOHelper_h
diff --git a/Modules/OpenCL/CMakeLists.txt b/Modules/OpenCL/CMakeLists.txt
index 25b7ef1cbd..c782ddf6d0 100644
--- a/Modules/OpenCL/CMakeLists.txt
+++ b/Modules/OpenCL/CMakeLists.txt
@@ -1,12 +1,11 @@
if(MITK_USE_OpenCL)
# create the module
MITK_CREATE_MODULE(
DEPENDS MitkCore
PACKAGE_DEPENDS
PUBLIC OpenCL
- PRIVATE ITK|ITKThresholding
)
add_subdirectory(Testing)
endif(MITK_USE_OpenCL)
diff --git a/Modules/OpenCVVideoSupport/CMakeLists.txt b/Modules/OpenCVVideoSupport/CMakeLists.txt
index c070905b75..2040203b4a 100644
--- a/Modules/OpenCVVideoSupport/CMakeLists.txt
+++ b/Modules/OpenCVVideoSupport/CMakeLists.txt
@@ -1,19 +1,19 @@
-set(dependencies ITK|ITKVideoBridgeOpenCV OpenCV)
+set(dependencies OpenCV)
if(MITK_USE_videoInput)
set(dependencies ${dependencies} videoInput)
endif(MITK_USE_videoInput)
mitk_create_module(
INCLUDE_DIRS Commands
DEPENDS MitkAlgorithmsExt
PACKAGE_DEPENDS PUBLIC ${dependencies}
ADDITIONAL_LIBS ${OPENCVVIDEOSUPPORT_ADDITIONAL_LIBS}
)
if(MODULE_IS_ENABLED)
if(MITK_USE_Qt5)
add_subdirectory(UI)
endif()
endif()
add_subdirectory(Testing)
diff --git a/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.cpp b/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.cpp
index d21581e8bf..213e8b4fc7 100644
--- a/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.cpp
+++ b/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.cpp
@@ -1,250 +1,263 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPropertyListsXmlFileReaderAndWriter.h"
#include "mitkProperties.h"
#include "mitkStandaloneDataStorage.h"
#include <itksys/SystemTools.hxx>
-#include <tinyxml.h>
+#include <tinyxml2.h>
+
+namespace
+{
+ std::string ReadStringAttribute(const tinyxml2::XMLElement* elem, const char *name)
+ {
+ const char* attrib = elem->Attribute(name);
+
+ return attrib != nullptr
+ ? attrib
+ : "";
+ }
+}
namespace mitk
{
bool PropertyListsXmlFileReaderAndWriter::PropertyFromXmlElem(std::string &name,
mitk::BaseProperty::Pointer &prop,
- TiXmlElement *elem) const
+ const tinyxml2::XMLElement *elem) const
{
- if (!elem)
+ if (nullptr == elem)
+ return false;
+
+ std::string type = ReadStringAttribute(elem, "type");
+
+ if (type.empty())
{
+ MITK_WARN << "type attribute not found in property";
return false;
}
+
+ name = ReadStringAttribute(elem, "name");
- bool readOp = false;
- std::string type = "";
- readOp = elem->QueryStringAttribute("type", &type) == TIXML_SUCCESS;
- if (readOp)
- readOp = elem->QueryStringAttribute("name", &name) == TIXML_SUCCESS;
- else
- MITK_WARN << "type"
- << " attribute not found in a property";
+ if (name.empty())
+ {
+ MITK_WARN << "name attribute not found in property";
+ return false;
+ }
- if (readOp)
+ tinyxml2::XMLError err = tinyxml2::XML_SUCCESS;
+
+ if (type == "BoolProperty")
{
- if (type == "BoolProperty")
+ int val = 0;
+ err = elem->QueryIntAttribute("value", &val);
+ if (tinyxml2::XML_SUCCESS == err)
{
- int val = 0;
- readOp = elem->QueryIntAttribute("value", &val) == TIXML_SUCCESS;
- if (readOp)
- {
- prop = mitk::BoolProperty::New(val == 1 ? true : false);
- }
+ prop = mitk::BoolProperty::New(val == 1 ? true : false);
}
- else if (type == "StringProperty")
+ }
+ else if (type == "StringProperty")
+ {
+ const auto* attrib = elem->FindAttribute("value");
+
+ if (nullptr == attrib)
{
- std::string val = "";
- readOp = elem->QueryStringAttribute("value", &val) == TIXML_SUCCESS;
- if (readOp)
- {
- prop = mitk::StringProperty::New(val);
- }
+ err = tinyxml2::XML_NO_ATTRIBUTE;
}
- else if (type == "IntProperty")
+ else
{
- int val = 0;
- readOp = elem->QueryIntAttribute("value", &val) == TIXML_SUCCESS;
- if (readOp)
- {
- prop = mitk::IntProperty::New(val);
- }
+ auto val = ReadStringAttribute(elem, "value");
+ prop = mitk::StringProperty::New(val);
}
- else if (type == "DoubleProperty")
+ }
+ else if (type == "IntProperty")
+ {
+ int val = 0;
+ err = elem->QueryIntAttribute("value", &val);
+ if (tinyxml2::XML_SUCCESS == err)
{
- double val = 0;
- readOp = elem->QueryDoubleAttribute("value", &val) == TIXML_SUCCESS;
- if (readOp)
- {
- prop = mitk::DoubleProperty::New(val);
- }
+ prop = mitk::IntProperty::New(val);
}
- else if (type == "FloatProperty")
+ }
+ else if (type == "DoubleProperty")
+ {
+ double val = 0;
+ err = elem->QueryDoubleAttribute("value", &val);
+ if (tinyxml2::XML_SUCCESS == err)
{
- float val = 0;
- readOp = elem->QueryFloatAttribute("value", &val) == TIXML_SUCCESS;
- if (readOp)
- {
- prop = mitk::FloatProperty::New(val);
- }
+ prop = mitk::DoubleProperty::New(val);
}
- else
+ }
+ else if (type == "FloatProperty")
+ {
+ float val = 0;
+ err = elem->QueryFloatAttribute("value", &val);
+ if (tinyxml2::XML_SUCCESS == err)
{
- readOp = false;
- MITK_WARN << "type"
- << " attribute unknown. Only BoolProperty, StringProperty, IntProperty, DoubleProperty or "
- "FloatProperty allowed.";
+ prop = mitk::FloatProperty::New(val);
}
}
else
- MITK_WARN << "name"
- << " attribute not found in a property";
-
- if (!readOp)
- MITK_WARN << "value"
- << " attribute not found in a property";
+ {
+ err = tinyxml2::XML_WRONG_ATTRIBUTE_TYPE;
+ MITK_WARN << "type attribute unknown. Only BoolProperty, StringProperty, IntProperty, DoubleProperty or FloatProperty allowed.";
+ }
- return readOp;
+ return tinyxml2::XML_SUCCESS == err;
}
+
bool PropertyListsXmlFileReaderAndWriter::PropertyToXmlElem(const std::string &name,
const mitk::BaseProperty *prop,
- TiXmlElement *elem) const
+ tinyxml2::XMLElement *elem) const
{
- if (!prop || !elem)
- {
+ if (nullptr == prop || nullptr == elem)
return false;
- }
const mitk::IntProperty *intProp = nullptr;
const mitk::FloatProperty *floatProp = nullptr;
const mitk::DoubleProperty *doubleProp = nullptr;
const mitk::BoolProperty *boolProp = nullptr;
const mitk::StringProperty *stringProp = nullptr;
bool writeOp = true;
- if ((boolProp = dynamic_cast<const BoolProperty *>(prop)))
+ if (nullptr != (boolProp = dynamic_cast<const BoolProperty *>(prop)))
{
- elem->SetAttribute(GetPropertyListIdElementName(), name);
+ elem->SetAttribute(GetPropertyListIdElementName(), name.c_str());
elem->SetAttribute("value", boolProp->GetValue() ? 1 : 0);
elem->SetAttribute("type", "BoolProperty");
}
- else if ((stringProp = dynamic_cast<const StringProperty *>(prop)))
+ else if (nullptr != (stringProp = dynamic_cast<const StringProperty *>(prop)))
{
- elem->SetAttribute(GetPropertyListIdElementName(), name);
+ elem->SetAttribute(GetPropertyListIdElementName(), name.c_str());
elem->SetAttribute("value", stringProp->GetValue());
elem->SetAttribute("type", "StringProperty");
}
- else if ((intProp = dynamic_cast<const IntProperty *>(prop)))
+ else if (nullptr != (intProp = dynamic_cast<const IntProperty *>(prop)))
{
- elem->SetAttribute(GetPropertyListIdElementName(), name);
+ elem->SetAttribute(GetPropertyListIdElementName(), name.c_str());
elem->SetAttribute("value", intProp->GetValue());
elem->SetAttribute("type", "IntProperty");
}
- else if ((doubleProp = dynamic_cast<const DoubleProperty *>(prop)))
+ else if (nullptr != (doubleProp = dynamic_cast<const DoubleProperty *>(prop)))
{
- elem->SetAttribute(GetPropertyListIdElementName(), name);
- elem->SetDoubleAttribute("value", doubleProp->GetValue());
+ elem->SetAttribute(GetPropertyListIdElementName(), name.c_str());
+ elem->SetAttribute("value", doubleProp->GetValue());
elem->SetAttribute("type", "DoubleProperty");
}
- else if ((floatProp = dynamic_cast<const FloatProperty *>(prop)))
+ else if (nullptr != (floatProp = dynamic_cast<const FloatProperty *>(prop)))
{
- elem->SetAttribute(GetPropertyListIdElementName(), name);
- elem->SetDoubleAttribute("value", static_cast<float>(floatProp->GetValue()));
+ elem->SetAttribute(GetPropertyListIdElementName(), name.c_str());
+ elem->SetAttribute("value", floatProp->GetValue());
elem->SetAttribute("type", "FloatProperty");
}
else
{
MITK_WARN("PropertyListImportFromXmlFile") << "Base property " << name << " is unknown";
writeOp = false;
}
return writeOp;
}
- bool PropertyListsXmlFileReaderAndWriter::WriteLists(
- const std::string &fileName, const std::map<std::string, mitk::PropertyList::Pointer> &_PropertyLists) const
+
+ bool PropertyListsXmlFileReaderAndWriter::WriteLists(const std::string &fileName,
+ const std::map<std::string, mitk::PropertyList::Pointer> &_PropertyLists) const
{
- TiXmlDocument doc;
+ tinyxml2::XMLDocument doc;
+ doc.InsertEndChild(doc.NewDeclaration());
- auto decl = new TiXmlDeclaration("1.0", "", "");
- doc.LinkEndChild(decl);
// create root
- auto propertyListsElem = new TiXmlElement("PropertyLists");
+ auto *propertyListsElem = doc.NewElement("PropertyLists");
bool allPropsConverted = true;
auto it = _PropertyLists.begin();
while (it != _PropertyLists.end())
{
const std::string &id = (*it).first;
const PropertyList *propList = (*it).second;
- auto propertyListElem = new TiXmlElement("PropertyList");
- propertyListElem->SetAttribute(GetPropertyListIdElementName(), id);
+ auto *propertyListElem = doc.NewElement("PropertyList");
+ propertyListElem->SetAttribute(GetPropertyListIdElementName(), id.c_str());
const std::map<std::string, BaseProperty::Pointer> *propMap = propList->GetMap();
auto propMapIt = propMap->begin();
while (propMapIt != propMap->end())
{
const std::string &propName = (*propMapIt).first;
const BaseProperty *prop = (*propMapIt).second;
- auto propertyElem = new TiXmlElement("Property");
+ auto *propertyElem = doc.NewElement("Property");
if (!this->PropertyToXmlElem(propName, prop, propertyElem))
allPropsConverted = false;
- propertyListElem->LinkEndChild(propertyElem);
+ propertyListElem->InsertEndChild(propertyElem);
++propMapIt;
}
- propertyListsElem->LinkEndChild(propertyListElem);
+ propertyListsElem->InsertEndChild(propertyListElem);
++it;
}
- doc.LinkEndChild(propertyListsElem);
+ doc.InsertEndChild(propertyListsElem);
- return (allPropsConverted && doc.SaveFile(fileName.c_str()));
+ return (allPropsConverted && tinyxml2::XML_SUCCESS == doc.SaveFile(fileName.c_str()));
}
- bool PropertyListsXmlFileReaderAndWriter::ReadLists(
- const std::string &fileName, std::map<std::string, mitk::PropertyList::Pointer> &_PropertyLists) const
+
+ bool PropertyListsXmlFileReaderAndWriter::ReadLists(const std::string &fileName,
+ std::map<std::string, mitk::PropertyList::Pointer> &_PropertyLists) const
{
// reread
- TiXmlDocument doc(fileName);
- doc.LoadFile();
+ tinyxml2::XMLDocument doc;
+ doc.LoadFile(fileName.c_str());
- TiXmlHandle docHandle(&doc);
- TiXmlElement *elem = docHandle.FirstChildElement("PropertyLists").FirstChildElement("PropertyList").ToElement();
+ tinyxml2::XMLHandle docHandle(&doc);
+ auto *elem = docHandle.FirstChildElement("PropertyLists").FirstChildElement("PropertyList").ToElement();
- if (!elem)
+ if (nullptr == elem)
{
MITK_WARN("PropertyListFromXml") << "Cannot find a PropertyList element (inside a PropertyLists element)";
return false;
}
bool opRead = false;
- while (elem)
+ while (nullptr != elem)
{
- std::string propListId;
- opRead = elem->QueryStringAttribute(GetPropertyListIdElementName(), &propListId) == TIXML_SUCCESS;
- if (!opRead)
+ std::string propListId = ReadStringAttribute(elem, GetPropertyListIdElementName());
+ if (propListId.empty())
break;
- mitk::PropertyList::Pointer propList = mitk::PropertyList::New();
+ opRead = true;
+
+ auto propList = mitk::PropertyList::New();
- TiXmlElement *propElem = elem->FirstChildElement("Property");
+ auto *propElem = elem->FirstChildElement("Property");
- while (propElem)
+ while (nullptr != propElem)
{
std::string name;
mitk::BaseProperty::Pointer prop;
opRead = this->PropertyFromXmlElem(name, prop, propElem);
if (!opRead)
break;
propList->SetProperty(name, prop);
propElem = propElem->NextSiblingElement("Property");
}
if (!opRead)
break;
_PropertyLists[propListId] = propList;
elem = elem->NextSiblingElement("PropertyList");
}
return opRead;
}
PropertyListsXmlFileReaderAndWriter::PropertyListsXmlFileReaderAndWriter() {}
PropertyListsXmlFileReaderAndWriter::~PropertyListsXmlFileReaderAndWriter() {}
const char *PropertyListsXmlFileReaderAndWriter::GetPropertyListIdElementName() { return "name"; }
}
diff --git a/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.h b/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.h
index 57de09355f..4534c2d1f6 100644
--- a/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.h
+++ b/Modules/Persistence/mitkPropertyListsXmlFileReaderAndWriter.h
@@ -1,47 +1,50 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkXmlSceneIO_h_included
#define mitkXmlSceneIO_h_included
#include "mitkDataStorage.h"
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLElement;
+}
namespace mitk
{
class PropertyListsXmlFileReaderAndWriter;
class PropertyListsXmlFileReaderAndWriter : public itk::Object
{
public:
static const char *GetPropertyListIdElementName();
mitkClassMacroItkParent(PropertyListsXmlFileReaderAndWriter, itk::Object);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
bool WriteLists(const std::string &fileName,
const std::map<std::string, mitk::PropertyList::Pointer> &_PropertyLists) const;
bool ReadLists(const std::string &fileName,
std::map<std::string, mitk::PropertyList::Pointer> &_PropertyLists) const;
protected:
PropertyListsXmlFileReaderAndWriter();
~PropertyListsXmlFileReaderAndWriter() override;
- bool PropertyFromXmlElem(std::string &name, mitk::BaseProperty::Pointer &prop, TiXmlElement *elem) const;
- bool PropertyToXmlElem(const std::string &name, const mitk::BaseProperty *prop, TiXmlElement *elem) const;
+ bool PropertyFromXmlElem(std::string &name, mitk::BaseProperty::Pointer &prop, const tinyxml2::XMLElement *elem) const;
+ bool PropertyToXmlElem(const std::string &name, const mitk::BaseProperty *prop, tinyxml2::XMLElement *elem) const;
};
}
#endif
diff --git a/Modules/Pharmacokinetics/CMakeLists.txt b/Modules/Pharmacokinetics/CMakeLists.txt
index ee417b64e2..6413f1948c 100644
--- a/Modules/Pharmacokinetics/CMakeLists.txt
+++ b/Modules/Pharmacokinetics/CMakeLists.txt
@@ -1,18 +1,15 @@
MITK_CREATE_MODULE(Pharmacokinetics
INCLUDE_DIRS
PUBLIC ${MITK_BINARY_DIR}
PRIVATE src/Common src/Functors src/Models src/DescriptionParameters src/SimulationFramework
DEPENDS
PUBLIC MitkCore MitkModelFit
PRIVATE MitkMultilabel
- PACKAGE_DEPENDS
- PUBLIC ITK|ITKOptimizers
- PRIVATE Boost
)
if(BUILD_TESTING)
ADD_SUBDIRECTORY(test)
endif(BUILD_TESTING)
ADD_SUBDIRECTORY(autoload/Models)
-ADD_SUBDIRECTORY(cmdapps)
\ No newline at end of file
+ADD_SUBDIRECTORY(cmdapps)
diff --git a/Modules/Pharmacokinetics/cmdapps/CMakeLists.txt b/Modules/Pharmacokinetics/cmdapps/CMakeLists.txt
index bbb4b7341c..c6425a4687 100644
--- a/Modules/Pharmacokinetics/cmdapps/CMakeLists.txt
+++ b/Modules/Pharmacokinetics/cmdapps/CMakeLists.txt
@@ -1,77 +1,76 @@
option(BUILD_PerfusionMiniApps "Build commandline tools for the perfusion module" OFF)
if(BUILD_PerfusionMiniApps)
# needed include directories
include_directories(
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR}
)
# list of miniapps
# if an app requires additional dependencies
# they are added after a "^^" and separated by "_"
set( miniapps
CurveDescriptorMiniApp^^
MRPerfusionMiniApp^^
MRSignal2ConcentrationMiniApp^^
)
foreach(miniapp ${miniapps})
# extract mini app name and dependencies
string(REPLACE "^^" "\\;" miniapp_info ${miniapp})
set(miniapp_info_list ${miniapp_info})
list(GET miniapp_info_list 0 appname)
list(GET miniapp_info_list 1 raw_dependencies)
string(REPLACE "_" "\\;" dependencies "${raw_dependencies}")
set(dependencies_list ${dependencies})
mitk_create_executable(${appname}
DEPENDS MitkModelFit MitkPharmacokinetics MitkCommandLine ${dependencies_list}
- PACKAGE_DEPENDS ITK
CPP_FILES ${appname}.cpp
)
if(EXECUTABLE_IS_ENABLED)
# On Linux, create a shell script to start a relocatable application
if(UNIX AND NOT APPLE)
install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${EXECUTABLE_TARGET}.sh)
endif()
get_target_property(_is_bundle ${EXECUTABLE_TARGET} MACOSX_BUNDLE)
if(APPLE)
if(_is_bundle)
set(_target_locations ${EXECUTABLE_TARGET}.app)
set(${_target_locations}_qt_plugins_install_dir ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_bundle_dest_dir ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_qt_plugins_for_current_bundle ${EXECUTABLE_TARGET}.app/Contents/MacOS)
set(_qt_conf_install_dirs ${EXECUTABLE_TARGET}.app/Contents/Resources)
install(TARGETS ${EXECUTABLE_TARGET} BUNDLE DESTINATION . )
else()
if(NOT MACOSX_BUNDLE_NAMES)
set(_qt_conf_install_dirs bin)
set(_target_locations bin/${EXECUTABLE_TARGET})
set(${_target_locations}_qt_plugins_install_dir bin)
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
else()
foreach(bundle_name ${MACOSX_BUNDLE_NAMES})
list(APPEND _qt_conf_install_dirs ${bundle_name}.app/Contents/Resources)
set(_current_target_location ${bundle_name}.app/Contents/MacOS/${EXECUTABLE_TARGET})
list(APPEND _target_locations ${_current_target_location})
set(${_current_target_location}_qt_plugins_install_dir ${bundle_name}.app/Contents/MacOS)
message( " set(${_current_target_location}_qt_plugins_install_dir ${bundle_name}.app/Contents/MacOS) ")
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION ${bundle_name}.app/Contents/MacOS/)
endforeach()
endif()
endif()
else()
set(_target_locations bin/${EXECUTABLE_TARGET}${CMAKE_EXECUTABLE_SUFFIX})
set(${_target_locations}_qt_plugins_install_dir bin)
set(_qt_conf_install_dirs bin)
install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
endif()
endif()
endforeach()
endif()
diff --git a/Modules/PharmacokineticsUI/CMakeLists.txt b/Modules/PharmacokineticsUI/CMakeLists.txt
index f9adf7c888..98b248743e 100644
--- a/Modules/PharmacokineticsUI/CMakeLists.txt
+++ b/Modules/PharmacokineticsUI/CMakeLists.txt
@@ -1,5 +1,5 @@
MITK_CREATE_MODULE(PharmacokineticsUI
INCLUDE_DIRS Common Qmitk
DEPENDS MitkPharmacokinetics MitkQtWidgets MitkQtWidgetsExt
- PACKAGE_DEPENDS Qt5|Core CTK|CTKWidgets Boost
+ PACKAGE_DEPENDS CTK|CTKWidgets
)
diff --git a/Modules/PhotoacousticsAlgorithms/CMakeLists.txt b/Modules/PhotoacousticsAlgorithms/CMakeLists.txt
deleted file mode 100644
index 16ebe278d0..0000000000
--- a/Modules/PhotoacousticsAlgorithms/CMakeLists.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-set(dependencies_list MitkCore MitkAlgorithmsExt MitkOpenCVVideoSupport)
-
-IF(MITK_USE_OpenCL)
- add_definitions(-DPHOTOACOUSTICS_USE_GPU)
- set(dependencies_list ${dependencies_list} MitkOpenCL)
- message("Using OpenCL in PhotoacousticAlgorithms")
-ENDIF(MITK_USE_OpenCL)
-
-MITK_CREATE_MODULE(
- DEPENDS ${dependencies_list}
- #AUTOLOAD_WITH MitkCore
- INCLUDE_DIRS PUBLIC include
- INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
- PACKAGE_DEPENDS ITK|ITKFFT+ITKImageCompose+ITKImageIntensity OpenCV tinyxml
-)
-
-add_subdirectory(test)
-add_subdirectory(MitkPABeamformingTool)
-add_subdirectory(MitkPAResampleCropTool)
diff --git a/Modules/PhotoacousticsAlgorithms/Documentation/doxygen/PAModule.dox b/Modules/PhotoacousticsAlgorithms/Documentation/doxygen/PAModule.dox
deleted file mode 100644
index 9cbcf6d54a..0000000000
--- a/Modules/PhotoacousticsAlgorithms/Documentation/doxygen/PAModule.dox
+++ /dev/null
@@ -1,45 +0,0 @@
-/**
-\page PAModulePage Photoacoustic Algorithms Module
-
-\tableofcontents
-
-\section PAModulePageOverview Overview
-
-The Photoacoustic Algorithms Module provides a <strong>set of filters for beamforming and post-processing of photoacoustic and ultrasound data</strong>.
-The main features are:
-<ul>
- <li> Management of all filters through a single class PhotoacousticImage
- <li> Beamforming of ultrasound and photoacoustic image data.
- <ul>
- <li> Beamforming using the DAS and DMAS Algorithms.
- <li> Optional real-time beamforming capabilities by the usage of openCL GPU computing
- </ul>
- <li> Post/Pre-Processing of any kind of images.
- <ul>
- <li> Crop Filter for removing artefacts in upper and lower edge of the image.
- <li> Multiple B-Mode Filter implementations with resampling and logarithmic filter.
- <li> Bandpass Filter
- </ul>
-</ul>
-
-To use the GPU capabilities of this module, openCL needs to be activated in CMAKE. The custom build option "camiPhotoacousticsWorkstation" activates all needed CMAKE options, as well as openCL.
-To build the project using openCL, the openCL libraries provided by your graphic card vendor need to be installed. The GPU capabilies of this module have been only tested using nvidia hardware, but, as openCL has been also implemented by AMD, this should work on either one. (Those are included in the CUDA package for nvidia graphic card owners)
-
-The \link org_mitk_gui_qt_photoacoustics_imageprocessing Photoacoustic Imageprocessing plugin \endlink provides a GUI to access all of thePhotoacoustic Algorithms Module's filters.
-
-\section PAModuleClasses The Photoacoustic Algorithms Module's Classes
-
-<ul>
- <li> mitk::PhotoacousticImage: The class where all filters are managed.
- <li> mitk::BeamformingSettings: The class used by many filters for storing the configuration to be used when applying them.
- <li> Five filters are currently implemented in the Photoacoustic Algorithms module:
- <ul>
- <li> mitk::PhotoacousticBModeFilter: A class for the B-Mode filter on GPU and CPU.
- <li> Resampling Filter: A resampling filter for post-processing.
- <li> mitk::BeamformingFilter: A filter with a switch for GPU/CPU computation, to compute the beamformed image out of raw ultrasound/photoacoustic data.
- <li> Crop Filter: A filter for cropping artifacts on the upper and lower edges of the image.
- <li> Bandpass Filter: A Filter to filter image data in the fourier domain, using a tukey window to cut off low or high frequency parts of the image.
- </ul>
- </li>
-</ul>
-*/
\ No newline at end of file
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/LICENSE b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/LICENSE
deleted file mode 100644
index d645695673..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/LICENSE
+++ /dev/null
@@ -1,202 +0,0 @@
-
- Apache License
- Version 2.0, January 2004
- http://www.apache.org/licenses/
-
- TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
-
- 1. Definitions.
-
- "License" shall mean the terms and conditions for use, reproduction,
- and distribution as defined by Sections 1 through 9 of this document.
-
- "Licensor" shall mean the copyright owner or entity authorized by
- the copyright owner that is granting the License.
-
- "Legal Entity" shall mean the union of the acting entity and all
- other entities that control, are controlled by, or are under common
- control with that entity. For the purposes of this definition,
- "control" means (i) the power, direct or indirect, to cause the
- direction or management of such entity, whether by contract or
- otherwise, or (ii) ownership of fifty percent (50%) or more of the
- outstanding shares, or (iii) beneficial ownership of such entity.
-
- "You" (or "Your") shall mean an individual or Legal Entity
- exercising permissions granted by this License.
-
- "Source" form shall mean the preferred form for making modifications,
- including but not limited to software source code, documentation
- source, and configuration files.
-
- "Object" form shall mean any form resulting from mechanical
- transformation or translation of a Source form, including but
- not limited to compiled object code, generated documentation,
- and conversions to other media types.
-
- "Work" shall mean the work of authorship, whether in Source or
- Object form, made available under the License, as indicated by a
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diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/README.rst b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/README.rst
deleted file mode 100644
index a008a380db..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/README.rst
+++ /dev/null
@@ -1,11 +0,0 @@
-==================
-ITKUltrasound
-==================
-
-Purpose
-=======
-
-This module contains filters for use with the `Insight Toolkit`_ (ITK) that
-may be particularly useful for the reconstruction and analysis of ultrasound.
-
-.. _Insight Toolkit: http://www.itk.org/
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.h
deleted file mode 100644
index a766265540..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.h
+++ /dev/null
@@ -1,139 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkAnalyticSignalImageFilter_h
-#define itkAnalyticSignalImageFilter_h
-
-#include <complex>
-
-#include "itkFFT1DComplexToComplexImageFilter.h"
-#include "itkFFT1DRealToComplexConjugateImageFilter.h"
-#include "itkImageRegionSplitterDirection.h"
-
-namespace itk
-{
-/** \class AnalyticSignalImageFilter
- * \brief Generates the analytic signal from one direction of an image.
- *
- * This filter generates the complex valued analytic signal along one direction
- * of an image. This input is a real valued image, and the output is a complex
- * image.
- *
- * The analytic signal is given by
- *
- * f_a(x) = f(x) - i f_H(x)
- *
- * Where i is the square root of one and f_H(x) is the Hibert transform of f(x).
- *
- * Since the Hilbert transform in the Fourier domain is
- *
- * F_H(k) = F(k) i sign(k),
- *
- * f_a(x) is calculated by
- *
- * f_a(x) = F^{-1}( F(k) 2 U(k) )
- *
- * where U(k) is the unit step function.
- *
- * \ingroup FourierTransform
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage >
-class AnalyticSignalImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension);
-
- typedef AnalyticSignalImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkTypeMacro( AnalyticSignalImageFilter, ImageToImageFilter );
- itkNewMacro( Self );
-
- /** Get the direction in which the filter is to be applied. */
- virtual unsigned int GetDirection() const
- {
- return this->m_FFTRealToComplexFilter->GetDirection();
- }
-
- /** Set the direction in which the filter is to be applied. */
- virtual void SetDirection( const unsigned int direction )
- {
- if( this->m_FFTRealToComplexFilter->GetDirection() != direction )
- {
- this->m_FFTRealToComplexFilter->SetDirection( direction );
- this->m_FFTComplexToComplexFilter->SetDirection( direction );
- this->Modified();
- }
- }
-
-protected:
- AnalyticSignalImageFilter();
- ~AnalyticSignalImageFilter() override {}
-
- void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- // These behave like their analogs in FFT1DRealToComplexConjugateImageFilter.
- void GenerateInputRequestedRegion() ITK_OVERRIDE;
- void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- void BeforeThreadedGenerateData() ITK_OVERRIDE;
- void ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId ) ITK_OVERRIDE;
- void AfterThreadedGenerateData() ITK_OVERRIDE;
-
- typedef FFT1DRealToComplexConjugateImageFilter< InputImageType, OutputImageType > FFTRealToComplexType;
- typedef FFT1DComplexToComplexImageFilter< OutputImageType, OutputImageType > FFTComplexToComplexType;
-
- typename FFTRealToComplexType::Pointer m_FFTRealToComplexFilter;
- typename FFTComplexToComplexType::Pointer m_FFTComplexToComplexFilter;
-
- /** Override to return a splitter that does not split along the direction we
- * are performing the transform. */
- const ImageRegionSplitterBase* GetImageRegionSplitter() const ITK_OVERRIDE;
-
-private:
- AnalyticSignalImageFilter( const Self& ); // purposely not implemented
- void operator=( const Self& ); // purposely not implemented
-
- ImageRegionSplitterDirection::Pointer m_ImageRegionSplitter;
-};
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkAnalyticSignalImageFilter.hxx"
-#endif
-
-#endif // itkAnalyticSignalImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.hxx
deleted file mode 100644
index 6f9bed0161..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkAnalyticSignalImageFilter.hxx
+++ /dev/null
@@ -1,267 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkAnalyticSignalImageFilter_hxx
-#define itkAnalyticSignalImageFilter_hxx
-
-#include "itkAnalyticSignalImageFilter.h"
-
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.h"
-#include "itkVnlFFT1DComplexToComplexImageFilter.h"
-
-#if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
-#include "itkFFTW1DRealToComplexConjugateImageFilter.h"
-#include "itkFFTW1DComplexToComplexImageFilter.h"
-#endif
-
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::AnalyticSignalImageFilter()
-{
- m_FFTRealToComplexFilter = FFTRealToComplexType::New();
- m_FFTComplexToComplexFilter = FFTComplexToComplexType::New();
-
- m_FFTComplexToComplexFilter->SetTransformDirection( FFTComplexToComplexType::INVERSE );
-
- this->SetDirection( 0 );
-
- this->m_ImageRegionSplitter = ImageRegionSplitterDirection::New();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- typename InputImageType::Pointer inputPtr =
- const_cast<InputImageType *> (this->GetInput());
- typename OutputImageType::Pointer outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->GetDirection();
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast< OutputImageType* >( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- const unsigned int direction = this->GetDirection ();
- enlargedSize[direction] = outputLargeSize[direction];
- enlargedIndex[direction] = outputLargeIndex[direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- const unsigned int direction = this->GetDirection();
- os << indent << "Direction: " << direction << std::endl;
-
- os << indent << "FFTRealToComplexFilter: " << std::endl;
- m_FFTRealToComplexFilter->Print( os, indent );
- os << indent << "FFTComplexToComplexFilter: " << std::endl;
- m_FFTComplexToComplexFilter->Print( os, indent );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-const ImageRegionSplitterBase *
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::GetImageRegionSplitter() const
-{
- return this->m_ImageRegionSplitter.GetPointer();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- this->m_ImageRegionSplitter->SetDirection( this->GetDirection() );
-
- m_FFTRealToComplexFilter->SetInput( this->GetInput() );
- m_FFTRealToComplexFilter->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
- m_FFTRealToComplexFilter->GetOutput()->SetLargestPossibleRegion( this->GetOutput()->GetLargestPossibleRegion() );
- m_FFTRealToComplexFilter->SetNumberOfThreads( this->GetNumberOfThreads() );
- m_FFTRealToComplexFilter->Update ();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType itkNotUsed( threadId ) )
-{
- // get pointers to the input and output
- const typename FFTRealToComplexType::OutputImageType * inputPtr = m_FFTRealToComplexFilter->GetOutput();
- OutputImageType * outputPtr = this->GetOutput();
-
- const typename FFTRealToComplexType::OutputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
- const unsigned int direction = this->GetDirection ();
- const unsigned int size = inputSize[direction];
- unsigned int dub_size;
- bool even;
- if( size % 2 == 0 )
- {
- even = true;
- dub_size = size / 2 - 1;
- }
- else
- {
- even = false;
- dub_size = (size + 1) / 2 - 1;
- }
-
- typedef ImageLinearConstIteratorWithIndex< typename FFTRealToComplexType::OutputImageType > InputIteratorType;
- typedef ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegionForThread );
- OutputIteratorType outputIt( outputPtr, outputRegionForThread );
- inputIt.SetDirection( direction );
- outputIt.SetDirection( direction );
-
- unsigned int i;
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- inputIt.GoToBeginOfLine();
- outputIt.GoToBeginOfLine();
-
- // DC
- outputIt.Set( inputIt.Get() );
- ++inputIt;
- ++outputIt;
-
- for( i = 0; i < dub_size; i++ )
- {
- outputIt.Set( inputIt.Get() * static_cast< typename TInputImage::PixelType >( 2 ) );
- ++outputIt;
- ++inputIt;
- }
- if( even )
- {
- outputIt.Set( inputIt.Get() );
- ++inputIt;
- ++outputIt;
- }
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( static_cast< typename TInputImage::PixelType >( 0 ) );
- ++outputIt;
- }
- }
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::AfterThreadedGenerateData()
-{
- // Trippy, eh?
- m_FFTComplexToComplexFilter->SetInput( this->GetOutput() );
- m_FFTComplexToComplexFilter->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
- m_FFTComplexToComplexFilter->GetOutput()->SetLargestPossibleRegion( this->GetOutput()->GetLargestPossibleRegion() );
- m_FFTComplexToComplexFilter->SetNumberOfThreads( this->GetNumberOfThreads() );
- m_FFTComplexToComplexFilter->Update ();
- this->GraftOutput( m_FFTComplexToComplexFilter->GetOutput() );
-}
-
-} // end namespace itk
-
-#endif // itkAnalyticSignalImageFilter_hxx
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.h
deleted file mode 100644
index baeb5c5e67..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.h
+++ /dev/null
@@ -1,152 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkBModeImageFilter_h
-#define itkBModeImageFilter_h
-
-#include "itkAddImageFilter.h"
-#include "itkComplexToModulusImageFilter.h"
-#include "itkConstantPadImageFilter.h"
-#include "itkRegionFromReferenceImageFilter.h"
-#include "itkImageToImageFilter.h"
-#include "itkImage.h"
-#include "itkLog10ImageFilter.h"
-
-#include "itkAnalyticSignalImageFilter.h"
-
-namespace itk
-{
-
-/**
- * \class BModeImageFilter
- *
- * \brief Create an ultrasound B-Mode (Brightness-Mode) image from raw
- * "RF" data. The RF's envelope is calculated from the analytic signal and
- * logarithmic intensity transform is applied.
- *
- * Use SetDirection() to define the axis of propagation.
- *
- * \ingroup Ultrasound
- *
- * \sa AnalyticSignalImageFilter
- *
- */
-template < typename TInputImage, typename TOutputImage=TInputImage, typename TComplexImage=Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
-class BModeImageFilter :
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef BModeImageFilter Self;
- typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- /** The type of input image. */
- typedef TInputImage InputImageType;
-
- /** Dimension of the input and output images. */
- itkStaticConstMacro (ImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- /** Typedef support for the input image scalar value type. */
- typedef typename InputImageType::PixelType InputPixelType;
-
- /** The type of output image. */
- typedef TOutputImage OutputImageType;
-
- /** Typedef support for the output image scalar value type. */
- typedef typename OutputImageType::PixelType OutputPixelType;
-
- /** Typedef of the image used for internal computations that has
- * std::complex pixels. */
- typedef TComplexImage ComplexImageType;
-
- /** Other convenient typedefs */
- typedef typename InputImageType::RegionType InputRegionType;
- typedef typename InputImageType::SizeType InputSizeType;
- typedef typename InputImageType::IndexType InputIndexType;
-
- /** Run-time type information (and related methods) */
- itkTypeMacro( BModeImageFilter, ImageToImageFilter );
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Set the direction in which the envelope is to be calculated. */
- virtual void SetDirection( unsigned int direction )
- {
- this->m_AnalyticFilter->SetDirection( direction );
- this->Modified();
- }
-
- /** Get the direction in which the envelope is to be calculated. */
- virtual unsigned int GetDirection() const
- {
- return m_AnalyticFilter->GetDirection();
- }
-
-protected:
- BModeImageFilter();
- ~BModeImageFilter() override {}
-
- void PrintSelf( std::ostream& os, Indent indent ) const ITK_OVERRIDE;
-
- void GenerateData() ITK_OVERRIDE;
-
- // These behave like their analogs in FFT1DRealToComplexConjugateImageFilter.
- void GenerateInputRequestedRegion() ITK_OVERRIDE;
- void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- /** Component filters. */
- typedef AnalyticSignalImageFilter< InputImageType, ComplexImageType > AnalyticType;
- typedef ComplexToModulusImageFilter< typename AnalyticType::OutputImageType, OutputImageType > ComplexToModulusType;
- typedef ConstantPadImageFilter< InputImageType, InputImageType > PadType;
- typedef AddImageFilter< InputImageType, InputImageType > AddConstantType;
- typedef Log10ImageFilter< InputImageType, OutputImageType > LogType;
- typedef RegionFromReferenceImageFilter< OutputImageType, OutputImageType > ROIType;
-
-private:
- BModeImageFilter( const Self& ); // purposely not implemented
- void operator=( const Self& ); // purposely not implemented
-
- typename AnalyticType::Pointer m_AnalyticFilter;
- typename ComplexToModulusType::Pointer m_ComplexToModulusFilter;
- typename PadType::Pointer m_PadFilter;
- typename AddConstantType::Pointer m_AddConstantFilter;
- typename LogType::Pointer m_LogFilter;
- typename ROIType::Pointer m_ROIFilter;
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkBModeImageFilter.hxx"
-#endif
-
-#endif // itkBModeImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.hxx
deleted file mode 100644
index f45b42fe37..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkBModeImageFilter.hxx
+++ /dev/null
@@ -1,208 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkBModeImageFilter_hxx
-#define itkBModeImageFilter_hxx
-
-#include "itkBModeImageFilter.h"
-
-#include "itkMetaDataDictionary.h"
-
-#include <algorithm>
-#include <sstream>
-#include <string>
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::BModeImageFilter()
-{
- m_AnalyticFilter = AnalyticType::New();
- m_ComplexToModulusFilter = ComplexToModulusType::New();
- m_PadFilter = PadType::New();
- m_AddConstantFilter = AddConstantType::New();
- m_LogFilter = LogType::New();
- m_ROIFilter = ROIType::New();
-
- // Avoid taking the log of zero. Assuming that the original input is coming
- // from a digitizer that outputs integer types, so 1 is small.
- m_AddConstantFilter->SetConstant2( 1 );
- m_PadFilter->SetConstant( 0. );
-
- m_ComplexToModulusFilter->SetInput( m_AnalyticFilter->GetOutput() );
- m_ROIFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
- m_LogFilter->SetInput( m_AddConstantFilter->GetOutput() );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- InputImageType * inputPtr = const_cast<InputImageType *> (this->GetInput());
- OutputImageType * outputPtr = this->GetOutput();
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->GetDirection();
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast< OutputImageType* >( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- const unsigned int direction = this->GetDirection ();
- enlargedSize[direction] = outputLargeSize[direction];
- enlargedIndex[direction] = outputLargeIndex[direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::GenerateData()
-{
- this->AllocateOutputs();
-
- const InputImageType * inputPtr = this->GetInput();
- OutputImageType * outputPtr = this->GetOutput();
-
- const unsigned int direction = m_AnalyticFilter->GetDirection();
- typename InputImageType::SizeType size = inputPtr->GetLargestPossibleRegion().GetSize();
-
- // Zero padding. FFT direction should be factorable by 2 for all FFT
- // implementations to work.
- unsigned int n = size[direction];
- while( n % 2 == 0 )
- {
- n /= 2;
- }
- bool doPadding;
- if( n == 1 )
- {
- doPadding = false;
- }
- else
- {
- doPadding = true;
- }
- if( doPadding )
- {
- n = size[direction];
- unsigned int newSizeDirection = 1;
- while( newSizeDirection < n )
- {
- newSizeDirection *= 2;
- }
- typename InputImageType::SizeType padSize;
- padSize.Fill( 0 );
- padSize[direction] = newSizeDirection - size[direction];
- size[direction] = newSizeDirection;
- m_PadFilter->SetPadUpperBound( padSize );
- m_PadFilter->SetInput( inputPtr );
- m_AnalyticFilter->SetInput( m_PadFilter->GetOutput() );
- m_ROIFilter->SetReferenceImage( inputPtr );
- m_ROIFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
- m_AddConstantFilter->SetInput( m_ROIFilter->GetOutput() );
- }
- else // padding is not required
- {
- m_AnalyticFilter->SetInput( inputPtr );
- m_AddConstantFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
- }
- m_LogFilter->GraftOutput( outputPtr );
- m_LogFilter->Update();
- this->GraftOutput( m_LogFilter->GetOutput() );
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.h
deleted file mode 100644
index 982f0397d5..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.h
+++ /dev/null
@@ -1,347 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkCurvilinearArraySpecialCoordinatesImage_h
-#define itkCurvilinearArraySpecialCoordinatesImage_h
-
-#include "itkSpecialCoordinatesImage.h"
-#include "itkPoint.h"
-#include "vnl/vnl_math.h"
-#include "itkNeighborhoodAccessorFunctor.h"
-
-namespace itk
-{
-/** \class CurvilinearArraySpecialCoordinatesImage
- *
- * \brief Templated 2D nonrectilinear-coordinate image class for
- * curvilinear/phased-array "range" images.
- *
- * \verbatim
- *
- * +---------------------> x-axis
- * |\
- * / | \
- * |-~\
- * / | \
- * | \
- * / | \
- * | lateral
- * |
- * v y-axis
- *
- * \endverbatim
- *
- * The equations form performing the conversion from Cartesian coordinates to
- * curvilinear/phased array coordinates are as follows:
- *
- * lateral = arctan(x/y)
- * radius = std::sqrt(x^2 + y^2)
- *
- * The reversed transforms are:
- *
- * x = radius * std::sin(lateral)
- * y = radius * std::cos(lateral)
- *
- * CurvilinearArraySpecialCoordinatesImages are templated over a pixel
- * type and follow the SpecialCoordinatesImage interface. The data in
- * an image is arranged in a 1D array as
- * [lateral-index][radius-index] with radius-index
- * varying most rapidly. The Index type reverses the order so that
- * Index[0] = radius-index, Index[1] = lateral-index.
- *
- * Lateral is discretized into m_LateralAngularSeparation intervals
- * per angular voxel, the most negative lateral interval containing
- * data is then mapped to lateral-index=0, and the largest lateral
- * interval containing data is then mapped to lateral-index=( number
- * of samples along lateral axis - 1 ). Elevation is discretized in
- * the same manner. This way, the mapping to Cartesian space is
- * symmetric about the x axis such that the line defined by
- * lateral/2 = x-axis. Radius is discretized into
- * m_RadiusSampleSize units per angular voxel. The smallest range
- * interval containing data is then mapped to radius-index=0, such
- * that radius = m_FirstSampleDistance + (radius-index *
- * m_RadiusSampleSize).
- *
- * \sa SpecialCoordinatesImage
- * \sa PhasedArray3DSpecialCoordinatesImage
- *
- * \ingroup Ultrasound
- *
- * \ingroup ImageObjects
- * \ingroup ITKCommon
- */
-template< typename TPixel, unsigned int VDimension >
-class CurvilinearArraySpecialCoordinatesImage:
- public SpecialCoordinatesImage< TPixel, VDimension >
-{
-public:
- /** Standard class typedefs */
- typedef CurvilinearArraySpecialCoordinatesImage Self;
- typedef SpecialCoordinatesImage< TPixel, VDimension > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
- typedef WeakPointer< const Self > ConstWeakPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(CurvilinearArraySpecialCoordinatesImage, SpecialCoordinatesImage);
-
- /** Pixel typedef support. Used to declare pixel type in filters
- * or other operations. */
- typedef TPixel PixelType;
-
- /** Typedef alias for PixelType */
- typedef TPixel ValueType;
-
- /** Internal Pixel representation. Used to maintain a uniform API
- * with Image Adaptors and allow to keep a particular internal
- * representation of data while showing a different external
- * representation. */
- typedef TPixel InternalPixelType;
-
- typedef typename Superclass::IOPixelType IOPixelType;
-
- /** Accessor type that convert data between internal and external
- * representations. */
- typedef DefaultPixelAccessor< PixelType > AccessorType;
-
- /** Accessor functor to choose between accessors: DefaultPixelAccessor for
- * the Image, and DefaultVectorPixelAccessor for the vector image. The
- * functor provides a generic API between the two accessors. */
- typedef DefaultPixelAccessorFunctor< Self > AccessorFunctorType;
-
- /** Typedef for the functor used to access a neighborhood of pixel
- * pointers. */
- typedef NeighborhoodAccessorFunctor< Self > NeighborhoodAccessorFunctorType;
-
- /** Dimension of the image. This constant is used by functions that are
- * templated over image type (as opposed to being templated over pixel type
- * and dimension) when they need compile time access to the dimension of
- * the image. */
- itkStaticConstMacro(ImageDimension, unsigned int, VDimension);
-
- /** Index typedef support. An index is used to access pixel values. */
- typedef typename Superclass::IndexType IndexType;
- typedef typename Superclass::IndexValueType IndexValueType;
-
- /** Offset typedef support. An offset is used to access pixel values. */
- typedef typename Superclass::OffsetType OffsetType;
-
- /** Size typedef support. A size is used to define region bounds. */
- typedef typename Superclass::SizeType SizeType;
- typedef typename Superclass::SizeValueType SizeValueType;
-
- /** Container used to store pixels in the image. */
- typedef ImportImageContainer< SizeValueType, PixelType > PixelContainer;
-
- /** Region typedef support. A region is used to specify a subset of
- * an image.
- */
- typedef typename Superclass::RegionType RegionType;
-
- /** Spacing typedef support. Spacing holds the "fake" size of a
- * pixel, making each pixel look like a 1 unit hyper-cube to filters
- * that were designed for normal images and that therefore use
- * m_Spacing. The spacing is the geometric distance between image
- * samples.
- */
- typedef typename Superclass::SpacingType SpacingType;
-
- /** Origin typedef support. The origin is the "fake" geometric
- * coordinates of the index (0,0). Also for use w/ filters designed
- * for normal images.
- */
- typedef typename Superclass::PointType PointType;
-
- /** A pointer to the pixel container. */
- typedef typename PixelContainer::Pointer PixelContainerPointer;
- typedef typename PixelContainer::ConstPointer PixelContainerConstPointer;
-
- /** Graft the data and information from one image to another. This
- * is a convenience method to setup a second image with all the meta
- * information of another image and use the same pixel
- * container. Note that this method is different than just using two
- * SmartPointers to the same image since separate DataObjects are
- * still maintained. This method is similar to
- * ImageSource::GraftOutput(). The implementation in ImageBase
- * simply calls CopyInformation() and copies the region ivars.
- * The implementation here refers to the superclass' implementation
- * and then copies over the pixel container. */
- virtual void Graft(const DataObject *data) ITK_OVERRIDE;
-
- /** \brief Get the continuous index from a physical point
- *
- * Returns true if the resulting index is within the image, false otherwise.
- * \sa Transform */
- template< typename TCoordRep >
- bool TransformPhysicalPointToContinuousIndex(
- const Point< TCoordRep, VDimension > & point,
- ContinuousIndex< TCoordRep, VDimension > & index) const
- {
- const RegionType & region = this->GetLargestPossibleRegion();
- const double maxLateral = region.GetSize(1) - 1;
-
- // Convert Cartesian coordinates into angular coordinates
- const TCoordRep lateral = std::atan(point[0] / point[1]);
- const TCoordRep radius = std::sqrt(point[0] * point[0] + point[1] * point[1] );
-
- // Convert the "proper" angular coordinates into index format
- index[0] = static_cast< TCoordRep >( ( ( radius - m_FirstSampleDistance )
- / m_RadiusSampleSize ) );
- index[1] = static_cast< TCoordRep >( ( lateral / m_LateralAngularSeparation )
- + ( maxLateral / 2.0 ) );
-
- // Now, check to see if the index is within allowed bounds
- const bool isInside = region.IsInside(index);
-
- return isInside;
- }
-
- /** Get the index (discrete) from a physical point.
- * Floating point index results are truncated to integers.
- * Returns true if the resulting index is within the image, false otherwise
- * \sa Transform */
- template< typename TCoordRep >
- bool TransformPhysicalPointToIndex(
- const Point< TCoordRep, VDimension > & point,
- IndexType & index) const
- {
- const RegionType & region = this->GetLargestPossibleRegion();
- const double maxLateral = region.GetSize(1) - 1;
-
- // Convert Cartesian coordinates into angular coordinates
- const TCoordRep lateral = std::atan(point[0] / point[1]);
- const TCoordRep radius = std::sqrt(point[0] * point[0] + point[1] * point[1] );
-
- // Convert the "proper" angular coordinates into index format
- index[0] = static_cast< IndexValueType >( ( ( radius - m_FirstSampleDistance )
- / m_RadiusSampleSize ) );
- index[1] = static_cast< IndexValueType >( ( lateral / m_LateralAngularSeparation )
- + ( maxLateral / 2.0 ) );
-
- // Now, check to see if the index is within allowed bounds
- const bool isInside = region.IsInside(index);
-
- return isInside;
- }
-
- /** Get a physical point (in the space which
- * the origin and spacing information comes from)
- * from a continuous index (in the index space)
- * \sa Transform */
- template< typename TCoordRep >
- void TransformContinuousIndexToPhysicalPoint(
- const ContinuousIndex< TCoordRep, VDimension > & index,
- Point< TCoordRep, VDimension > & point) const
- {
- const RegionType & region = this->GetLargestPossibleRegion();
- const double maxLateral = region.GetSize(1) - 1;
-
- // Convert the index into proper angular coordinates
- const TCoordRep radius = ( index[0] * m_RadiusSampleSize ) + m_FirstSampleDistance;
- const TCoordRep lateral = ( index[1] - ( maxLateral / 2.0 ) ) * m_LateralAngularSeparation;
-
- // Convert the angular coordinates into Cartesian coordinates
- point[0] = static_cast< TCoordRep >( radius * std::sin(lateral) );
- point[1] = static_cast< TCoordRep >( radius * std::cos(lateral) );
- }
-
- /** Get a physical point (in the space which
- * the origin and spacing information comes from)
- * from a discrete index (in the index space)
- *
- * \sa Transform */
- template< typename TCoordRep >
- void TransformIndexToPhysicalPoint(
- const IndexType & index,
- Point< TCoordRep, VDimension > & point) const
- {
- const RegionType & region = this->GetLargestPossibleRegion();
- const double maxLateral = region.GetSize(1) - 1;
-
- // Convert the index into proper angular coordinates
- const TCoordRep radius = ( index[0] * m_RadiusSampleSize ) + m_FirstSampleDistance;
- const TCoordRep lateral = ( index[1] - ( maxLateral / 2.0 ) ) * m_LateralAngularSeparation;
-
- // Convert the angular coordinates into Cartesian coordinates
- point[0] = static_cast< TCoordRep >( radius * std::sin(lateral) );
- point[1] = static_cast< TCoordRep >( radius * std::cos(lateral) );
- }
-
- /** Set/Get the number of radians between each lateral unit. */
- itkSetMacro(LateralAngularSeparation, double);
- itkGetConstMacro(LateralAngularSeparation, double);
-
- /** Set/Get the number of cartesian units between each unit along the R . */
- itkSetMacro(RadiusSampleSize, double);
- itkGetConstMacro(RadiusSampleSize, double);
-
- /** Set the distance to add to the radius. */
- itkSetMacro(FirstSampleDistance, double);
- itkGetConstMacro(FirstSampleDistance, double);
-
- template< typename TCoordRep >
- void TransformLocalVectorToPhysicalVector(
- FixedArray< TCoordRep, VDimension > & ) const
- {}
-
- template< typename TCoordRep >
- void TransformPhysicalVectorToLocalVector(
- const FixedArray< TCoordRep, VDimension > & ,
- FixedArray< TCoordRep, VDimension > & ) const
- {}
-
-protected:
- CurvilinearArraySpecialCoordinatesImage()
- {
- m_RadiusSampleSize = 1;
- m_LateralAngularSeparation = 1 * ( 2.0 * vnl_math::pi / 360.0 ); // 1
- // degree
- m_FirstSampleDistance = 0;
- }
-
- virtual ~CurvilinearArraySpecialCoordinatesImage() {}
- virtual void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;
-
-private:
- CurvilinearArraySpecialCoordinatesImage(const Self &); // purposely not implemented
- void operator=(const Self &); // purposely not implemented
-
- double m_LateralAngularSeparation; // in radians
- double m_RadiusSampleSize;
- double m_FirstSampleDistance;
-};
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkCurvilinearArraySpecialCoordinatesImage.hxx"
-#endif
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.hxx
deleted file mode 100644
index f543e172a0..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkCurvilinearArraySpecialCoordinatesImage.hxx
+++ /dev/null
@@ -1,98 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-/*=========================================================================
- *
- * Portions of this file are subject to the VTK Toolkit Version 3 copyright.
- *
- * Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
- *
- * For complete copyright, license and disclaimer of warranty information
- * please refer to the NOTICE file at the top of the ITK source tree.
- *
- *=========================================================================*/
-#ifndef itkCurvilinearArraySpecialCoordinatesImage_hxx
-#define itkCurvilinearArraySpecialCoordinatesImage_hxx
-#include "itkCurvilinearArraySpecialCoordinatesImage.h"
-
-namespace itk
-{
-
-template< typename TPixel, unsigned int VDimension >
-void
-CurvilinearArraySpecialCoordinatesImage< TPixel, VDimension >
-::PrintSelf(std::ostream & os, Indent indent) const
-{
- Superclass::PrintSelf(os, indent);
-
- os << indent
- << "RadiusSampleSize = " << m_RadiusSampleSize
- << std::endl;
- os << indent
- << "LateralAngularSeparation = "
- << m_LateralAngularSeparation
- << std::endl;
- os << indent
- << "FirstSampleDistance = "
- << m_FirstSampleDistance
- << std::endl;
-}
-
-
-template< typename TPixel, unsigned int VDimension >
-void
-CurvilinearArraySpecialCoordinatesImage< TPixel, VDimension >
-::Graft(const DataObject *data)
-{
- // call the superclass' implementation
- Superclass::Graft(data);
-
- if ( data )
- {
- // Attempt to cast data to a CurvilinearArraySpecialCoordinatesImage
- const Self * const imgData = dynamic_cast< const Self * >( data );
-
- if ( imgData )
- {
- // Now copy anything remaining that is needed
- this->SetPixelContainer( const_cast< PixelContainer * >
- ( imgData->GetPixelContainer() ) );
- }
- else
- {
- // pointer could not be cast back down
- itkExceptionMacro( << "itk::Image::Graft() cannot cast "
- << typeid( data ).name() << " to "
- << typeid( const Self * ).name() );
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h
deleted file mode 100644
index c363c456f4..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h
+++ /dev/null
@@ -1,117 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DComplexConjugateToRealImageFilter_h
-#define itkFFT1DComplexConjugateToRealImageFilter_h
-
-#include <complex>
-
-#include "itkImageToImageFilter.h"
-#include "itkImageRegionSplitterDirection.h"
-
-namespace itk
-{
-/** \class FFT1DComplexConjugateToRealImageFilter
- * \brief Perform the Fast Fourier Transform, in the reverse direction, with
- * real output, but only along one dimension.
- *
- * \ingroup FourierTransform
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=Image< typename NumericTraits< typename TInputImage::PixelType >::ValueType, TInputImage::ImageDimension > >
-class FFT1DComplexConjugateToRealImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- typedef FFT1DComplexConjugateToRealImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension );
-
- itkTypeMacro( FFT1DComplexConjugateToRealImageFilter, ImageToImageFilter );
-
- /** Customized object creation methods that support configuration-based
- * selection of FFT implementation.
- *
- * Default implementation is VnlFFT1D.
- */
- static Pointer New(void);
-
- /** Get the direction in which the filter is to be applied. */
- itkGetMacro(Direction, unsigned int);
-
- /** Set the direction in which the filter is to be applied. */
- itkSetClampMacro(Direction, unsigned int, 0, ImageDimension - 1);
-
-protected:
- FFT1DComplexConjugateToRealImageFilter();
- ~FFT1DComplexConjugateToRealImageFilter() override {}
-
- void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- void GenerateInputRequestedRegion() ITK_OVERRIDE;
- void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- void BeforeThreadedGenerateData() ITK_OVERRIDE;
-
- /** Override to return a splitter that does not split along the direction we
- * are performing the transform. */
- const ImageRegionSplitterBase* GetImageRegionSplitter() const ITK_OVERRIDE;
-
- /** Direction in which the filter is to be applied
- * this should be in the range [0,ImageDimension-1]. */
- unsigned int m_Direction;
-
-private:
- FFT1DComplexConjugateToRealImageFilter( const Self& );
- void operator=( const Self& );
-
- ImageRegionSplitterDirection::Pointer m_ImageRegionSplitter;
-};
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#ifndef itkVnlFFT1DComplexConjugateToRealImageFilter_h
-#ifndef itkVnlFFT1DComplexConjugateToRealImageFilter_hxx
-#ifndef itkFFTW1DComplexConjugateToRealImageFilter_h
-#ifndef itkFFTW1DComplexConjugateToRealImageFilter_hxx
-#include "itkFFT1DComplexConjugateToRealImageFilter.hxx"
-#endif
-#endif
-#endif
-#endif
-#endif
-
-#endif // itkFFT1DComplexConjugateToRealImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.hxx
deleted file mode 100644
index e2c87d77da..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.hxx
+++ /dev/null
@@ -1,204 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DComplexConjugateToRealImageFilter_hxx
-#define itkFFT1DComplexConjugateToRealImageFilter_hxx
-
-#include "itkFFT1DComplexConjugateToRealImageFilter.h"
-
-#include "itkVnlFFT1DComplexConjugateToRealImageFilter.h"
-
-#if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
-#include "itkFFTW1DComplexConjugateToRealImageFilter.h"
-#endif
-
-#include "itkMetaDataDictionary.h"
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage >
-typename FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >::Pointer
-FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::New()
-{
- Pointer smartPtr = ::itk::ObjectFactory< Self >::Create();
-
-#ifdef ITK_USE_FFTWD
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( double ) )
- {
- smartPtr = dynamic_cast< Self* >(
- FFTW1DComplexConjugateToRealImageFilter< double, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-#ifdef ITK_USE_FFTWF
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( float ) )
- {
- smartPtr = dynamic_cast<Self *>(
- FFTW1DComplexConjugateToRealImageFilter< float, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-
- if( smartPtr.IsNull() )
- {
- smartPtr = VnlFFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
- ::New().GetPointer();
- }
-
- return smartPtr;
-}
-
-
-template < typename TInputImage, typename TOutputImage >
-FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::FFT1DComplexConjugateToRealImageFilter():
- m_Direction( 0 )
-{
- this->m_ImageRegionSplitter = ImageRegionSplitterDirection::New();
-}
-
-
-template <typename TInputImage, typename TOutputImage>
-const ImageRegionSplitterBase*
-FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::GetImageRegionSplitter() const
-{
- return this->m_ImageRegionSplitter.GetPointer();
-}
-
-
-template<typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- this->m_ImageRegionSplitter->SetDirection( this->GetDirection() );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- typename InputImageType::Pointer inputPtr =
- const_cast<InputImageType *> (this->GetInput());
- typename OutputImageType::Pointer outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->m_Direction;
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast<OutputImageType*>( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- enlargedSize[this->m_Direction] = outputLargeSize[this->m_Direction];
- enlargedIndex[this->m_Direction] = outputLargeIndex[this->m_Direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Direction: " << m_Direction << std::endl;
-}
-
-} // end namespace itk
-
-#endif // itkFFT1DComplexConjugateToRealImageFilter_hxx
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h
deleted file mode 100644
index 9c130d753e..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h
+++ /dev/null
@@ -1,138 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DComplexToComplexImageFilter_h
-#define itkFFT1DComplexToComplexImageFilter_h
-
-#include <complex>
-
-#include "itkImage.h"
-#include "itkImageToImageFilter.h"
-#include "itkImageRegionSplitterDirection.h"
-
-namespace itk
-{
-/** \class FFT1DComplexToComplexImageFilter
- * \brief Perform the Fast Fourier Transform, complex input to complex output,
- * but only along one dimension.
- *
- * The direction of the transform, 'Forward' or 'Inverse', can be set with
- * SetTransformDirection() and GetTransformDirection().
- *
- * The dimension along which to apply to filter can be specified with
- * SetDirection() and GetDirection().
- *
- * \ingroup FourierTransform
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=TInputImage >
-class FFT1DComplexToComplexImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- typedef FFT1DComplexToComplexImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension );
-
- itkTypeMacro( FFT1DComplexToComplexImageFilter, ImageToImageFilter );
-
- /** Customized object creation methods that support configuration-based
- * selection of FFT implementation.
- *
- * Default implementation is VnlFFT1D.
- */
- static Pointer New();
-
- /** Transform direction. */
- typedef enum { DIRECT = 1, INVERSE } TransformDirectionType;
-
- /** Set/Get the direction in which the transform will be applied.
- * By selecting DIRECT, this filter will perform a direct (forward) Fourier
- * Transform.
- * By selecting INVERSE, this filter will perform an inverse Fourier
- * Transform. */
- itkSetMacro( TransformDirection, TransformDirectionType );
- itkGetConstMacro( TransformDirection, TransformDirectionType );
-
- /** Get the direction in which the filter is to be applied. */
- itkGetMacro(Direction, unsigned int);
-
- /** Set the direction in which the filter is to be applied. */
- itkSetClampMacro(Direction, unsigned int, 0, ImageDimension - 1);
-
-protected:
- FFT1DComplexToComplexImageFilter();
- ~FFT1DComplexToComplexImageFilter() override {}
-
- void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- void GenerateInputRequestedRegion() ITK_OVERRIDE;
- void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- void BeforeThreadedGenerateData() ITK_OVERRIDE;
-
- /** Override to return a splitter that does not split along the direction we
- * are performing the transform. */
- const ImageRegionSplitterBase* GetImageRegionSplitter() const ITK_OVERRIDE;
-
- /** Direction in which the filter is to be applied
- * this should be in the range [0,ImageDimension-1]. */
- unsigned int m_Direction;
-
- /** Direction to apply the transform (forward/inverse). */
- TransformDirectionType m_TransformDirection;
-
-private:
- FFT1DComplexToComplexImageFilter( const Self& );
- void operator=( const Self& );
-
- ImageRegionSplitterDirection::Pointer m_ImageRegionSplitter;
-};
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_h
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_hxx
-#ifndef itkFFTW1DComplexToComplexImageFilter_h
-#ifndef itkFFTW1DComplexToComplexImageFilter_hxx
-#include "itkFFT1DComplexToComplexImageFilter.hxx"
-#endif
-#endif
-#endif
-#endif
-#endif
-
-#endif // itkFFT1DComplexToComplexImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx
deleted file mode 100644
index af4c9d7b1c..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx
+++ /dev/null
@@ -1,206 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DComplexToComplexImageFilter_hxx
-#define itkFFT1DComplexToComplexImageFilter_hxx
-
-#include "itkFFT1DComplexToComplexImageFilter.h"
-
-#include "itkVnlFFT1DComplexToComplexImageFilter.h"
-
-#if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
-#include "itkFFTW1DComplexToComplexImageFilter.h"
-#endif
-
-#include "itkMetaDataDictionary.h"
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage >
-typename FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >::Pointer
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::New()
-{
- Pointer smartPtr = ::itk::ObjectFactory< Self >::Create();
-
-#ifdef ITK_USE_FFTWD
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( double ) )
- {
- smartPtr = dynamic_cast< Self* >(
- FFTW1DComplexToComplexImageFilter< double, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-#ifdef ITK_USE_FFTWF
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( float ) )
- {
- smartPtr = dynamic_cast<Self *>(
- FFTW1DComplexToComplexImageFilter< float, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-
- if( smartPtr.IsNull() )
- {
- smartPtr = VnlFFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
- ::New().GetPointer();
- }
-
- return smartPtr;
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::FFT1DComplexToComplexImageFilter():
- m_Direction(0), m_TransformDirection( DIRECT )
-{
- this->m_ImageRegionSplitter = ImageRegionSplitterDirection::New();
-}
-
-
-template <typename TInputImage, typename TOutputImage>
-const ImageRegionSplitterBase*
-FFT1DComplexToComplexImageFilter < TInputImage, TOutputImage >
-::GetImageRegionSplitter(void) const
-{
- return this->m_ImageRegionSplitter.GetPointer();
-}
-
-
-template<typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter < TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- this->m_ImageRegionSplitter->SetDirection( this->GetDirection() );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- typename InputImageType::Pointer inputPtr =
- const_cast<InputImageType *> (this->GetInput());
- typename OutputImageType::Pointer outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->m_Direction;
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast<OutputImageType*>( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- enlargedSize[this->m_Direction] = outputLargeSize[this->m_Direction];
- enlargedIndex[this->m_Direction] = outputLargeIndex[this->m_Direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Direction: " << m_Direction << std::endl;
- os << indent << "TransformDirection: " << m_TransformDirection << std::endl;
-}
-
-
-} // end namespace itk
-
-#endif // itkFFT1DComplexToComplexImageFilter_hxx
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h
deleted file mode 100644
index a388268a68..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h
+++ /dev/null
@@ -1,119 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DRealToComplexConjugateImageFilter_h
-#define itkFFT1DRealToComplexConjugateImageFilter_h
-
-#include <complex>
-
-#include "itkImageToImageFilter.h"
-#include "itkImageRegionSplitterDirection.h"
-
-namespace itk
-{
-/** \class FFT1DRealToComplexConjugateImageFilter
- * \brief Perform the Fast Fourier Transform, in the forward direction, with
- * real inputs, but only along one dimension.
- *
- * \ingroup FourierTransform
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
-class FFT1DRealToComplexConjugateImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
-
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- typedef FFT1DRealToComplexConjugateImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkStaticConstMacro( ImageDimension, unsigned int, InputImageType::ImageDimension );
-
- itkTypeMacro( FFT1DRealToComplexConjugateImageFilter, ImageToImageFilter );
-
- /** Customized object creation methods that support configuration-based
- * selection of FFT implementation.
- *
- * Default implementation is VnlFFT1D.
- */
- static Pointer New();
-
- /** Get the direction in which the filter is to be applied. */
- itkGetMacro(Direction, unsigned int);
-
- /** Set the direction in which the filter is to be applied. */
- itkSetClampMacro(Direction, unsigned int, 0, ImageDimension - 1);
-
-protected:
- FFT1DRealToComplexConjugateImageFilter();
- ~FFT1DRealToComplexConjugateImageFilter() override {}
-
- void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- void GenerateInputRequestedRegion() ITK_OVERRIDE;
- void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- void BeforeThreadedGenerateData() ITK_OVERRIDE;
-
- /** Override to return a splitter that does not split along the direction we
- * are performing the transform. */
- const ImageRegionSplitterBase* GetImageRegionSplitter() const ITK_OVERRIDE;
-
-private:
- FFT1DRealToComplexConjugateImageFilter( const Self& );
- void operator=( const Self& );
-
- ImageRegionSplitterDirection::Pointer m_ImageRegionSplitter;
-
- /** Direction in which the filter is to be applied
- * this should be in the range [0,ImageDimension-1]. */
- unsigned int m_Direction;
-
-};
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_h
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_hxx
-#ifndef itkFFTW1DRealToComplexConjugateImageFilter_h
-#ifndef itkFFTW1DRealToComplexConjugateImageFilter_hxx
-#include "itkFFT1DRealToComplexConjugateImageFilter.hxx"
-#endif
-#endif
-#endif
-#endif
-#endif
-
-#endif // itkFFT1DRealToComplexConjugateImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx
deleted file mode 100644
index 469f702479..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx
+++ /dev/null
@@ -1,203 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DRealToComplexConjugateImageFilter_hxx
-#define itkFFT1DRealToComplexConjugateImageFilter_hxx
-
-#include "itkFFT1DRealToComplexConjugateImageFilter.h"
-
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.h"
-
-#if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
-#include "itkFFTW1DRealToComplexConjugateImageFilter.h"
-#endif
-
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage >
-typename FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >::Pointer
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::New()
-{
- Pointer smartPtr = ::itk::ObjectFactory< Self >::Create();
-
-#ifdef ITK_USE_FFTWD
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( double ) )
- {
- smartPtr = dynamic_cast< Self* >(
- FFTW1DRealToComplexConjugateImageFilter< double, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-#ifdef ITK_USE_FFTWF
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( float ) )
- {
- smartPtr = dynamic_cast<Self *>(
- FFTW1DRealToComplexConjugateImageFilter< float, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-
- if( smartPtr.IsNull() )
- {
- smartPtr = VnlFFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
- ::New().GetPointer();
- }
-
- return smartPtr;
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::FFT1DRealToComplexConjugateImageFilter():
- m_Direction( 0 )
-{
- this->m_ImageRegionSplitter = ImageRegionSplitterDirection::New();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-const ImageRegionSplitterBase*
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::GetImageRegionSplitter() const
-{
- return this->m_ImageRegionSplitter.GetPointer();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- this->m_ImageRegionSplitter->SetDirection( this->GetDirection() );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- typename InputImageType::Pointer inputPtr =
- const_cast<InputImageType *> (this->GetInput());
- typename OutputImageType::Pointer outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->m_Direction;
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter < TInputImage, TOutputImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast< OutputImageType * >( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- enlargedSize[this->m_Direction] = outputLargeSize[this->m_Direction];
- enlargedIndex[this->m_Direction] = outputLargeIndex[this->m_Direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter < TInputImage, TOutputImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Direction: " << m_Direction << std::endl;
-}
-
-} // end namespace itk
-
-#endif // itkFFT1DRealToComplexConjugateImageFilter_hxx
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.h
deleted file mode 100644
index 976f59ac76..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.h
+++ /dev/null
@@ -1,139 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkRegionFromReferenceImageFilter_h
-#define itkRegionFromReferenceImageFilter_h
-
-#include "itkExtractImageFilter.h"
-
-namespace itk
-{
-
-/** \class RegionFromReferenceImageFilter
- * \brief Decrease the image size by cropping the image by an itk::Size at
- * both the upper and lower bounds of the largest possible region.
- *
- * RegionFromReferenceImageFilter changes the image boundary of an image by removing
- * pixels outside the target region. The target region is not specified in
- * advance, but calculated in BeforeThreadedGenerateData().
- *
- * This filter uses ExtractImageFilter to perform the cropping.
- *
- * \ingroup GeometricTransforms
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=TInputImage >
-class RegionFromReferenceImageFilter:
- public ExtractImageFilter<TInputImage,TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef RegionFromReferenceImageFilter Self;
- typedef ExtractImageFilter<TInputImage,TOutputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(RegionFromReferenceImageFilter, ExtractImageFilter);
-
- /** Typedef to describe the output and input image region types. */
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::InputImageRegionType InputImageRegionType;
-
- /** Typedef to describe the type of pixel. */
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
- typedef typename Superclass::InputImagePixelType InputImagePixelType;
-
- /** Typedef to describe the output and input image index and size types. */
- typedef typename Superclass::OutputImageIndexType OutputImageIndexType;
- typedef typename Superclass::InputImageIndexType InputImageIndexType;
- typedef typename Superclass::OutputImageSizeType OutputImageSizeType;
- typedef typename Superclass::InputImageSizeType InputImageSizeType;
- typedef InputImageSizeType SizeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- Superclass::InputImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- Superclass::OutputImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- Superclass::OutputImageDimension);
-
- typedef ImageBase< itkGetStaticConstMacro( ImageDimension ) > ReferenceImageType;
-
- /** Copy the output information from another Image. */
- void SetReferenceImage ( const ReferenceImageType *image );
-
- const ReferenceImageType * GetReferenceImage() const;
-
- /** Set the input image */
- void SetInput1(const TInputImage *input)
- {
- this->SetInput( input );
- }
-
- /** Set the reference image */
- void SetInput2(const ReferenceImageType *input)
- {
- this->SetReferenceImage( input );
- }
-
-
-#ifdef ITK_USE_CONCEPT_CHECKING
- /** Begin concept checking */
- itkConceptMacro(InputConvertibleToOutputCheck,
- (Concept::Convertible<InputImagePixelType, OutputImagePixelType>));
- itkConceptMacro(SameDimensionCheck,
- (Concept::SameDimension<InputImageDimension, OutputImageDimension>));
- /** End concept checking */
-#endif
-
-protected:
- RegionFromReferenceImageFilter()
- {
- this->SetNumberOfRequiredInputs(2);
- }
- ~RegionFromReferenceImageFilter() override {}
-
- void GenerateOutputInformation() ITK_OVERRIDE;
-
-private:
- RegionFromReferenceImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkRegionFromReferenceImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx
deleted file mode 100644
index 277794c7f2..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkRegionFromReferenceImageFilter_hxx
-#define itkRegionFromReferenceImageFilter_hxx
-
-#include "itkRegionFromReferenceImageFilter.h"
-
-namespace itk
-{
-
-template <typename TInputImage, typename TOutputImage>
-void
-RegionFromReferenceImageFilter<TInputImage, TOutputImage>
-::GenerateOutputInformation()
-{
- if( !this->GetInput() || !this->GetReferenceImage() )
- {
- return;
- }
-
- // Superclass::Superclass::GenerateOutputInformation();
- this->SetExtractionRegion( this->GetReferenceImage()->GetLargestPossibleRegion() );
- Superclass::GenerateOutputInformation();
-}
-
-
-template <typename TInputImage, typename TOutputImage>
-void
-RegionFromReferenceImageFilter<TInputImage,TOutputImage>
-::SetReferenceImage ( const ReferenceImageType *image )
-{
- itkDebugMacro("setting input ReferenceImage to " << image);
- if( image != static_cast<const ReferenceImageType *>(this->GetInput( 1 )) )
- {
- this->ProcessObject::SetNthInput(1, const_cast< ReferenceImageType *>( image ) );
- this->Modified();
- }
-}
-
-
-template <typename TInputImage, typename TOutputImage>
-const typename RegionFromReferenceImageFilter<TInputImage,TOutputImage>::ReferenceImageType *
-RegionFromReferenceImageFilter<TInputImage,TOutputImage>
-::GetReferenceImage() const
-{
- Self * surrogate = const_cast< Self * >( this );
-
- const DataObject * input = surrogate->ProcessObject::GetInput(1);
-
- const ReferenceImageType * referenceImage = static_cast<const ReferenceImageType *>( input );
-
- return referenceImage;
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.h
deleted file mode 100644
index cf23fc58bf..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.h
+++ /dev/null
@@ -1,135 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkSpectra1DImageFilter_h
-#define itkSpectra1DImageFilter_h
-
-#include "itkImageToImageFilter.h"
-#include "itkDefaultConvertPixelTraits.h"
-#include "itkImageRegionConstIterator.h"
-
-#include "vnl/algo/vnl_fft_base.h"
-#include "vnl/algo/vnl_fft_1d.h"
-
-#include <utility>
-#include <map>
-
-#include "itkSpectra1DSupportWindowImageFilter.h"
-
-namespace itk
-{
-
-/** \class Spectra1DImageFilter
- * \brief Generate an image of local spectra.
- *
- * This image takes in the input image and image that has indexes of the local
- * lines used to compute the local spectra.
- *
- * \ingroup Ultrasound
- *
- * \sa Spectra1DSupportWindowImageFilter
- */
-template< typename TInputImage, typename TSupportWindowImage, typename TOutputImage >
-class Spectra1DImageFilter:
- public ImageToImageFilter< TInputImage,
- TOutputImage >
-{
-public:
- itkStaticConstMacro( ImageDimension, unsigned int, TInputImage::ImageDimension );
-
- typedef TInputImage InputImageType;
- typedef TSupportWindowImage SupportWindowImageType;
- typedef TOutputImage OutputImageType;
-
- typedef typename DefaultConvertPixelTraits< typename OutputImageType::PixelType >::ComponentType
- ScalarType;
-
- /** Standard class typedefs. */
- typedef Spectra1DImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkTypeMacro( Spectra1DImageFilter, ImageToImageFilter );
- itkNewMacro( Self );
-
- /** Set/get the input image containning the support window for local spectra
- * computation. */
- itkSetInputMacro( SupportWindowImage, SupportWindowImageType );
- itkGetInputMacro( SupportWindowImage, SupportWindowImageType );
-
-protected:
- Spectra1DImageFilter();
- virtual ~Spectra1DImageFilter() {};
-
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- virtual void GenerateOutputInformation() ITK_OVERRIDE;
- virtual void BeforeThreadedGenerateData() ITK_OVERRIDE;
- virtual void ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId ) ITK_OVERRIDE;
-
-private:
- Spectra1DImageFilter( const Self & ); // purposely not implemented
- void operator=( const Self & ); // purposely not implemented
-
- typedef vcl_complex< ScalarType > ComplexType;
- typedef vnl_vector< ComplexType > ComplexVectorType;
- typedef vnl_vector< ScalarType > SpectraVectorType;
- typedef typename InputImageType::IndexType IndexType;
- typedef std::pair< IndexType, SpectraVectorType > SpectraLineType;
- typedef std::deque< SpectraLineType > SpectraLinesContainerType;
- typedef typename SupportWindowImageType::PixelType SupportWindowType;
- typedef ImageRegionConstIterator< InputImageType > InputImageIteratorType;
- typedef vnl_fft_1d< ScalarType > FFT1DType;
-
- typedef Spectra1DSupportWindowImageFilter< OutputImageType > Spectra1DSupportWindowFilterType;
- typedef typename Spectra1DSupportWindowFilterType::FFT1DSizeType FFT1DSizeType;
-
- typedef std::map< FFT1DSizeType, SpectraVectorType > LineWindowMapType;
-
- struct PerThreadData
- {
- ComplexVectorType ComplexVector;
- SpectraVectorType SpectraVector;
- typename InputImageType::SizeType LineImageRegionSize;
- LineWindowMapType LineWindowMap;
- };
- typedef std::vector< PerThreadData > PerThreadDataContainerType;
- PerThreadDataContainerType m_PerThreadDataContainer;
-
- SpectraLineType ComputeSpectra( const IndexType & lineIndex, ThreadIdType threadId );
- void AddLineWindow( FFT1DSizeType length, LineWindowMapType & lineWindowMap );
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkSpectra1DImageFilter.hxx"
-#endif
-
-#endif // itkSpectra1DImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.hxx
deleted file mode 100644
index 7830428ef8..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DImageFilter.hxx
+++ /dev/null
@@ -1,273 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkSpectra1DImageFilter_hxx
-#define itkSpectra1DImageFilter_hxx
-
-#include "itkSpectra1DImageFilter.h"
-
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkImageRegionConstIterator.h"
-#include "itkMetaDataObject.h"
-
-#include "itkSpectra1DSupportWindowImageFilter.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TSupportWindowImage, typename TOutputImage >
-Spectra1DImageFilter< TInputImage, TSupportWindowImage, TOutputImage >
-::Spectra1DImageFilter()
-{
- this->AddRequiredInputName( "SupportWindowImage" );
-}
-
-
-template< typename TInputImage, typename TSupportWindowImage, typename TOutputImage >
-void
-Spectra1DImageFilter< TInputImage, TSupportWindowImage, TOutputImage >
-::GenerateOutputInformation()
-{
- Superclass::GenerateOutputInformation();
-
- const SupportWindowImageType * supportWindowImage = this->GetSupportWindowImage();
- const MetaDataDictionary & dict = supportWindowImage->GetMetaDataDictionary();
- FFT1DSizeType fft1DSize = 32;
- ExposeMetaData< FFT1DSizeType >( dict, "FFT1DSize", fft1DSize );
- const FFT1DSizeType spectraComponents = fft1DSize / 2 - 1;
-
- OutputImageType * output = this->GetOutput();
- output->SetVectorLength( spectraComponents );
-}
-
-
-template< typename TInputImage, typename TSupportWindowImage, typename TOutputImage >
-void
-Spectra1DImageFilter< TInputImage, TSupportWindowImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- const SupportWindowImageType * supportWindowImage = this->GetSupportWindowImage();
- const MetaDataDictionary & dict = supportWindowImage->GetMetaDataDictionary();
- FFT1DSizeType fft1DSize = 32;
- ExposeMetaData< FFT1DSizeType >( dict, "FFT1DSize", fft1DSize );
- const FFT1DSizeType spectraComponents = fft1DSize / 2 - 1;
-
- const ThreadIdType numberOfThreads = this->GetNumberOfThreads();
- this->m_PerThreadDataContainer.resize( numberOfThreads );
- for( ThreadIdType threadId = 0; threadId < numberOfThreads; ++threadId )
- {
- PerThreadData & perThreadData = this->m_PerThreadDataContainer[threadId];
- perThreadData.ComplexVector.set_size( fft1DSize );
- perThreadData.SpectraVector.set_size( spectraComponents );
- perThreadData.LineImageRegionSize.Fill( 1 );
- perThreadData.LineImageRegionSize[0] = fft1DSize;
- }
-}
-
-
-template< typename TInputImage, typename TSupportWindowImage, typename TOutputImage >
-void
-Spectra1DImageFilter< TInputImage, TSupportWindowImage, TOutputImage >
-::AddLineWindow( FFT1DSizeType length, LineWindowMapType & lineWindowMap )
-{
- if( lineWindowMap.count( length ) == 1 )
- {
- return;
- }
- // Currently using a Hamming Window
- SpectraVectorType window( length );
- ScalarType sum = NumericTraits< ScalarType >::ZeroValue();
- const ScalarType twopi = 2 * vnl_math::pi;
- for( FFT1DSizeType sample = 0; sample < length; ++sample )
- {
- window[sample] = 0.54 + 0.46 * std::cos( (twopi * sample) / (length - 1) );
- sum += window[sample];
- }
- for( FFT1DSizeType sample = 0; sample < length; ++sample )
- {
- window[sample] /= sum;
- }
- lineWindowMap[length] = window;
-}
-
-
-template< typename TInputImage, typename TSupportWindowImage, typename TOutputImage >
-typename Spectra1DImageFilter< TInputImage, TSupportWindowImage, TOutputImage >::SpectraLineType
-Spectra1DImageFilter< TInputImage, TSupportWindowImage, TOutputImage >
-::ComputeSpectra( const IndexType & lineIndex, ThreadIdType threadId )
-{
- const InputImageType * input = this->GetInput();
- PerThreadData & perThreadData = this->m_PerThreadDataContainer[threadId];
-
- const FFT1DSizeType fft1DSize = static_cast< FFT1DSizeType >( perThreadData.ComplexVector.size() );
-
- const typename InputImageType::RegionType lineRegion( lineIndex, perThreadData.LineImageRegionSize );
- InputImageIteratorType inputIt( input, lineRegion );
- inputIt.GoToBegin();
- perThreadData.ComplexVector.fill( 0 );
- typename ComplexVectorType::iterator complexVectorIt = perThreadData.ComplexVector.begin();
- typename SpectraVectorType::const_iterator windowIt = perThreadData.LineWindowMap[fft1DSize].begin();
- while( !inputIt.IsAtEnd() )
- {
- *complexVectorIt = inputIt.Value() * *windowIt;
- ++inputIt;
- ++complexVectorIt;
- ++windowIt;
- }
- FFT1DType fft1D( fft1DSize );
- fft1D.bwd_transform( perThreadData.ComplexVector );
- typename ComplexVectorType::const_iterator complexVectorConstIt = perThreadData.ComplexVector.begin();
- typename SpectraVectorType::iterator spectraVectorIt = perThreadData.SpectraVector.begin();
- // drop DC component
- ++complexVectorConstIt;
- const size_t highFreq = perThreadData.SpectraVector.size();
- for( size_t freq = 0; freq < highFreq; ++freq )
- {
- spectraVectorIt[freq] = std::real(*complexVectorConstIt * std::conj(*complexVectorConstIt));
- ++complexVectorConstIt;
- }
- return std::make_pair( lineIndex, perThreadData.SpectraVector );
-}
-
-
-template< typename TInputImage, typename TSupportWindowImage, typename TOutputImage >
-void
-Spectra1DImageFilter< TInputImage, TSupportWindowImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId )
-{
- OutputImageType * output = this->GetOutput();
- const SupportWindowImageType * supportWindowImage = this->GetSupportWindowImage();
-
- typedef ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- OutputIteratorType outputIt( output, outputRegionForThread );
- outputIt.SetDirection( 1 );
-
- const MetaDataDictionary & dict = supportWindowImage->GetMetaDataDictionary();
- FFT1DSizeType fft1DSize = 32;
- ExposeMetaData< FFT1DSizeType >( dict, "FFT1DSize", fft1DSize );
- PerThreadData & perThreadData = this->m_PerThreadDataContainer[threadId];
- this->AddLineWindow( fft1DSize, perThreadData.LineWindowMap );
-
- ComplexVectorType complexVector( fft1DSize );
- SpectraVectorType spectraVector( fft1DSize );
- typename InputImageType::SizeType lineImageRegionSize;
- lineImageRegionSize.Fill( 1 );
- lineImageRegionSize[0] = fft1DSize;
- vnl_fft_1d< ScalarType > fft1D( fft1DSize );
- SpectraLinesContainerType spectraLines;
-
- typedef ImageLinearConstIteratorWithIndex< SupportWindowImageType > SupportWindowIteratorType;
- SupportWindowIteratorType supportWindowIt( supportWindowImage, outputRegionForThread );
- supportWindowIt.SetDirection( 1 );
-
- for( outputIt.GoToBegin(), supportWindowIt.GoToBegin();
- !outputIt.IsAtEnd();
- outputIt.NextLine(), supportWindowIt.NextLine() )
- {
- spectraLines.clear();
- while( ! outputIt.IsAtEndOfLine() )
- {
- // Compute the per line spectra.
- const SupportWindowType & supportWindow = supportWindowIt.Value();
- if( spectraLines.size() == 0 ) // first window in this lateral direction
- {
- const typename SupportWindowType::const_iterator windowLineEnd = supportWindow.end();
- for( typename SupportWindowType::const_iterator windowLine = supportWindow.begin();
- windowLine != windowLineEnd;
- ++windowLine )
- {
- const IndexType & lineIndex = *windowLine;
- const SpectraLineType & spectraLine = this->ComputeSpectra( lineIndex, threadId );
- spectraLines.push_back( spectraLine );
- }
- }
- else // subsequent window along a line
- {
- const IndexValueType desiredFirstLine = supportWindow[0][1];
- while( spectraLines[0].first[1] < desiredFirstLine )
- {
- spectraLines.pop_front();
- }
- const typename SupportWindowType::const_iterator windowLineEnd = supportWindow.end();
- typename SpectraLinesContainerType::iterator spectraLinesIt = spectraLines.begin();
- const typename SpectraLinesContainerType::iterator spectraLinesEnd = spectraLines.end();
- for( typename SupportWindowType::const_iterator windowLine = supportWindow.begin();
- windowLine != windowLineEnd;
- ++windowLine )
- {
- const IndexType & lineIndex = *windowLine;
- if( spectraLinesIt == spectraLinesEnd ) // past the end of the previously processed lines
- {
- const SpectraLineType & spectraLine = this->ComputeSpectra( lineIndex, threadId );
- spectraLines.push_back( spectraLine );
- }
- else if( lineIndex[1] == (spectraLinesIt->first)[1] ) // one of the same lines that was previously computed
- {
- if( lineIndex[0] != (spectraLinesIt->first)[0] )
- {
- const SpectraLineType & spectraLine = this->ComputeSpectra( lineIndex, threadId );
- *spectraLinesIt = spectraLine;
- }
- ++spectraLinesIt;
- }
- else
- {
- itkExceptionMacro( "Unexpected line" );
- }
- }
- }
-
- const size_t spectraLinesCount = spectraLines.size();
- this->AddLineWindow( spectraLinesCount, perThreadData.LineWindowMap );
- typename OutputImageType::PixelType outputPixel;
- outputPixel.SetSize( fft1DSize );
- outputPixel.Fill( NumericTraits< ScalarType >::ZeroValue() );
- typename SpectraVectorType::const_iterator windowIt = perThreadData.LineWindowMap[spectraLinesCount].begin();
- for( size_t line = 0; line < spectraLinesCount; ++line )
- {
- typename SpectraVectorType::const_iterator spectraIt = spectraLines[line].second.begin();
- for( FFT1DSizeType sample = 0; sample < fft1DSize; ++sample )
- {
- outputPixel[sample] += *windowIt * *spectraIt;
- ++spectraIt;
- }
- ++windowIt;
- }
- outputIt.Set( outputPixel );
-
- ++outputIt;
- ++supportWindowIt;
- }
- }
-}
-
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.h
deleted file mode 100644
index d9b0d65807..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.h
+++ /dev/null
@@ -1,113 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkSpectra1DSupportWindowImageFilter_h
-#define itkSpectra1DSupportWindowImageFilter_h
-
-#include <deque>
-
-#include "itkImageToImageFilter.h"
-
-namespace itk
-{
-
-/** \class Spectra1DSupportWindowImageFilter
- * \brief Generate an image of local spectra computation support windows.
- *
- * The information from the input image is used to determine the output image
- * information. The pixel value of the input image is used to specify the
- * nominal number of lines on either side of the central FFT line to add to
- * the window. The nominal size of the 1D FFT is specified with SetFFTSize()
- *
- * The overlap between windows is specified with SetStep(). By default, the
- * Step is only one sample.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage >
-class Spectra1DSupportWindowImageFilter:
- public ImageToImageFilter< TInputImage,
- Image< std::deque< typename TInputImage::IndexType >, TInputImage::ImageDimension > >
-{
-public:
- itkStaticConstMacro( ImageDimension, unsigned int, TInputImage::ImageDimension );
-
- typedef TInputImage InputImageType;
- typedef typename InputImageType::IndexType IndexType;
-
- typedef std::deque< IndexType > OutputPixelType;
- typedef Image< OutputPixelType, ImageDimension > OutputImageType;
-
- typedef unsigned int FFT1DSizeType;
-
- /** Standard class typedefs. */
- typedef Spectra1DSupportWindowImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkTypeMacro( Spectra1DSupportWindowImageFilter, ImageToImageFilter );
- itkNewMacro( Self );
-
- /** Set/Get the nominal size of the FFT. This will be truncated at the
- * boundary of image. */
- itkGetConstMacro( FFT1DSize, FFT1DSizeType );
- itkSetMacro( FFT1DSize, FFT1DSizeType );
-
- /** Set/Get the number of samples between windows -- defaults to 1. */
- itkGetConstMacro( Step, SizeValueType );
- itkSetMacro( Step, SizeValueType );
-
-protected:
- Spectra1DSupportWindowImageFilter();
- virtual ~Spectra1DSupportWindowImageFilter() {};
-
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- virtual void GenerateOutputInformation() ITK_OVERRIDE;
-
- virtual void ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId ) ITK_OVERRIDE;
- virtual void AfterThreadedGenerateData() ITK_OVERRIDE;
-
- virtual void PrintSelf( std::ostream & os, Indent indent ) const ITK_OVERRIDE;
-
-private:
- Spectra1DSupportWindowImageFilter( const Self & ); // purposely not implemented
- void operator=( const Self & ); // purposely not implemented
-
- FFT1DSizeType m_FFT1DSize;
- SizeValueType m_Step;
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkSpectra1DSupportWindowImageFilter.hxx"
-#endif
-
-#endif // itkSpectra1DSupportWindowImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.hxx
deleted file mode 100644
index 1a8521fad1..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowImageFilter.hxx
+++ /dev/null
@@ -1,168 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkSpectra1DSupportWindowImageFilter_hxx
-#define itkSpectra1DSupportWindowImageFilter_hxx
-
-#include "itkSpectra1DSupportWindowImageFilter.h"
-#include "itkImageRegionIterator.h"
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkMetaDataObject.h"
-#include "itkImageScanlineIterator.h"
-
-namespace itk
-{
-
-template< typename TInputImage >
-Spectra1DSupportWindowImageFilter< TInputImage >
-::Spectra1DSupportWindowImageFilter():
- m_FFT1DSize( 32 ),
- m_Step( 1 )
-{
-}
-
-
-template< typename TInputImage >
-void
-Spectra1DSupportWindowImageFilter< TInputImage >
-::GenerateOutputInformation()
-{
- Superclass::GenerateOutputInformation();
-
- OutputImageType * output = this->GetOutput();
- const InputImageType * input = this->GetInput();
-
- OutputImageRegionType outputRegion = input->GetLargestPossibleRegion();
- typename OutputImageType::SizeType outputSize = outputRegion.GetSize();
- outputSize[0] /= this->GetStep();
- outputRegion.SetSize( outputSize );
- output->SetLargestPossibleRegion( outputRegion );
-
- typename OutputImageType::SpacingType outputSpacing = input->GetSpacing();
- outputSpacing[0] *= this->GetStep();
- output->SetSpacing( outputSpacing );
-}
-
-
-template< typename TInputImage >
-void
-Spectra1DSupportWindowImageFilter< TInputImage >
-::ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, ThreadIdType itkNotUsed( threadId ) )
-{
- OutputImageType * output = this->GetOutput();
- const InputImageType * input = this->GetInput();
-
- const OutputImageRegionType outputLargestRegion = output->GetLargestPossibleRegion();
- typedef typename OutputImageType::IndexType IndexType;
- const IndexType largestIndexStart = outputLargestRegion.GetIndex();
- IndexType largestIndexStop = largestIndexStart + outputLargestRegion.GetSize();
- for( unsigned int dim = 0; dim < ImageDimension; ++dim )
- {
- largestIndexStop[dim] -= 1;
- }
-
- typedef ImageLinearConstIteratorWithIndex< InputImageType > InputIteratorType;
- InputIteratorType inputIt( input, outputRegionForThread );
- typedef ImageScanlineIterator< OutputImageType > OutputIteratorType;
- OutputIteratorType outputIt( output, outputRegionForThread );
- const FFT1DSizeType fftSize = this->GetFFT1DSize();
- const SizeValueType sampleStep = this->GetStep();
- if( outputLargestRegion.GetSize()[0] < fftSize )
- {
- itkExceptionMacro( "Insufficient size in the FFT direction." );
- }
- for( inputIt.GoToBegin(), outputIt.GoToBegin(); !outputIt.IsAtEnd(); )
- {
- while( !outputIt.IsAtEndOfLine() )
- {
- OutputPixelType & supportWindow = outputIt.Value();
- supportWindow.clear();
-
- const IndexType inputIndex = inputIt.GetIndex();
-
- IndexType lineIndex;
- lineIndex[0] = inputIndex[0] - fftSize / 2;
- if( lineIndex[0] < largestIndexStart[0] )
- {
- lineIndex[0] = largestIndexStart[0];
- }
-
- if( lineIndex[0] + fftSize > largestIndexStop[0] )
- {
- lineIndex[0] = largestIndexStop[0] - fftSize;
- }
-
- const IndexValueType sideLines = static_cast< IndexValueType >( inputIt.Get() );
- for( IndexValueType line = inputIndex[1] - sideLines;
- line < inputIndex[1] + sideLines;
- ++line )
- {
- if( line < largestIndexStart[1] || line > largestIndexStop[1] )
- {
- continue;
- }
- lineIndex[1] = line;
- supportWindow.push_back( lineIndex );
- }
- for( SizeValueType ii = 0; ii < sampleStep; ++ii )
- {
- ++inputIt;
- }
- ++outputIt;
- }
- inputIt.NextLine();
- outputIt.NextLine();
- }
-}
-
-
-template< typename TInputImage >
-void
-Spectra1DSupportWindowImageFilter< TInputImage >
-::AfterThreadedGenerateData()
-{
- OutputImageType * output = this->GetOutput();
- MetaDataDictionary & dict = output->GetMetaDataDictionary();
- EncapsulateMetaData< FFT1DSizeType >( dict, "FFT1DSize", this->GetFFT1DSize() );
-}
-
-
-template< typename TInputImage >
-void
-Spectra1DSupportWindowImageFilter< TInputImage >
-::PrintSelf( std::ostream & os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- os << indent << "FFT1DSize: " << this->GetFFT1DSize() << std::endl;
- os << indent << "Step: " << this->GetStep() << std::endl;
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.h
deleted file mode 100644
index 1132a46300..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.h
+++ /dev/null
@@ -1,101 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkSpectra1DSupportWindowToMaskImageFilter_h
-#define itkSpectra1DSupportWindowToMaskImageFilter_h
-
-#include "itkImageToImageFilter.h"
-
-namespace itk
-{
-
-/** \class Spectra1DSupportWindowToMaskImageFilter
- * \brief Generate a mask image from the support window at a given index.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage >
-class Spectra1DSupportWindowToMaskImageFilter:
- public ImageToImageFilter< TInputImage,
- TOutputImage >
-{
-public:
- itkStaticConstMacro( ImageDimension, unsigned int, TInputImage::ImageDimension );
-
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
-
- typedef typename InputImageType::IndexType IndexType;
- typedef typename OutputImageType::PixelType OutputPixelType;
-
- /** Standard class typedefs. */
- typedef Spectra1DSupportWindowToMaskImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkTypeMacro( Spectra1DSupportWindowToMaskImageFilter, ImageToImageFilter );
- itkNewMacro( Self );
-
- /** Set/Get the index of the support window to create the mask for. */
- itkGetConstReferenceMacro( MaskIndex, IndexType );
- itkSetMacro( MaskIndex, IndexType );
-
- /** Set/Get the value to consider as "background". Defaults to zero. */
- itkSetMacro( BackgroundValue, OutputPixelType );
- itkGetConstMacro( BackgroundValue, OutputPixelType );
-
- /** Set/Get the value in the image to consider as "foreground". Defaults to
- * maximum value of the OutputPixelType. */
- itkSetMacro( ForegroundValue, OutputPixelType );
- itkGetConstMacro( ForegroundValue, OutputPixelType );
-
-
-protected:
- Spectra1DSupportWindowToMaskImageFilter();
- virtual ~Spectra1DSupportWindowToMaskImageFilter() {};
-
- virtual void GenerateData() ITK_OVERRIDE;
-
-private:
- Spectra1DSupportWindowToMaskImageFilter( const Self & ); // purposely not implemented
- void operator=( const Self & ); // purposely not implemented
-
- IndexType m_MaskIndex;
-
- OutputPixelType m_BackgroundValue;
- OutputPixelType m_ForegroundValue;
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkSpectra1DSupportWindowToMaskImageFilter.hxx"
-#endif
-
-#endif // itkSpectra1DSupportWindowToMaskImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.hxx
deleted file mode 100644
index 165cda2b6f..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkSpectra1DSupportWindowToMaskImageFilter.hxx
+++ /dev/null
@@ -1,86 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkSpectra1DSupportWindowToMaskImageFilter_hxx
-#define itkSpectra1DSupportWindowToMaskImageFilter_hxx
-
-#include "itkSpectra1DSupportWindowToMaskImageFilter.h"
-#include "itkSpectra1DSupportWindowImageFilter.h"
-#include "itkImageRegionIterator.h"
-#include "itkImageRegionConstIteratorWithIndex.h"
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-Spectra1DSupportWindowToMaskImageFilter< TInputImage, TOutputImage >
-::Spectra1DSupportWindowToMaskImageFilter():
- m_BackgroundValue( NumericTraits< OutputPixelType >::ZeroValue() ),
- m_ForegroundValue( NumericTraits< OutputPixelType >::max() )
-{
- m_MaskIndex.Fill( 0 );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-Spectra1DSupportWindowToMaskImageFilter< TInputImage, TOutputImage >
-::GenerateData()
-{
- this->AllocateOutputs();
-
- const InputImageType * input = this->GetInput();
- typedef typename InputImageType::PixelType InputPixelType;
- const InputPixelType & inputPixel = input->GetPixel( this->GetMaskIndex() );
-
- typedef Spectra1DSupportWindowImageFilter< OutputImageType > Spectra1DSupportWindowFilterType;
- typedef typename Spectra1DSupportWindowFilterType::FFT1DSizeType FFT1DSizeType;
-
- const MetaDataDictionary & dict = input->GetMetaDataDictionary();
- FFT1DSizeType fft1DSize = 32;
- ExposeMetaData< FFT1DSizeType >( dict, "FFT1DSize", fft1DSize );
-
- OutputImageType * output = this->GetOutput();
- output->FillBuffer( this->GetBackgroundValue() );
-
- for( typename InputPixelType::const_iterator lineIt = inputPixel.begin(); lineIt != inputPixel.end(); ++lineIt )
- {
- const IndexType startIndex = *lineIt;
- IndexType index = startIndex;
- for( FFT1DSizeType sampleIndex = 0; sampleIndex < fft1DSize; ++sampleIndex )
- {
- index[0] = startIndex[0] + sampleIndex;
- output->SetPixel( index, this->GetForegroundValue() );
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.h
deleted file mode 100644
index 46a5f1f0fa..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.h
+++ /dev/null
@@ -1,97 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkTimeGainCompensationImageFilter_h
-#define itkTimeGainCompensationImageFilter_h
-
-#include "itkImageToImageFilter.h"
-
-#include "itkArray2D.h"
-
-namespace itk
-{
-
-/**
- * \class TimeGainCompensationImageFilter
- * \brief Applies a linear piecewise time gain compensation.
- *
- * This filter applies a linear piecewise gain with depth. The depth
- * direction is assumed to be the first direction (0th direction).
- *
- * \ingroup Ultrasound
- * */
-template< typename TInputImage, typename TOutputImage = TInputImage >
-class TimeGainCompensationImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
-
- typedef TimeGainCompensationImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
-
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkTypeMacro( TimeGainCompensationImageFilter, ImageToImageFilter );
- itkNewMacro( Self );
-
- typedef Array2D< double > GainType;
-
- /** Set/Get the gain. The first column specifies the depth. The second
- * column specifies the gain. */
- itkSetMacro( Gain, GainType );
- itkGetConstReferenceMacro( Gain, GainType );
-
-protected:
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- TimeGainCompensationImageFilter();
- virtual ~TimeGainCompensationImageFilter() {}
-
- void PrintSelf( std::ostream & os, Indent indent ) const ITK_OVERRIDE;
-
- virtual void BeforeThreadedGenerateData() ITK_OVERRIDE;
- virtual void ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId ) ITK_OVERRIDE;
-
-private:
- TimeGainCompensationImageFilter( const Self& ); // purposely not implemented
- void operator=( const Self& ); // purposely not implemented
-
- GainType m_Gain;
-};
-
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkTimeGainCompensationImageFilter.hxx"
-#endif
-
-#endif // itkTimeGainCompensationImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.hxx
deleted file mode 100644
index c6df4bacc3..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkTimeGainCompensationImageFilter.hxx
+++ /dev/null
@@ -1,176 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkTimeGainCompensationImageFilter_hxx
-#define itkTimeGainCompensationImageFilter_hxx
-
-#include "itkTimeGainCompensationImageFilter.h"
-
-#include "itkImageScanlineIterator.h"
-#include "itkImageScanlineConstIterator.h"
-#include "itkArray.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-TimeGainCompensationImageFilter< TInputImage, TOutputImage >
-::TimeGainCompensationImageFilter():
- m_Gain( 2, 2 )
-{
- m_Gain(0, 0) = NumericTraits< double >::min();
- m_Gain(0, 1) = NumericTraits< double >::OneValue();
- m_Gain(1, 0) = NumericTraits< double >::max();
- m_Gain(1, 1) = NumericTraits< double >::OneValue();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-TimeGainCompensationImageFilter< TInputImage, TOutputImage >
-::PrintSelf( std::ostream & os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Gain:" << std::endl;
- for( unsigned int ii = 0; ii < m_Gain.rows(); ++ii )
- {
- os << indent.GetNextIndent() << "[" << m_Gain( ii, 0 ) << ", " << m_Gain( ii, 1 ) << "]" << std::endl;
- }
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-TimeGainCompensationImageFilter< TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- const GainType & gain = this->GetGain();
- if( gain.cols() != 2 )
- {
- itkExceptionMacro( "Gain should have two columns." );
- }
- if( gain.rows() < 2 )
- {
- itkExceptionMacro( "Insufficient depths specified in Gain." );
- }
- double depth = gain( 0, 0 );
- for( unsigned int ii = 1; ii < gain.rows(); ++ii )
- {
- if( gain( ii, 0 ) <= depth )
- {
- itkExceptionMacro( "Gain depths must be strictly increasing." );
- }
- depth = gain( ii, 0 );
- }
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-TimeGainCompensationImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType & outputRegionForThread, ThreadIdType itkNotUsed( threadId ) )
-{
- const InputImageType * inputImage = this->GetInput();
- OutputImageType * outputImage = this->GetOutput();
-
- // Compute the line gain once.
- const GainType & gain = this->GetGain();
- double pieceStart = gain( 0, 0 );
- double pieceEnd = gain( 1, 0 );
- double gainStart = gain( 0, 1 );
- double gainEnd = gain( 1, 1 );
- SizeValueType gainSegment = 1;
-
- typedef Array< double > LineGainType;
- const SizeValueType lineGainSize = outputRegionForThread.GetSize()[0];
- const typename InputImageType::RegionType & inputRegion = inputImage->GetLargestPossibleRegion();
- const IndexValueType imageStartIndex = inputRegion.GetIndex()[0];
- const typename InputImageType::PointType origin = inputImage->GetOrigin();
- const SpacePrecisionType pixelSpacing = inputImage->GetSpacing()[0];
- IndexValueType indexOffset = outputRegionForThread.GetIndex()[0] - imageStartIndex;
- LineGainType lineGain( lineGainSize );
- for( SizeValueType lineGainIndex = 0; lineGainIndex < lineGainSize; ++lineGainIndex )
- {
- const SpacePrecisionType pixelLocation = origin[0] + pixelSpacing * indexOffset;
- if( pixelLocation <= pieceStart )
- {
- lineGain[lineGainIndex] = gainStart;
- }
- else if( pixelLocation > pieceEnd )
- {
- if( gainSegment >= gain.rows() - 1 )
- {
- lineGain[lineGainIndex] = gainEnd;
- }
- else
- {
- ++gainSegment;
- pieceStart = gain( gainSegment - 1, 0 );
- pieceEnd = gain( gainSegment, 0 );
- gainStart = gain( gainSegment - 1, 1 );
- gainEnd = gain( gainSegment, 1 );
-
- const SpacePrecisionType offset = static_cast< SpacePrecisionType >( pixelLocation - pieceStart );
- lineGain[lineGainIndex] = offset * ( gainEnd - gainStart ) / ( pieceEnd - pieceStart ) + gainStart;
- }
- }
- else
- {
- const SpacePrecisionType offset = static_cast< SpacePrecisionType >( pixelLocation - pieceStart );
- lineGain[lineGainIndex] = offset * ( gainEnd - gainStart ) / ( pieceEnd - pieceStart ) + gainStart;
- }
- ++indexOffset;
- }
-
- typedef ImageScanlineConstIterator< InputImageType > InputIteratorType;
- InputIteratorType inputIt( inputImage, outputRegionForThread );
-
- typedef ImageScanlineIterator< OutputImageType > OutputIteratorType;
- OutputIteratorType outputIt( outputImage, outputRegionForThread );
-
- for( inputIt.GoToBegin(), outputIt.GoToBegin();
- !outputIt.IsAtEnd();
- inputIt.NextLine(), outputIt.NextLine() )
- {
- inputIt.GoToBeginOfLine();
- outputIt.GoToBeginOfLine();
- SizeValueType lineGainIndex = 0;
- while( ! outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( inputIt.Value() * lineGain[lineGainIndex] );
- ++inputIt;
- ++outputIt;
- ++lineGainIndex;
- }
- }
-}
-
-} // end namespace itk
-
-#endif // itkTimeGainCompensationImageFilter_hxx
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h
deleted file mode 100644
index 1ccada5222..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexConjugateToRealImageFilter_h
-#define itkVnlFFT1DComplexConjugateToRealImageFilter_h
-
-#include "itkFFT1DComplexConjugateToRealImageFilter.h"
-#include <complex>
-
-namespace itk
-{
-
-/** \class VnlFFT1DComplexConjugateToRealImageFilter
- *
- * \brief Perform the FFT along one dimension of an image using Vnl as a
- * backend.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=Image< typename NumericTraits< typename TInputImage::PixelType >::ValueType, TInputImage::ImageDimension > >
-class VnlFFT1DComplexConjugateToRealImageFilter:
- public FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef VnlFFT1DComplexConjugateToRealImageFilter Self;
- typedef FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- typedef typename Superclass::InputImageType InputImageType;
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Run-time type information (and related methods). */
- itkTypeMacro( VnlFFT1DComplexConjugateToRealImageFilter, FFT1DComplexConjugateToRealImageFilter );
-
-protected:
- void ThreadedGenerateData( const OutputImageRegionType&, ThreadIdType threadID ) override; // generates output from input
-
- VnlFFT1DComplexConjugateToRealImageFilter() { }
- ~VnlFFT1DComplexConjugateToRealImageFilter() override { }
-
-private:
- VnlFFT1DComplexConjugateToRealImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkVnlFFT1DComplexConjugateToRealImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx
deleted file mode 100644
index d77ad681a1..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx
+++ /dev/null
@@ -1,110 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexConjugateToRealImageFilter_hxx
-#define itkVnlFFT1DComplexConjugateToRealImageFilter_hxx
-
-#include "itkVnlFFT1DComplexConjugateToRealImageFilter.h"
-
-#include "itkFFT1DComplexConjugateToRealImageFilter.hxx"
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkIndent.h"
-#include "itkMetaDataObject.h"
-#include "itkExceptionObject.h"
-#include "vnl/algo/vnl_fft_base.h"
-#include "vnl/algo/vnl_fft_1d.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-void
-VnlFFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegion, ThreadIdType itkNotUsed( threadID ) )
-{
- // get pointers to the input and output
- const typename Superclass::InputImageType * inputPtr = this->GetInput();
- typename Superclass::OutputImageType * outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- const typename Superclass::InputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
-
- unsigned int vec_size = inputSize[this->m_Direction];
-
- typedef itk::ImageLinearConstIteratorWithIndex< InputImageType > InputIteratorType;
- typedef itk::ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegion );
- OutputIteratorType outputIt( outputPtr, outputRegion );
-
- inputIt.SetDirection(this->m_Direction);
- outputIt.SetDirection(this->m_Direction);
-
- typedef typename TOutputImage::PixelType OutputPixelType;
- vnl_vector< vcl_complex< OutputPixelType > > inputBuffer( vec_size );
- typename vnl_vector< vcl_complex< OutputPixelType > >::iterator inputBufferIt = inputBuffer.begin();
- // fft is done in-place
- typename vnl_vector< vcl_complex< OutputPixelType > >::iterator outputBufferIt = inputBuffer.begin();
- vnl_fft_1d< OutputPixelType > v1d(vec_size);
-
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- // copy the input line into our buffer
- inputIt.GoToBeginOfLine();
- inputBufferIt = inputBuffer.begin();
- while( !inputIt.IsAtEndOfLine() )
- {
- *inputBufferIt = inputIt.Get();
- ++inputIt;
- ++inputBufferIt;
- }
-
- // do the transform
- v1d.fwd_transform(inputBuffer);
-
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( (*outputBufferIt).real() / vec_size );
- ++outputIt;
- ++outputBufferIt;
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h
deleted file mode 100644
index 4fbbbd10b0..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h
+++ /dev/null
@@ -1,85 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_h
-#define itkVnlFFT1DComplexToComplexImageFilter_h
-
-#include "itkFFT1DComplexToComplexImageFilter.h"
-#include <complex>
-
-namespace itk
-{
-
-/** \class VnlFFT1DComplexToComplexImageFilter
- *
- * \brief Perform the FFT along one dimension of an image using Vnl as a
- * backend.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage >
-class VnlFFT1DComplexToComplexImageFilter:
- public FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef VnlFFT1DComplexToComplexImageFilter Self;
- typedef FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- typedef typename Superclass::InputImageType InputImageType;
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- typedef typename Superclass::TransformDirectionType TransformDirectionType;
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Run-time type information (and related methods). */
- itkTypeMacro( VnlFFT1DComplexToComplexImageFilter, FFT1DComplexToComplexImageFilter );
-
-protected:
- VnlFFT1DComplexToComplexImageFilter() {}
- ~VnlFFT1DComplexToComplexImageFilter() override {}
-
- void ThreadedGenerateData( const OutputImageRegionType&, ThreadIdType threadID ) ITK_OVERRIDE;
-
-private:
- VnlFFT1DComplexToComplexImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkVnlFFT1DComplexToComplexImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx
deleted file mode 100644
index 3ab41c2caa..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx
+++ /dev/null
@@ -1,127 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_hxx
-#define itkVnlFFT1DComplexToComplexImageFilter_hxx
-
-#include "itkVnlFFT1DComplexToComplexImageFilter.h"
-
-#include "itkFFT1DComplexToComplexImageFilter.hxx"
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkIndent.h"
-#include "itkMetaDataObject.h"
-#include "itkExceptionObject.h"
-#include "vnl/algo/vnl_fft_base.h"
-#include "vnl/algo/vnl_fft_1d.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-void
-VnlFFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegion, ThreadIdType itkNotUsed( threadID ) )
-{
- // get pointers to the input and output
- const typename Superclass::InputImageType * inputPtr = this->GetInput();
- typename Superclass::OutputImageType * outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- const typename Superclass::InputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
-
- const unsigned int direction = this->GetDirection();
- const unsigned int vectorSize = inputSize[direction];
-
- typedef itk::ImageLinearConstIteratorWithIndex< InputImageType > InputIteratorType;
- typedef itk::ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegion );
- OutputIteratorType outputIt( outputPtr, outputRegion );
-
- inputIt.SetDirection( direction );
- outputIt.SetDirection( direction );
-
- typedef typename TInputImage::PixelType PixelType;
- typedef vnl_vector< PixelType > VNLVectorType;
- VNLVectorType inputBuffer( vectorSize );
- typename VNLVectorType::iterator inputBufferIt = inputBuffer.begin();
- // fft is done in-place
- typename VNLVectorType::iterator outputBufferIt = inputBuffer.begin();
- vnl_fft_1d< typename NumericTraits< PixelType >::ValueType > v1d(vectorSize);
-
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- // copy the input line into our buffer
- inputIt.GoToBeginOfLine();
- inputBufferIt = inputBuffer.begin();
- while( !inputIt.IsAtEndOfLine() )
- {
- *inputBufferIt = inputIt.Get();
- ++inputIt;
- ++inputBufferIt;
- }
-
- // do the transform
- if( this->m_TransformDirection == Superclass::DIRECT )
- {
- v1d.bwd_transform(inputBuffer);
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( *outputBufferIt );
- ++outputIt;
- ++outputBufferIt;
- }
- }
- else // m_TransformDirection == INVERSE
- {
- v1d.fwd_transform(inputBuffer);
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( (*outputBufferIt) / static_cast< PixelType >( vectorSize ));
- ++outputIt;
- ++outputBufferIt;
- }
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h
deleted file mode 100644
index 1d8c15ab2d..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_h
-#define itkVnlFFT1DRealToComplexConjugateImageFilter_h
-
-#include "itkFFT1DRealToComplexConjugateImageFilter.h"
-#include <complex>
-
-namespace itk
-{
-
-/** \class VnlFFT1DRealToComplexConjugateImageFilter
- *
- * \brief Perform the FFT along one dimension of an image using Vnl as a
- * backend.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
-class VnlFFT1DRealToComplexConjugateImageFilter :
- public FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef VnlFFT1DRealToComplexConjugateImageFilter Self;
- typedef FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- typedef typename Superclass::InputImageType InputImageType;
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Run-time type information (and related methods). */
- itkTypeMacro( VnlFFT1DRealToComplexConjugateImageFilter, FFT1DRealToComplexConjugateImageFilter );
-
-protected:
- void ThreadedGenerateData( const OutputImageRegionType&, ThreadIdType threadID ) ITK_OVERRIDE;
-
- VnlFFT1DRealToComplexConjugateImageFilter() { }
- ~VnlFFT1DRealToComplexConjugateImageFilter() override { }
-
-private:
- VnlFFT1DRealToComplexConjugateImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx
deleted file mode 100644
index 0d38c0d745..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx
+++ /dev/null
@@ -1,115 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_hxx
-#define itkVnlFFT1DRealToComplexConjugateImageFilter_hxx
-
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.h"
-
-#include "itkFFT1DRealToComplexConjugateImageFilter.hxx"
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkIndent.h"
-#include "itkMetaDataObject.h"
-#include "itkExceptionObject.h"
-#include "itkVnlFFTCommon.h"
-#include "vnl/algo/vnl_fft_base.h"
-#include "vnl/algo/vnl_fft_1d.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-void
-VnlFFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegion, ThreadIdType itkNotUsed( threadID ) )
-{
- // get pointers to the input and output
- const typename Superclass::InputImageType * inputPtr = this->GetInput();
- typename Superclass::OutputImageType * outputPtr = this->GetOutput();
-
- const typename Superclass::InputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
-
- const unsigned int direction = this->GetDirection();
- unsigned int vectorSize = inputSize[direction];
- if( ! VnlFFTCommon::IsDimensionSizeLegal(vectorSize) )
- {
- itkExceptionMacro("Illegal Array DIM for FFT");
- }
-
-
- typedef ImageLinearConstIteratorWithIndex< InputImageType > InputIteratorType;
- typedef ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegion );
- OutputIteratorType outputIt( outputPtr, outputRegion );
-
- inputIt.SetDirection( direction );
- outputIt.SetDirection( direction );
-
- typedef typename TInputImage::PixelType PixelType;
- typedef vcl_complex< PixelType > ComplexType;
- typedef vnl_vector< ComplexType > ComplexVectorType;
- ComplexVectorType inputBuffer( vectorSize );
- typename ComplexVectorType::iterator inputBufferIt = inputBuffer.begin();
- // fft is done in-place
- typename ComplexVectorType::iterator outputBufferIt = inputBuffer.begin();
- vnl_fft_1d< PixelType > v1d( vectorSize );
-
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin();
- !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- // copy the input line into our buffer
- inputIt.GoToBeginOfLine();
- inputBufferIt = inputBuffer.begin();
- while( !inputIt.IsAtEndOfLine() )
- {
- *inputBufferIt = inputIt.Value();
- ++inputIt;
- ++inputBufferIt;
- }
-
- // do the transform
- v1d.bwd_transform( inputBuffer );
-
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( *outputBufferIt );
- ++outputIt;
- ++outputBufferIt;
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.h b/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.h
deleted file mode 100644
index 00f14ab7fc..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.h
+++ /dev/null
@@ -1,143 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkPhotoacousticBModeImageFilter_h
-#define itkPhotoacousticBModeImageFilter_h
-
-#include "itkComplexToModulusImageFilter.h"
-#include "itkConstantPadImageFilter.h"
-#include "itkImageToImageFilter.h"
-#include "itkImage.h"
-
-#include "ITKUltrasound/itkRegionFromReferenceImageFilter.h"
-#include "ITKUltrasound/itkAnalyticSignalImageFilter.h"
-
-namespace itk
-{
-
-/**
- * \class PhotoacousticBModeImageFilter
- *
- * \brief Create an Photoacoustic B-Mode (Brightness-Mode) image from raw
- * "RF" data. The RF's envelope is calculated from the analytic signal and
- * logarithmic intensity transform is NOT applied. This is for now the only
- * difference to the "normal" BModeImageFilter.
- *
- * Use SetDirection() to define the axis of propagation.
- *
- */
-template < typename TInputImage, typename TOutputImage=TInputImage, typename TComplexImage=Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
-class PhotoacousticBModeImageFilter :
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef PhotoacousticBModeImageFilter Self;
- typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- /** The type of input image. */
- typedef TInputImage InputImageType;
-
- /** Dimension of the input and output images. */
- itkStaticConstMacro (ImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- /** Typedef support for the input image scalar value type. */
- typedef typename InputImageType::PixelType InputPixelType;
-
- /** The type of output image. */
- typedef TOutputImage OutputImageType;
-
- /** Typedef support for the output image scalar value type. */
- typedef typename OutputImageType::PixelType OutputPixelType;
-
- /** Typedef of the image used for internal computations that has
- * std::complex pixels. */
- typedef TComplexImage ComplexImageType;
-
- /** Other convenient typedefs */
- typedef typename InputImageType::RegionType InputRegionType;
- typedef typename InputImageType::SizeType InputSizeType;
- typedef typename InputImageType::IndexType InputIndexType;
-
- /** Run-time type information (and related methods) */
- itkTypeMacro( PhotoacousticBModeImageFilter, ImageToImageFilter );
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Set the direction in which the envelope is to be calculated. */
- virtual void SetDirection( unsigned int direction )
- {
- this->m_AnalyticFilter->SetDirection( direction );
- this->Modified();
- }
-
- /** Get the direction in which the envelope is to be calculated. */
- virtual unsigned int GetDirection() const
- {
- return m_AnalyticFilter->GetDirection();
- }
-
-protected:
- PhotoacousticBModeImageFilter();
- ~PhotoacousticBModeImageFilter() override {}
-
- void PrintSelf( std::ostream& os, Indent indent ) const ITK_OVERRIDE;
-
- void GenerateData() ITK_OVERRIDE;
-
- // These behave like their analogs in FFT1DRealToComplexConjugateImageFilter.
- void GenerateInputRequestedRegion() ITK_OVERRIDE;
- void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- /** Component filters. */
- typedef AnalyticSignalImageFilter< InputImageType, ComplexImageType > AnalyticType;
- typedef ComplexToModulusImageFilter< typename AnalyticType::OutputImageType, OutputImageType > ComplexToModulusType;
- typedef ConstantPadImageFilter< InputImageType, InputImageType > PadType;
- typedef RegionFromReferenceImageFilter< OutputImageType, OutputImageType > ROIType;
-
-private:
- PhotoacousticBModeImageFilter( const Self& ); // purposely not implemented
- void operator=( const Self& ); // purposely not implemented
-
- typename AnalyticType::Pointer m_AnalyticFilter;
- typename ComplexToModulusType::Pointer m_ComplexToModulusFilter;
- typename PadType::Pointer m_PadFilter;
- typename ROIType::Pointer m_ROIFilter;
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkPhotoacousticBModeImageFilter.hxx"
-#endif
-
-#endif // itkPhotoacousticBModeImageFilter_h
diff --git a/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.hxx b/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.hxx
deleted file mode 100644
index cf58bf31eb..0000000000
--- a/Modules/PhotoacousticsAlgorithms/ITKFilter/itkPhotoacousticBModeImageFilter.hxx
+++ /dev/null
@@ -1,203 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkPhotoacousticBModeImageFilter_hxx
-#define itkPhotoacousticBModeImageFilter_hxx
-
-#include "itkPhotoacousticBModeImageFilter.h"
-
-#include "itkMetaDataDictionary.h"
-
-#include <algorithm>
-#include <sstream>
-#include <string>
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::PhotoacousticBModeImageFilter()
-{
- m_AnalyticFilter = AnalyticType::New();
- m_ComplexToModulusFilter = ComplexToModulusType::New();
- m_PadFilter = PadType::New();
- m_ROIFilter = ROIType::New();
-
- m_PadFilter->SetConstant( 0. );
- m_ComplexToModulusFilter->SetInput( m_AnalyticFilter->GetOutput() );
- m_ROIFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- InputImageType * inputPtr = const_cast<InputImageType *> (this->GetInput());
- OutputImageType * outputPtr = this->GetOutput();
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->GetDirection();
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast< OutputImageType* >( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- const unsigned int direction = this->GetDirection ();
- enlargedSize[direction] = outputLargeSize[direction];
- enlargedIndex[direction] = outputLargeIndex[direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::GenerateData()
-{
- this->AllocateOutputs();
-
- const InputImageType * inputPtr = this->GetInput();
- OutputImageType * outputPtr = this->GetOutput();
-
- const unsigned int direction = m_AnalyticFilter->GetDirection();
- typename InputImageType::SizeType size = inputPtr->GetLargestPossibleRegion().GetSize();
-
- // Zero padding. FFT direction should be factorable by 2 for all FFT
- // implementations to work.
- unsigned int n = size[direction];
- while( n % 2 == 0 )
- {
- n /= 2;
- }
- bool doPadding;
- if( n == 1 )
- {
- doPadding = false;
- }
- else
- {
- doPadding = true;
- }
- if( doPadding )
- {
- n = size[direction];
- unsigned int newSizeDirection = 1;
- while( newSizeDirection < n )
- {
- newSizeDirection *= 2;
- }
- typename InputImageType::SizeType padSize;
- padSize.Fill( 0 );
- padSize[direction] = newSizeDirection - size[direction];
- size[direction] = newSizeDirection;
- m_PadFilter->SetPadUpperBound( padSize );
- m_PadFilter->SetInput( inputPtr );
- m_AnalyticFilter->SetInput( m_PadFilter->GetOutput() );
- m_ROIFilter->SetReferenceImage( inputPtr );
- m_ROIFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
- m_ROIFilter->GraftOutput( outputPtr );
- m_ROIFilter->Update();
- this->GraftOutput( m_ROIFilter->GetOutput() );
- }
- else // padding is not required
- {
- m_AnalyticFilter->SetInput( inputPtr );
- m_ComplexToModulusFilter->GraftOutput( outputPtr );
- m_ComplexToModulusFilter->Update();
- this->GraftOutput( m_ComplexToModulusFilter->GetOutput() );
- }
-
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/CMakeLists.txt b/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/CMakeLists.txt
deleted file mode 100644
index ba56da85ab..0000000000
--- a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-OPTION(BUILD_PhotoacousticBeamformingTool "Build MiniApp for beamforming of a PA image" OFF)
-
-IF(BUILD_PhotoacousticBeamformingTool)
- PROJECT( MitkPABeamformingTool )
- mitk_create_executable(PABeamformingTool
- DEPENDS MitkCommandLine MitkCore MitkPhotoacousticsAlgorithms
- PACKAGE_DEPENDS tinyxml
- CPP_FILES PABeamformingTool.cpp)
-
- install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
- ENDIF()
diff --git a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/PABeamformingTool.cpp b/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/PABeamformingTool.cpp
deleted file mode 100644
index 3fe1900be7..0000000000
--- a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/PABeamformingTool.cpp
+++ /dev/null
@@ -1,397 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkCommon.h>
-#include <chrono>
-#include <mitkIOUtil.h>
-#include <mitkCommandLineParser.h>
-#include <mitkException.h>
-
-#include <mitkPhotoacousticFilterService.h>
-#include <mitkBeamformingSettings.h>
-#include <mitkCastToFloatImageFilter.h>
-
-#include <itksys/SystemTools.hxx>
-#include <tinyxml/tinyxml.h>
-
-struct InputParameters
-{
- mitk::Image::Pointer inputImage;
- std::string outputFilename;
- bool verbose;
- std::string settingsFile;
- std::string imageType;
-};
-
-struct BandpassSettings
-{
- float highPass;
- float lowPass;
- float alphaLow;
- float alphaHigh;
- float speedOfSound;
-};
-
-struct CropSettings
-{
- int above;
- int below;
- int right;
- int left;
- int zStart;
- int zEnd;
-};
-
-struct ResampleSettings
-{
- double spacing;
- unsigned int dimX;
-};
-
-struct BModeSettings
-{
- mitk::PhotoacousticFilterService::BModeMethod method;
- bool UseLogFilter;
-};
-
-struct ProcessSettings
-{
- bool DoBeamforming;
- bool DoBandpass;
- bool DoCropping;
- bool DoResampling;
- bool DoBmode;
-};
-
-InputParameters parseInput(int argc, char* argv[])
-{
- mitkCommandLineParser parser;
- parser.setCategory("MITK-Photoacoustics");
- parser.setTitle("Mitk Photoacoustics Beamforming Tool");
- parser.setDescription("Reads a nrrd file as an input and applies a beamforming method as set with the parameters defined in an additionally provided xml file.");
- parser.setContributor("Computer Assisted Medical Interventions, DKFZ");
-
- parser.setArgumentPrefix("--", "-");
-
- parser.beginGroup("Required parameters");
- parser.addArgument(
- "inputImage", "i", mitkCommandLineParser::Image,
- "Input image (mitk::Image)", "input image (.nrrd file)",
- us::Any(), false, false, false, mitkCommandLineParser::Input);
- parser.addArgument(
- "output", "o", mitkCommandLineParser::File,
- "Output filename", "output image (.nrrd file)",
- us::Any(), false, false, false, mitkCommandLineParser::Output);
- parser.addArgument(
- "settings", "s", mitkCommandLineParser::String,
- "settings file", "file containing beamforming and other specifications(.xml file)",
- us::Any(), false);
- parser.addArgument(
- "type", "t", mitkCommandLineParser::String,
- "image type", "Specifies whether to use the PA or US subsection of the xml file must be 'PA' or 'US'",
- us::Any(), false);
- parser.endGroup();
-
- parser.beginGroup("Optional parameters");
- parser.addArgument(
- "verbose", "v", mitkCommandLineParser::Bool,
- "Verbose Output", "Whether to produce verbose, or rather debug output. (default: false)");
- parser.endGroup();
-
- InputParameters input;
-
- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
- if (parsedArgs.size() == 0)
- exit(-1);
-
- input.verbose = (bool)parsedArgs.count("verbose");
- MITK_INFO(input.verbose) << "### VERBOSE OUTPUT ENABLED ###";
-
- if (parsedArgs.count("inputImage"))
- {
- MITK_INFO(input.verbose) << "Reading input image...";
- input.inputImage = mitk::IOUtil::Load<mitk::Image>(us::any_cast<std::string>(parsedArgs["inputImage"]));
- MITK_INFO(input.verbose) << "Reading input image...[Done]";
- }
- else
- mitkThrow() << "No input image given.";
-
- if (parsedArgs.count("output"))
- input.outputFilename = us::any_cast<std::string>(parsedArgs["output"]);
- else
- mitkThrow() << "No output image path given..";
-
- if (parsedArgs.count("settings"))
- input.settingsFile = us::any_cast<std::string>(parsedArgs["settings"]);
- else
- mitkThrow() << "No settings image path given..";
-
- if (parsedArgs.count("type"))
- input.imageType = us::any_cast<std::string>(parsedArgs["type"]);
- else
- mitkThrow() << "No settings image type given..";
-
- return input;
-}
-
-TiXmlElement* getRootChild(TiXmlElement* root, std::string childName)
-{
- for (TiXmlElement* elem = root->FirstChildElement(); elem != NULL; elem = elem->NextSiblingElement())
- {
- if (elem->Value() == childName)
- return elem;
- }
- return nullptr;
-}
-
-void ParseXML(std::string xmlFile, InputParameters input, mitk::BeamformingSettings::Pointer *bfSet, BandpassSettings& bandpassSet, CropSettings& cropSet, ResampleSettings& resSet, BModeSettings& bmodeSet, ProcessSettings& processSet)
-{
- MITK_INFO << "Loading configuration File \"" << xmlFile << "\"";
- TiXmlDocument doc(xmlFile);
- if (!doc.LoadFile())
- mitkThrow() << "Failed to load settings file \"" << xmlFile << "\" Error: " << doc.ErrorDesc();
-
- TiXmlElement* root = doc.FirstChildElement();
- if (root == NULL)
- {
- mitkThrow() << "Failed to load file: No root element.";
- doc.Clear();
- }
-
- TiXmlElement* elemtop = getRootChild(root, input.imageType);
- if(elemtop == nullptr)
- mitkThrow() << "The xml file is wrongly formatted, no element \"" << input.imageType << "\" found";
-
- for (TiXmlElement* elem = elemtop->FirstChildElement(); elem != NULL; elem = elem->NextSiblingElement())
- {
- std::string elemName = elem->Value();
- if (elemName == "Beamforming")
- {
- processSet.DoBeamforming = std::stoi(elem->Attribute("do"));
- if (!processSet.DoBeamforming)
- continue;
-
- float SpeedOfSound = std::stof(elem->Attribute("speedOfSoundMeterPerSecond"));
- float PitchMeter = std::stof(elem->Attribute("pitchMilliMeter"))/1000;
- float TimeSpacingMicroSecond = (float)(input.inputImage->GetGeometry()->GetSpacing()[1] / 1000000);
-
- if (std::stof(elem->Attribute("timeSpacingMicroSecond")) > 0) {
- TimeSpacingMicroSecond = std::stof(elem->Attribute("timeSpacingMicroSecond"));
- MITK_INFO << "TIME: " << TimeSpacingMicroSecond;
- }
-
- float Angle = std::stof(elem->Attribute("apodizationAngle"));
- bool IsPhotoacousticImage = true;
- if (std::string(elem->Attribute("imageType")).compare("US") == 0) {
- IsPhotoacousticImage = false;
- MITK_INFO << "US IMAGE";
- }
-
- unsigned int SamplesPerLine = std::stoi(elem->Attribute("reconstructedYDimension"));
- unsigned int ReconstructionLines = std::stoi(elem->Attribute("reconstructedXDimension"));
-
-
- float ReconstructionDepth = std::stof(elem->Attribute("reconstructionDepthMeter"));
- bool UseGPU = std::stoi(elem->Attribute("useGPU"));
- unsigned int GPUBatchSize = std::stoi(elem->Attribute("GPUBatchSize"));
-
- std::string apodizationStr = elem->Attribute("apodizationFunction");
- mitk::BeamformingSettings::Apodization Apodization = mitk::BeamformingSettings::Apodization::Box;
- if (apodizationStr == "Box")
- Apodization = mitk::BeamformingSettings::Apodization::Box;
- else if (apodizationStr == "Hann")
- Apodization = mitk::BeamformingSettings::Apodization::Hann;
- else if (apodizationStr == "Hamm")
- Apodization = mitk::BeamformingSettings::Apodization::Hamm;
- else
- mitkThrow() << "Apodization incorrectly defined in settings";
-
- std::string geomStr = elem->Attribute("probeGeometry");
- mitk::BeamformingSettings::ProbeGeometry ProbeGeometry = mitk::BeamformingSettings::ProbeGeometry::Linear;
- if (geomStr == "linear")
- ProbeGeometry = mitk::BeamformingSettings::ProbeGeometry::Linear;
- else if(geomStr == "concave")
- ProbeGeometry = mitk::BeamformingSettings::ProbeGeometry::Concave;
- else
- mitkThrow() << "geometry incorrectly defined in settings";
-
- float radius = std::stof(elem->Attribute("radiusMilliMeter"))/1000;
-
- unsigned int ApodizationArraySize = ReconstructionLines;
-
- std::string algorithmStr = elem->Attribute("algorithm");
- mitk::BeamformingSettings::BeamformingAlgorithm Algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS;
- if (algorithmStr == "DAS")
- Algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS;
- else if (algorithmStr == "DMAS")
- Algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DMAS;
- else if (algorithmStr == "sDMAS")
- Algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS;
- else
- mitkThrow() << "Beamforming algorithm incorrectly defined in settings";
-
- *bfSet = mitk::BeamformingSettings::New(
- PitchMeter,
- SpeedOfSound,
- TimeSpacingMicroSecond,
- Angle,
- IsPhotoacousticImage,
- SamplesPerLine,
- ReconstructionLines,
- input.inputImage->GetDimensions(),
- ReconstructionDepth,
- UseGPU,
- GPUBatchSize,
- Apodization,
- ApodizationArraySize,
- Algorithm,
- ProbeGeometry,
- radius
- );
- }
- if (elemName == "Bandpass")
- {
- processSet.DoBandpass = std::stoi(elem->Attribute("do"));
- if (!processSet.DoBandpass)
- continue;
-
- bandpassSet.highPass = std::stof(elem->Attribute("highPass"));
- bandpassSet.lowPass = std::stof(elem->Attribute("lowPass"));
- bandpassSet.alphaLow = std::stof(elem->Attribute("alphaLow"));
- bandpassSet.alphaHigh = std::stof(elem->Attribute("alphaHigh"));
- }
- if (elemName == "Cropping")
- {
- processSet.DoCropping = std::stoi(elem->Attribute("do"));
- if (!processSet.DoCropping)
- continue;
-
- cropSet.above = std::stoi(elem->Attribute("cutAbove"));
- cropSet.below = std::stoi(elem->Attribute("cutBelow"));
- cropSet.right = std::stoi(elem->Attribute("cutRight"));
- cropSet.left = std::stoi(elem->Attribute("cutLeft"));
- cropSet.zStart = std::stoi(elem->Attribute("firstSlice"));
- cropSet.zEnd = std::stoi(elem->Attribute("cutSlices"));
- }
- if (elemName == "Resampling")
- {
- processSet.DoResampling = std::stoi(elem->Attribute("do"));
- if (!processSet.DoResampling)
- continue;
-
- resSet.spacing = std::stod(elem->Attribute("spacing"));
- resSet.dimX = std::stoi(elem->Attribute("dimX"));
- }
- if (elemName == "BMode")
- {
- processSet.DoBmode = std::stoi(elem->Attribute("do"));
- if (!processSet.DoBmode)
- continue;
-
- std::string methodStr = elem->Attribute("method");
- if (methodStr == "EnvelopeDetection")
- bmodeSet.method = mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection;
- else if (methodStr == "Abs")
- bmodeSet.method = mitk::PhotoacousticFilterService::BModeMethod::Abs;
- else
- mitkThrow() << "BMode method incorrectly set in configuration file";
- bmodeSet.UseLogFilter = (bool)std::stoi(elem->Attribute("useLogFilter"));
- }
- }
-}
-
-int main(int argc, char * argv[])
-{
- auto input = parseInput(argc, argv);
-
- mitk::BeamformingSettings::Pointer bfSettings;
- BandpassSettings bandpassSettings{5,10,1,1,1540};
- BModeSettings bmodeSettings{ mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection, false };
- CropSettings cropSettings{ 0,0,0,0,0,0 };
- ResampleSettings resSettings{ 0.15 , 256};
- ProcessSettings processSettings{ false, false, false, false, false };
-
- MITK_INFO << "Parsing settings XML...";
- try
- {
- ParseXML(input.settingsFile, input, &bfSettings, bandpassSettings, cropSettings, resSettings, bmodeSettings, processSettings);
- }
- catch (mitk::Exception e)
- {
- MITK_INFO << e;
- return -1;
- }
-
- MITK_INFO << "Parsing settings XML...[Done]";
-
- MITK_INFO(input.verbose) << "Beamforming input image...";
- mitk::Image::Pointer inputImage = input.inputImage;
- if (!(inputImage->GetPixelType().GetTypeAsString() == "scalar (float)" || inputImage->GetPixelType().GetTypeAsString() == " (float)"))
- {
- // we need a float image, so cast it here
- MITK_INFO(input.verbose) << "Casting input image to float...";
- mitk::CastToFloatImageFilter::Pointer castFilter = mitk::CastToFloatImageFilter::New();
- castFilter->SetInput(inputImage);
- castFilter->Update();
- inputImage = castFilter->GetOutput();
- MITK_INFO << inputImage->GetPixelType().GetPixelTypeAsString();
- MITK_INFO(input.verbose) << "Casting input image to float...[Done]";
- }
-
- mitk::PhotoacousticFilterService::Pointer m_FilterService = mitk::PhotoacousticFilterService::New();
-
- mitk::Image::Pointer output = inputImage;
- if (processSettings.DoBandpass)
- {
- MITK_INFO(input.verbose) << "Bandpassing input image...";
- output = m_FilterService->ApplyBandpassFilter(output, bandpassSettings.highPass*1e6, bandpassSettings.lowPass*1e6, bandpassSettings.alphaHigh, bandpassSettings.alphaLow, 1, bandpassSettings.speedOfSound, true);
- MITK_INFO(input.verbose) << "Bandpassing input image...[Done]";
- }
- if (processSettings.DoBeamforming)
- {
- MITK_INFO(input.verbose) << "Beamforming input image...";
- output = m_FilterService->ApplyBeamforming(output, bfSettings);
- MITK_INFO(input.verbose) << "Beamforming input image...[Done]";
- }
- if (processSettings.DoCropping)
- {
- int err;
- MITK_INFO(input.verbose) << "Applying Crop filter to image...";
- output = m_FilterService->ApplyCropping(output,
- cropSettings.above, cropSettings.below, cropSettings.right, cropSettings.left, cropSettings.zStart, cropSettings.zEnd, &err);
- MITK_INFO(input.verbose) << "Applying Crop filter to image...[Done]";
- }
- if (processSettings.DoBmode)
- {
- MITK_INFO(input.verbose) << "Applying BModeFilter to image...";
- output = m_FilterService->ApplyBmodeFilter(output, bmodeSettings.method, bmodeSettings.UseLogFilter);
- MITK_INFO(input.verbose) << "Applying BModeFilter to image...[Done]";
- }
- if (processSettings.DoResampling)
- {
- double spacing[3] = { output->GetGeometry()->GetSpacing()[0] * output->GetDimension(0) / resSettings.dimX, resSettings.spacing, output->GetGeometry()->GetSpacing()[2] };
- MITK_INFO(input.verbose) << "Applying Resample filter to image...";
- output = m_FilterService->ApplyResampling(output, spacing);
- if (output->GetDimension(0) != resSettings.dimX)
- {
- double dim[3] = { (double)resSettings.dimX, (double)output->GetDimension(1), (double)output->GetDimension(2) };
- output = m_FilterService->ApplyResamplingToDim(output, dim);
- }
- MITK_INFO(input.verbose) << "Applying Resample filter to image...[Done]";
- }
-
- MITK_INFO(input.verbose) << "Saving image...";
- mitk::IOUtil::Save(output, input.outputFilename);
- MITK_INFO(input.verbose) << "Saving image...[Done]";
-
- MITK_INFO(input.verbose) << "Beamforming input image...[Done]";
-}
diff --git a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/files.cmake b/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/files.cmake
deleted file mode 100644
index 1bed148e42..0000000000
--- a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/files.cmake
+++ /dev/null
@@ -1,3 +0,0 @@
-set(CPP_FILES
- PABeamformingTool.cpp
-)
diff --git a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/name.options.xml b/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/name.options.xml
deleted file mode 100644
index ec367585b5..0000000000
--- a/Modules/PhotoacousticsAlgorithms/MitkPABeamformingTool/name.options.xml
+++ /dev/null
@@ -1,131 +0,0 @@
-<?xml version="1.0" ?>
-<ProcessingPipeline>
- <OneTool
- StartWith="sort"
- StopAfter="video"
- CorrectedWavelength="False"
- FirstFileNumber="1"
- MitkPath="E:/NH3/sb/"
- AverageSequences="1"
- PyroTStoSeconds="1000"
- ImageTStoSeconds="1000"
- />
- <!-- stage 1: "sort"
- stage 2: "beamform"
- stage 3: "motion"
- stage 4: "average"
- stage 5: "unmix"
- -->
-
- <WavelengthSequence
- sequence="700 710 720 730 740 750 760 770 780 790 800 810 820 830 840 850 860 870 880 890 900 910 920 930 940 950"
- firstWavelength="0"
- />
-
- <PA>
- <Beamforming
- do="1"
- pitchInMeters="0.3"
- speedOfSound="1540"
- angle="27"
- isPhotoacousticImage="1"
- samplesPerLine="2048"
- reconstructionLines="512"
- reconstructionDepth="0.04"
- useGPU="1"
- GPUBatchSize="32"
- apodization="Hann"
- apodizationArraySize="512"
- algorithm="DAS"
- geometry="linear"
- radiusInMm="40"/>
- <!--apodization = "Box","Hann","Hamm"
- algorithm = "DAS","sDMAS","DMAS"
- geometry="linear","concave"
- -->
-
- <Bandpass
- do="0"
- highPass="5"
- lowPass="10"
- alphaLow="1"
- alphaHigh="1"
- speedOfSound="1540"
- />
-
- <Cropping
- do="1"
- cutAbove="400"
- cutBelow="100"
- cutRight="0"
- cutLeft="0"
- firstSlice="0"
- cutSlices="0"/>
-
- <Resampling
- do="1"
- spacing="0.075"
- dimX="512"/>
-
- <BMode
- do="1"
- method="EnvelopeDetection"
- useLogFilter="0"/>
- <!--method = "Abs","EnvelopeDetection"
- -->
- </PA>
-
- <US>
- <Beamforming
- do="0"/>
-
- <Bandpass
- do="1"
- highPass="5"
- lowPass="10"
- alphaLow="1"
- alphaHigh="1"
- speedOfSound="1540"
- />
-
- <Cropping
- do="1"
- cutAbove="400"
- cutBelow="100"
- cutRight="0"
- cutLeft="0"
- firstSlice="0"
- cutSlices="0"/>
-
- <Resampling
- do="1"
- spacing="0.075"
- dimX="512"
- />
-
- <BMode
- do="1"
- method="EnvelopeDetection"
- useLogFilter="1"/>
- </US>
-
- <Video
- cmap="viridis"
- image_idx_test_image = "0"
- vmin = "0"
- vmax = "1"
- fps = "36"
- dpi = "150"
- ticks_xaxis = "0 10 20 30 40"
- ticks_yaxis = "0 5 10 25"
- fig_title = "$\mathrm{sO_2}$ estimation by PA unmixing [%]"
- laser_freq = "20"
- crop_top="8"
- crop_bottom="8"
- crop_left="0"
- crop_right="0"
- image_type="sO2"
- auto_ROI="False"
- />
- <!-- #sO2', 'tHb', or 'both' -->
-</ProcessingPipeline>
diff --git a/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/CMakeLists.txt b/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/CMakeLists.txt
deleted file mode 100644
index eedce28006..0000000000
--- a/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-OPTION(BUILD_PhotoacousticResampleCropTool "Build MiniApp for resampling and cropping of images" OFF)
-
-IF(BUILD_PhotoacousticResampleCropTool)
- PROJECT( MitkPAResampleCropTool )
- mitk_create_executable(PAResampleCropTool
- DEPENDS MitkCommandLine MitkCore MitkPhotoacousticsAlgorithms
- PACKAGE_DEPENDS tinyxml
- CPP_FILES PAResampleCropTool.cpp)
-
- install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
- ENDIF()
diff --git a/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/PAResampleCropTool.cpp b/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/PAResampleCropTool.cpp
deleted file mode 100644
index 7fef39afe0..0000000000
--- a/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/PAResampleCropTool.cpp
+++ /dev/null
@@ -1,194 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkCommon.h>
-#include <chrono>
-#include <mitkIOUtil.h>
-#include <mitkCommandLineParser.h>
-#include <mitkException.h>
-
-#include <mitkPhotoacousticFilterService.h>
-#include <mitkBeamformingSettings.h>
-#include <mitkCastToFloatImageFilter.h>
-
-#include <itksys/SystemTools.hxx>
-#include <tinyxml\tinyxml.h>
-
-struct InputParameters
-{
- mitk::Image::Pointer inputImage;
- std::string outputFilename;
- bool verbose;
- std::string settingsFile;
-};
-
-struct CropSettings
-{
- unsigned int dimX;
- unsigned int dimY;
- unsigned int cutAbove;
-};
-
-struct ResamplingSettings
-{
- double spacing[3];
-};
-
-
-InputParameters parseInput(int argc, char* argv[])
-{
- mitkCommandLineParser parser;
- parser.setCategory("MITK-Photoacoustics");
- parser.setTitle("Mitk Photoacoustics Resample and Crop Tool");
- parser.setDescription("Reads a nrrd file as an input and crops and resamples it as set with the parameters defined in an additionally provided xml file.");
- parser.setContributor("Computer Assisted Medical Interventions, DKFZ");
-
- parser.setArgumentPrefix("--", "-");
-
- parser.beginGroup("Required parameters");
- parser.addArgument(
- "inputImage", "i", mitkCommandLineParser::Image,
- "Input image (mitk::Image)", "input image (.nrrd file)",
- us::Any(), false, false, false, mitkCommandLineParser::Input);
- parser.addArgument(
- "output", "o", mitkCommandLineParser::File,
- "Output filename", "output image (.nrrd file)",
- us::Any(), false, false, false, mitkCommandLineParser::Output);
- parser.addArgument(
- "settings", "s", mitkCommandLineParser::String,
- "settings file", "file containing specifications (.xml file)",
- us::Any(), false);
- parser.endGroup();
-
- parser.beginGroup("Optional parameters");
- parser.addArgument(
- "verbose", "v", mitkCommandLineParser::Bool,
- "Verbose Output", "Whether to produce verbose, or rather debug output. (default: false)");
- parser.endGroup();
-
- InputParameters input;
-
- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
- if (parsedArgs.size() == 0)
- exit(-1);
-
- input.verbose = (bool)parsedArgs.count("verbose");
- MITK_INFO(input.verbose) << "### VERBOSE OUTPUT ENABLED ###";
-
- if (parsedArgs.count("inputImage"))
- {
- MITK_INFO(input.verbose) << "Reading input image...";
- input.inputImage = mitk::IOUtil::Load<mitk::Image>(us::any_cast<std::string>(parsedArgs["inputImage"]));
- MITK_INFO(input.verbose) << "Reading input image...[Done]";
- }
- else
- mitkThrow() << "No input image given.";
-
- if (parsedArgs.count("output"))
- input.outputFilename = us::any_cast<std::string>(parsedArgs["output"]);
- else
- mitkThrow() << "No output image path given..";
-
- if (parsedArgs.count("settings"))
- input.settingsFile = us::any_cast<std::string>(parsedArgs["settings"]);
- else
- mitkThrow() << "No settings image path given..";
-
- return input;
-}
-
-void ParseXML(std::string xmlFile, InputParameters input, CropSettings& cropSet, ResamplingSettings& resSet)
-{
- MITK_INFO << "Loading configuration File \"" << xmlFile << "\"";
- TiXmlDocument doc(xmlFile);
- if (!doc.LoadFile())
- mitkThrow() << "Failed to load settings file \"" << xmlFile << "\" Error: " << doc.ErrorDesc();
-
- TiXmlElement* root = doc.FirstChildElement();
- if (root == NULL)
- {
- mitkThrow() << "Failed to load file: No root element.";
- doc.Clear();
- }
- for (TiXmlElement* elem = root->FirstChildElement(); elem != NULL; elem = elem->NextSiblingElement())
- {
- std::string elemName = elem->Value();
- if (elemName == "ResampleCrop")
- {
- cropSet.dimX = std::stoi(elem->Attribute("dimX"));
- cropSet.dimY = std::stoi(elem->Attribute("dimY"));
- cropSet.cutAbove = std::stoi(elem->Attribute("cutAbove"));
- resSet.spacing[0] = std::stod(elem->Attribute("spacingX"));
- resSet.spacing[1] = std::stod(elem->Attribute("spacingY"));
- resSet.spacing[2] = std::stod(elem->Attribute("spacingZ"));
- }
- }
-}
-
-int main(int argc, char * argv[])
-{
- auto input = parseInput(argc, argv);
-
- CropSettings cropSettings{ 0,0,0 };
- ResamplingSettings resSettings{ 0 };
-
- MITK_INFO << "Parsing settings XML...";
- try
- {
- ParseXML(input.settingsFile, input, cropSettings, resSettings);
- }
- catch (mitk::Exception e)
- {
- MITK_INFO << e;
- return -1;
- }
-
- MITK_INFO << "Parsing settings XML...[Done]";
-
- MITK_INFO(input.verbose) << "Processing input image...";
-
- mitk::PhotoacousticFilterService::Pointer m_FilterService = mitk::PhotoacousticFilterService::New();
-
- mitk::Image::Pointer output = input.inputImage;
- MITK_INFO(input.verbose) << "Resampling input image...";
- MITK_INFO << resSettings.spacing[0];
- output = m_FilterService->ApplyResampling(output, resSettings.spacing);
- MITK_INFO(input.verbose) << "Resampling input image...[Done]";
-
- if (output->GetDimension(0) != cropSettings.dimX)
- {
- double outputDim[] = {(double)cropSettings.dimX, (double)output->GetDimension(1), (double)output->GetDimension(2)};
- output = m_FilterService->ApplyResamplingToDim(output, outputDim);
- }
-
- int err = 0;
- int below = output->GetDimension(1) - cropSettings.dimY - cropSettings.cutAbove;
- if (below < 0)
- {
- MITK_INFO(input.verbose) << "Extending input image...";
- output = m_FilterService->ExtendImage(output, 0, cropSettings.dimY);
- MITK_INFO(input.verbose) << "Extending input image...[Done]";
- }
- else
- {
- MITK_INFO(input.verbose) << "Cropping input image...";
- output = m_FilterService->ApplyCropping(output, cropSettings.cutAbove, below, 0, 0, 0, 0, &err);
- MITK_INFO(input.verbose) << "Cropping input image...[Done]";
- }
-
-
- MITK_INFO(input.verbose) << "Saving image...";
- mitk::IOUtil::Save(output, input.outputFilename);
- MITK_INFO(input.verbose) << "Saving image...[Done]";
-
- MITK_INFO(input.verbose) << "Processing input image...[Done]";
-}
diff --git a/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/files.cmake b/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/files.cmake
deleted file mode 100644
index f8bb3ffe66..0000000000
--- a/Modules/PhotoacousticsAlgorithms/MitkPAResampleCropTool/files.cmake
+++ /dev/null
@@ -1,3 +0,0 @@
-set(CPP_FILES
- PAResampleCropTool.cpp
-)
diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DAS.cl b/Modules/PhotoacousticsAlgorithms/Resources/DAS.cl
deleted file mode 100644
index b814242b05..0000000000
--- a/Modules/PhotoacousticsAlgorithms/Resources/DAS.cl
+++ /dev/null
@@ -1,120 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-__kernel void ckDAS(
- __global float* dSource, // input image
- __global float* dDest, // output buffer
- __global unsigned short* usedLines,
- __global unsigned short* delays,
- __constant float* apodArray,
- unsigned short apodArraySize,
- unsigned int inputL,
- unsigned int inputS,
- unsigned int Slices,
- unsigned int outputL,
- unsigned int outputS // parameters
-)
-{
- // get thread identifier
- unsigned int globalPosX = get_global_id(0);
- unsigned int globalPosY = get_global_id(1);
- unsigned int globalPosZ = get_global_id(2);
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices )
- {
- float l_i = (float)globalPosX / (float)outputL * (float)inputL;
-
- unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX];
- unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1];
- unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2];
-
- float apod_mult = (float)apodArraySize / (float)curUsedLines;
-
- unsigned short Delay = 0;
-
- float output = 0;
- float mult = 0;
-
- for (short l_s = minLine; l_s < maxLine; ++l_s)
- {
- Delay = delays[globalPosY * (outputL / 2) + (int)(fabs(l_s - l_i)/(float)inputL * (float)outputL)];
- if (Delay < inputS && Delay >= 0) {
- output += apodArray[(int)((l_s - minLine)*apod_mult)] * dSource[(int)(globalPosZ * inputL * inputS + Delay * inputL + l_s)];
- }
- else
- --curUsedLines;
- }
-
- dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)curUsedLines;
- }
-}
-
-__kernel void ckDAS_g(
- __global float* dSource, // input image
- __global float* dDest, // output buffer
- __global float* elementHeights,
- __global float* elementPositions,
- __constant float* apodArray,
- unsigned short apodArraySize,
- unsigned int inputL,
- unsigned int inputS,
- int Slices,
- int outputL,
- int outputS,
- float totalSamples_i,
- float horizontalExtent,
- float mult,
- char isPAImage,
- __global unsigned short* usedLines // parameters
-)
-{
- // get thread identifier
- int globalPosX = get_global_id(0);
- int globalPosY = get_global_id(1);
- int globalPosZ = get_global_id(2);
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices )
- {
- int AddSample = 0;
- float l_p = 0;
- float s_i = 0;
-
- float apod_mult = 1;
-
- float output = 0;
-
- l_p = (float)globalPosX / outputL * horizontalExtent;
- s_i = (float)globalPosY / outputS * totalSamples_i;
-
- unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX];
- unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1];
- unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2];
-
- apod_mult = (float)apodArraySize / curUsedLines;
-
- for (int l_s = minLine; l_s < maxLine; ++l_s)
- {
- AddSample = (int)sqrt(
- pow(s_i-elementHeights[l_s]*mult, 2)
- +
- pow(mult * (l_p - elementPositions[l_s]), 2)
- ) + (1 - isPAImage)*s_i;
- if (AddSample < inputS && AddSample >= 0)
- output += dSource[(int)(globalPosZ * inputL * inputS + l_s + AddSample*inputL)] * apodArray[(int)((l_s - minLine)*apod_mult)];
- else
- --curUsedLines;
- }
- dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / curUsedLines;
- }
-}
diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DMAS.cl b/Modules/PhotoacousticsAlgorithms/Resources/DMAS.cl
deleted file mode 100644
index a4fecfda31..0000000000
--- a/Modules/PhotoacousticsAlgorithms/Resources/DMAS.cl
+++ /dev/null
@@ -1,163 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-__kernel void ckDMAS(
- __global float* dSource, // input image
- __global float* dDest, // output buffer
- __global unsigned short* usedLines,
- __global unsigned short* AddSamples,
- __constant float* apodArray,
- unsigned short apodArraySize,
- unsigned int inputL,
- unsigned int inputS,
- unsigned int Slices,
- unsigned int outputL,
- unsigned int outputS // parameters
-)
-{
- // get thread identifier
- unsigned int globalPosX = get_global_id(0);
- unsigned int globalPosY = get_global_id(1);
- unsigned int globalPosZ = get_global_id(2);
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices )
- {
- float l_i = (float)globalPosX / (float)outputL * (float)inputL;
-
- unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX];
- unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1];
- unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2];
-
- float apod_mult = (float)apodArraySize / (float)curUsedLines;
-
- unsigned short Delay1 = 0;
- unsigned short Delay2 = 0;
-
- float output = 0;
- float mult = 0;
-
- float s_1 = 0;
- float s_2 = 0;
- float apod_1 = 0;
-
- for (short l_s1 = minLine; l_s1 < maxLine; ++l_s1)
- {
- Delay1 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s1 - l_i)/(float)inputL * (float)outputL)];
- if (Delay1 < inputS && Delay1 >= 0)
- {
- s_1 = dSource[(int)(globalPosZ * inputL * inputS + Delay1 * inputL + l_s1)];
- apod_1 = apodArray[(int)((l_s1 - minLine)*apod_mult)];
-
- for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2)
- {
- Delay2 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s2 - l_i)/(float)inputL * (float)outputL)];
- if (Delay2 < inputS && Delay2 >= 0)
- {
- s_2 = dSource[(int)(globalPosZ * inputL * inputS + Delay2 * inputL + l_s2)];
-
- mult = apodArray[(int)((l_s2 - minLine)*apod_mult)] * s_2 * apod_1 * s_1;
-
- output += sqrt(fabs(mult)) * sign(mult);
- }
- }
- }
- else
- --curUsedLines;
- }
-
- dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)(curUsedLines * curUsedLines - (curUsedLines - 1));
- }
-}
-
-__kernel void ckDMAS_g(
- __global float* dSource, // input image
- __global float* dDest, // output buffer
- __global float* elementHeights,
- __global float* elementPositions,
- __constant float* apodArray,
- unsigned short apodArraySize,
- unsigned int inputL,
- unsigned int inputS,
- int Slices,
- int outputL,
- int outputS,
- float totalSamples_i,
- float horizontalExtent,
- float mult,
- char isPAImage,
- __global unsigned short* usedLines // parameters
-)
-{
- // get thread identifier
- int globalPosX = get_global_id(0);
- int globalPosY = get_global_id(1);
- int globalPosZ = get_global_id(2);
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices )
- {
- int AddSample1 = 0;
- int AddSample2 = 0;
-
- float output = 0;
-
- float s_1 = 0;
- float s_2 = 0;
- float apod_1 = 0;
-
- float l_p = (float)globalPosX / outputL * horizontalExtent;
- float s_i = (float)globalPosY / outputS * totalSamples_i;
-
- unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX];
- unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1];
- unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2];
-
- float apod_mult = (float)apodArraySize / curUsedLines;
-
- float multiplication = 0;
-
- for (int l_s1 = minLine; l_s1 < maxLine; ++l_s1)
- {
- AddSample1 = (int)sqrt(
- pow(s_i-elementHeights[l_s1]*mult, 2)
- +
- pow(mult * (l_p - elementPositions[l_s1]), 2)
- ) + (1 - isPAImage)*s_i;
-
- if (AddSample1 < inputS && AddSample1 >= 0)
- {
- s_1 = dSource[(int)(globalPosZ * inputL * inputS + AddSample1 * inputL + l_s1)];
- apod_1 = apodArray[(int)((l_s1 - minLine)*apod_mult)];
-
- for (int l_s2 = minLine; l_s2 < maxLine; ++l_s2)
- {
- AddSample2 = (int)sqrt(
- pow(s_i-elementHeights[l_s2]*mult, 2)
- +
- pow(mult * (l_p - elementPositions[l_s2]), 2)
- ) + (1 - isPAImage)*s_i;
- if (AddSample2 < inputS && AddSample2 >= 0)
- {
- s_2 = dSource[(int)(globalPosZ * inputL * inputS + AddSample2 * inputL + l_s2)];
- multiplication = apodArray[(int)((l_s2 - minLine)*apod_mult)] * s_2 * apod_1 * s_1;
-
- output += sqrt(fabs(multiplication)) * sign(multiplication);
- }
- }
- }
- else
- --curUsedLines;
- }
- dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)(pow((float)curUsedLines, 2) - (curUsedLines - 1));
- }
-}
diff --git a/Modules/PhotoacousticsAlgorithms/Resources/DelayCalculation.cl b/Modules/PhotoacousticsAlgorithms/Resources/DelayCalculation.cl
deleted file mode 100644
index 0ecda5781e..0000000000
--- a/Modules/PhotoacousticsAlgorithms/Resources/DelayCalculation.cl
+++ /dev/null
@@ -1,40 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-__kernel void ckDelayCalculationSphe( __global unsigned short *gDest,
- __global unsigned short *usedLines,
- unsigned int inputL,
- unsigned int inputS,
- unsigned int outputL,
- unsigned int outputS,
- char isPAImage,
- float delayMultiplicatorRaw,
- float totalSamples_i // parameters
- )
-{
- uint globalPosX = get_global_id(0);
- uint globalPosY = get_global_id(1);
-
- if (globalPosX * 2 < outputL && globalPosY < outputS)
- {
- float l_i = 0; // we calculate the delays relative to line zero
- float s_i = (float)globalPosY / (float)outputS * totalSamples_i;
- float l_s = (float)globalPosX / (float)outputL * (float)inputL; // the currently calculated line
-
- gDest[globalPosY * (outputL / 2) + globalPosX] =
- sqrt(
- pow(s_i, 2)
- +
- pow((delayMultiplicatorRaw * ((l_s - l_i)) / inputL), 2)
- ) + (1-isPAImage)*s_i;
- }
-}
diff --git a/Modules/PhotoacousticsAlgorithms/Resources/UsedLinesCalculation.cl b/Modules/PhotoacousticsAlgorithms/Resources/UsedLinesCalculation.cl
deleted file mode 100644
index 46d4629000..0000000000
--- a/Modules/PhotoacousticsAlgorithms/Resources/UsedLinesCalculation.cl
+++ /dev/null
@@ -1,128 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-__kernel void ckUsedLines(
- __global unsigned short* dDest, // output buffer
- float partMult,
- unsigned int inputL,
- unsigned int inputS,
- unsigned int outputL,
- unsigned int outputS,
- float totalSamples_i // parameters
-)
-{
- // get thread identifier
- unsigned int globalPosX = get_global_id(0);
- unsigned int globalPosY = get_global_id(1);
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS)
- {
- float l_i = (float)globalPosX / outputL * inputL;
- float s_i = (float)globalPosY / (float)outputS * totalSamples_i;
-
- float part = partMult * s_i;
- if (part < 1)
- part = 1;
-
- unsigned short maxLine = min((l_i + part) + 1, (float)inputL);
- unsigned short minLine = max((l_i - part), 0.0f);
-
- dDest[globalPosY * 3 * outputL + 3 * globalPosX] = (maxLine - minLine); //usedLines
- dDest[globalPosY * 3 * outputL + 3 * globalPosX + 1] = minLine; //minLine
- dDest[globalPosY * 3 * outputL + 3 * globalPosX + 2] = maxLine; //maxLine
- }
-}
-
-__kernel void ckUsedLines_g(
- __global unsigned short* dDest, // output buffer
- __global float* elementHeights,
- __global float* elementPositions,
- float sin_deg,
- float probeRadius,
- unsigned int inputL,
- unsigned int inputS,
- unsigned int outputL,
- unsigned int outputS,
- float horizontalExtent,
- float verticalExtent
-)
-{
- // get thread identifier
- unsigned int globalPosX = get_global_id(0);
- unsigned int globalPosY = get_global_id(1);
-
- float x_sensor_pos = 0;
- float y_sensor_pos = 0;
- float center_to_sensor_a = 0;
- float center_to_sensor_b = 0;
- float center_to_sensor_c = 0;
- float distance_to_sensor_direction = 0;
- float distance_sensor_target = 0;
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS)
- {
- float x_cm = (float)globalPosX / outputL * horizontalExtent; // x*Xspacing
- float y_cm = (float)globalPosY / (float)outputS * verticalExtent; // y*Yspacing
-
- int maxLine = inputL;
- int minLine = 0;
-
- float x_center_pos = horizontalExtent / 2.0;
- float y_center_pos = probeRadius;
-
- for (int l_s = minLine; l_s <= inputL; l_s += 1)
- {
- x_sensor_pos = elementPositions[l_s];
- y_sensor_pos = elementHeights[l_s];
-
- distance_sensor_target = sqrt((x_cm - x_sensor_pos)*(x_cm - x_sensor_pos) + (y_cm - y_sensor_pos)*(y_cm - y_sensor_pos));
-
- // solving line equation
- center_to_sensor_a = y_sensor_pos - y_center_pos;
- center_to_sensor_b = x_center_pos - x_sensor_pos;
- center_to_sensor_c = -(center_to_sensor_a * x_center_pos + center_to_sensor_b * y_center_pos);
- distance_to_sensor_direction = fabs((center_to_sensor_a * x_cm + center_to_sensor_b * y_cm + center_to_sensor_c)) / (sqrt(center_to_sensor_a*center_to_sensor_a + center_to_sensor_b*center_to_sensor_b));
-
- if (distance_to_sensor_direction < (sin_deg*distance_sensor_target))
- {
- minLine = l_s;
- break;
- }
- }
-
- for (int l_s = maxLine - 1; l_s > minLine; l_s -= 1) // start with maxline-1 otherwise elementPositions[] will go out of range
- {
- x_sensor_pos = elementPositions[l_s];
- y_sensor_pos = elementHeights[l_s];
-
- distance_sensor_target = sqrt((x_cm - x_sensor_pos)*(x_cm - x_sensor_pos) + (y_cm - y_sensor_pos)*(y_cm - y_sensor_pos));
-
- // solving line equation
- center_to_sensor_a = y_sensor_pos - y_center_pos;
- center_to_sensor_b = x_center_pos - x_sensor_pos;
- center_to_sensor_c = -(center_to_sensor_a * x_center_pos + center_to_sensor_b * y_center_pos);
- distance_to_sensor_direction = fabs((center_to_sensor_a * x_cm + center_to_sensor_b * y_cm + center_to_sensor_c)) / (sqrt(center_to_sensor_a*center_to_sensor_a + center_to_sensor_b*center_to_sensor_b));
-
- if (distance_to_sensor_direction < sin_deg*distance_sensor_target)
- {
- maxLine = l_s;
- break;
- }
- }
-
- dDest[globalPosY * 3 * outputL + 3 * globalPosX] = (maxLine - minLine); //usedLines
- dDest[globalPosY * 3 * outputL + 3 * globalPosX + 1] = minLine; //minLine
- dDest[globalPosY * 3 * outputL + 3 * globalPosX + 2] = maxLine; //maxLine
- }
-}
diff --git a/Modules/PhotoacousticsAlgorithms/Resources/sDMAS.cl b/Modules/PhotoacousticsAlgorithms/Resources/sDMAS.cl
deleted file mode 100644
index ab37ae7e0a..0000000000
--- a/Modules/PhotoacousticsAlgorithms/Resources/sDMAS.cl
+++ /dev/null
@@ -1,167 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-__kernel void cksDMAS(
- __global float* dSource, // input image
- __global float* dDest, // output buffer
- __global unsigned short* usedLines,
- __global unsigned short* AddSamples,
- __constant float* apodArray,
- unsigned short apodArraySize,
- unsigned int inputL,
- unsigned int inputS,
- unsigned int Slices,
- unsigned int outputL,
- unsigned int outputS // parameters
-)
-{
- // get thread identifier
- unsigned int globalPosX = get_global_id(0);
- unsigned int globalPosY = get_global_id(1);
- unsigned int globalPosZ = get_global_id(2);
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices )
- {
- float l_i = (float)globalPosX / (float)outputL * (float)inputL;
-
- unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX];
- unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1];
- unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2];
-
- float apod_mult = (float)apodArraySize / (float)curUsedLines;
-
- unsigned short Delay1 = 0;
- unsigned short Delay2 = 0;
-
- float output = 0;
- float mult = 0;
-
- float s_1 = 0;
- float s_2 = 0;
- float dSign = 0;
- float apod_1 = 0;
-
- for (short l_s1 = minLine; l_s1 < maxLine; ++l_s1)
- {
- Delay1 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s1 - l_i)/(float)inputL * (float)outputL)];
- if (Delay1 < inputS && Delay1 >= 0)
- {
- s_1 = dSource[(int)(globalPosZ * inputL * inputS + Delay1 * inputL + l_s1)];
- apod_1 = apodArray[(int)((l_s1 - minLine)*apod_mult)];
- dSign += s_1;
-
- for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2)
- {
- Delay2 = AddSamples[globalPosY * (outputL / 2) + (int)(fabs(l_s2 - l_i)/(float)inputL * (float)outputL)];
- if (Delay2 < inputS && Delay2 >= 0)
- {
- s_2 = dSource[(int)(globalPosZ * inputL * inputS + Delay2 * inputL + l_s2)];
-
- mult = apodArray[(int)((l_s2 - minLine)*apod_mult)] * s_2 * apod_1 * s_1;
-
- output += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0));
- }
- }
- }
- else
- --curUsedLines;
- }
-
- dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)(curUsedLines * curUsedLines - (curUsedLines - 1)) * sign(dSign);
- }
-}
-
-__kernel void cksDMAS_g(
- __global float* dSource, // input image
- __global float* dDest, // output buffer
- __global float* elementHeights,
- __global float* elementPositions,
- __constant float* apodArray,
- unsigned short apodArraySize,
- unsigned int inputL,
- unsigned int inputS,
- int Slices,
- int outputL,
- int outputS,
- float totalSamples_i,
- float horizontalExtent,
- float mult,
- char isPAImage,
- __global unsigned short* usedLines // parameters
-)
-{
- // get thread identifier
- int globalPosX = get_global_id(0);
- int globalPosY = get_global_id(1);
- int globalPosZ = get_global_id(2);
-
- // terminate non-valid threads
- if ( globalPosX < outputL && globalPosY < outputS && globalPosZ < Slices )
- {
- int AddSample1 = 0;
- int AddSample2 = 0;
-
- float output = 0;
-
- float s_1 = 0;
- float s_2 = 0;
- float apod_1 = 0;
-
- float l_p = (float)globalPosX / outputL * horizontalExtent;
- float s_i = (float)globalPosY / outputS * totalSamples_i;
-
- unsigned short curUsedLines = usedLines[globalPosY * 3 * outputL + 3 * globalPosX];
- unsigned short minLine = usedLines[globalPosY * 3 * outputL + 3 * globalPosX + 1];
- unsigned short maxLine = usedLines[globalPosY * 3 *outputL + 3 * globalPosX + 2];
-
- float apod_mult = (float)apodArraySize / curUsedLines;
- float dSign = 0;
-
- float multiplication = 0;
-
- for (int l_s1 = minLine; l_s1 < maxLine; ++l_s1)
- {
- AddSample1 = (int)sqrt(
- pow(s_i-elementHeights[l_s1]*mult, 2)
- +
- pow(mult * (l_p - elementPositions[l_s1]), 2)
- ) + (1 - isPAImage)*s_i;
-
- if (AddSample1 < inputS && AddSample1 >= 0)
- {
- s_1 = dSource[(int)(globalPosZ * inputL * inputS + AddSample1 * inputL + l_s1)];
- apod_1 = apodArray[(int)((l_s1 - minLine)*apod_mult)];
- dSign += s_1;
-
- for (int l_s2 = minLine; l_s2 < maxLine; ++l_s2)
- {
- AddSample2 = (int)sqrt(
- pow(s_i-elementHeights[l_s2]*mult, 2)
- +
- pow(mult * (l_p - elementPositions[l_s2]), 2)
- ) + (1 - isPAImage)*s_i;
- if (AddSample2 < inputS && AddSample2 >= 0)
- {
- s_2 = dSource[(int)(globalPosZ * inputL * inputS + AddSample2 * inputL + l_s2)];
- multiplication = apodArray[(int)((l_s2 - minLine)*apod_mult)] * s_2 * apod_1 * s_1;
-
- output += sqrt(fabs(multiplication)) * sign(multiplication);
- }
- }
- }
- else
- --curUsedLines;
- }
- dDest[ globalPosZ * outputL * outputS + globalPosY * outputL + globalPosX ] = output / (float)(pow((float)curUsedLines, 2) - (curUsedLines - 1)) * sign(dSign);
- }
-}
diff --git a/Modules/PhotoacousticsAlgorithms/files.cmake b/Modules/PhotoacousticsAlgorithms/files.cmake
deleted file mode 100644
index 87f8116092..0000000000
--- a/Modules/PhotoacousticsAlgorithms/files.cmake
+++ /dev/null
@@ -1,31 +0,0 @@
-
-file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*")
-
-set(CPP_FILES
- source/filters/mitkBeamformingFilter.cpp
- source/filters/mitkBeamformingSettings.cpp
- source/filters/mitkImageSliceSelectionFilter.cpp
- source/filters/mitkCastToFloatImageFilter.cpp
- source/filters/mitkCropImageFilter.cpp
- source/filters/mitkBandpassFilter.cpp
- source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp
- source/utils/mitkPhotoacousticFilterService.cpp
- source/utils/mitkBeamformingUtils.cpp
- source/mitkPhotoacousticMotionCorrectionFilter.cpp
-)
-
-IF(MITK_USE_OpenCL)
-list(APPEND CPP_FILES
- source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp
- source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp
- source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp
-)
-ENDIF(MITK_USE_OpenCL)
-
-set(RESOURCE_FILES
- UsedLinesCalculation.cl
- DelayCalculation.cl
- DMAS.cl
- DAS.cl
- sDMAS.cl
-)
diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticBModeFilter.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticBModeFilter.h
deleted file mode 100644
index 63c239e9f3..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticBModeFilter.h
+++ /dev/null
@@ -1,63 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef _MITKPHOTOACOUSTICSBMODEFILTER_H_
-#define _MITKPHOTOACOUSTICSBMODEFILTER_H_
-
-#include <itkObject.h>
-#include "mitkImageToImageFilter.h"
-
-namespace mitk
-{
- /*!
- * \brief Class implementing a mitk::ImageToImageFilter for BMode filtering on CPU
- *
- * The only parameter that needs to be provided is whether it should use a logfilter.
- * Currently this class only performs an absolute BMode filter.
- */
- class PhotoacousticBModeFilter : public ImageToImageFilter
- {
- public:
- mitkClassMacro(PhotoacousticBModeFilter, ImageToImageFilter);
-
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- /** \brief Set parameters for the filter
- *
- * @param useLogFilter If true, the filter will apply a logfilter on the processed image
- */
- void UseLogFilter(bool useLogFilter)
- {
- m_UseLogFilter = useLogFilter;
- }
-
- protected:
-
- PhotoacousticBModeFilter();
-
- ~PhotoacousticBModeFilter() override;
-
- void GenerateInputRequestedRegion() override;
-
- void GenerateOutputInformation() override;
-
- void GenerateData() override;
-
- //##Description
- //## @brief Time when Header was last initialized
- itk::TimeStamp m_TimeOfHeaderInitialization;
-
- bool m_UseLogFilter;
- };
-}
-#endif /* _MITKPHOTOACOUSTICSBMODEFILTER_H_ */
diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h
deleted file mode 100644
index 2c2bd99680..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h
+++ /dev/null
@@ -1,143 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_
-#define _MITKPHOTOACOUSTICSOCLBEAMFORMER_H_
-
-#include <itkObject.h>
-
-#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN
-
-#include "mitkOclDataSetToDataSetFilter.h"
-#include "mitkBeamformingSettings.h"
-#include "mitkPhotoacousticOCLDelayCalculation.h"
-#include "mitkPhotoacousticOCLUsedLinesCalculation.h"
-
-#include <chrono>
-
-namespace mitk
-{
- /*!
- * \brief Class implementing a mitk::OclDataSetToDataSetFilter for beamforming on GPU
- *
- * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::PhotoacousticOCLBeamformingFilter::SetConfig(BeamformingSettings settings)
- * Additional configuration of the apodisation function is needed.
- */
-
- class PhotoacousticOCLBeamformingFilter : public OclDataSetToDataSetFilter, public itk::Object
- {
- public:
- mitkClassMacroItkParent(PhotoacousticOCLBeamformingFilter, itk::Object);
- mitkNewMacro1Param(Self, BeamformingSettings::Pointer);
-
- /**
- * @brief SetInput Set the input data through an image. Arbitrary images are supported
- */
- void SetInput(Image::Pointer image);
- /**
- * brief SetInput Manually set the input data while providing 3 dimensions and memory size of the input data (Bytes per element).
- */
- void SetInput(void* data, unsigned int* dimensions, unsigned int BpE);
- /**
- * @brief GetOutput Get a pointer to the processed data. The standard datatype is float.
- */
- void* GetOutput();
-
- /**
- * @brief GetOutputAsImage Returns an mitk::Image constructed from the processed data
- */
- mitk::Image::Pointer GetOutputAsImage();
-
- /** \brief Update the filter */
- void Update();
-
- /** \brief Set the Apodisation function to apply when beamforming */
- void SetApodisation(const float* apodisation, unsigned short apodArraySize)
- {
- m_ApodArraySize = apodArraySize;
- m_Apodisation = apodisation;
- }
-
- protected:
-
- PhotoacousticOCLBeamformingFilter(BeamformingSettings::Pointer settings);
- virtual ~PhotoacousticOCLBeamformingFilter();
-
- /** \brief Initialize the filter */
- bool Initialize();
-
- /** \brief Updated the used data for beamforming depending on whether the configuration has significantly changed */
- void UpdateDataBuffers();
-
- /** \brief Execute the filter */
- void Execute();
-
- mitk::PixelType GetOutputType()
- {
- return mitk::MakeScalarPixelType<float>();
- }
-
- int GetBytesPerElem()
- {
- return sizeof(float);
- }
-
- virtual us::Module* GetModule();
-
- private:
- /** The OpenCL kernel for the filter */
- cl_kernel m_PixelCalculation;
-
- unsigned int m_OutputDim[3];
-
- const float* m_Apodisation;
- unsigned short m_ApodArraySize;
- unsigned int m_inputSlices;
-
- unsigned short m_PAImage;
-
- BeamformingSettings::Pointer m_Conf;
-
- mitk::Image::Pointer m_InputImage;
-
- size_t m_ChunkSize[3];
-
- mitk::OCLUsedLinesCalculation::Pointer m_UsedLinesCalculation;
- mitk::OCLDelayCalculation::Pointer m_DelayCalculation;
-
- cl_mem m_ApodizationBuffer;
- cl_mem m_DelaysBuffer;
- cl_mem m_UsedLinesBuffer;
- cl_mem m_ElementHeightsBuffer;
- cl_mem m_ElementPositionsBuffer;
-
- };
-}
-#else
-namespace mitk
-{
- class PhotoacousticOCLBeamformingFilter : public itk::Object
- {
- public:
- mitkClassMacroItkParent(mitk::PhotoacousticOCLBeamformingFilter, itk::Object);
- itkNewMacro(Self);
-
- protected:
- /** Constructor */
- PhotoacousticOCLBeamformingFilter() {}
-
- /** Destructor */
- ~PhotoacousticOCLBeamformingFilter() override {}
- };
-}
-#endif
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h
deleted file mode 100644
index 3b0bb88905..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h
+++ /dev/null
@@ -1,85 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef _MITKPHOTOACOUSTICSDELAYCALC_H_
-#define _MITKPHOTOACOUSTICSDELAYCALC_H_
-
-#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN
-
-#include "mitkOclDataSetToDataSetFilter.h"
-#include <itkObject.h>
-#include "mitkBeamformingSettings.h"
-
-namespace mitk
-{
- /*!
- * \brief Class implementing a mitk::OclDataSetToDataSetFilter to calculate the delays used for beamforming.
- *
- * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::OCLDelayCalculation::SetConfig(BeamformingSettings conf)
- * Additionally the output of an instance of mitk::OCLUsedLinesCalculation is needed to calculate the delays.
- */
-
- class OCLDelayCalculation : public OclDataSetToDataSetFilter, public itk::Object
- {
- public:
- mitkClassMacroItkParent(OCLDelayCalculation, itk::Object);
- mitkNewMacro1Param(Self, mitk::BeamformingSettings::Pointer);
-
- void Update();
-
- /** \brief Sets the usedLines buffer object to use for the calculation of the delays.
- *
- * @param usedLines An buffer generated as the output of an instance of mitk::OCLUsedLinesCalculation.
- */
- void SetInputs(cl_mem usedLines)
- {
- m_UsedLines = usedLines;
- }
-
- protected:
-
- OCLDelayCalculation(mitk::BeamformingSettings::Pointer settings);
- virtual ~OCLDelayCalculation();
-
- /** Initialize the filter */
- bool Initialize();
-
- void Execute();
-
- mitk::PixelType GetOutputType()
- {
- return mitk::MakeScalarPixelType<unsigned short>();
- }
-
- int GetBytesPerElem()
- {
- return sizeof(unsigned short);
- }
-
- virtual us::Module* GetModule();
-
- int m_sizeThis;
-
- private:
- /** The OpenCL kernel for the filter */
- cl_kernel m_PixelCalculation;
-
- BeamformingSettings::Pointer m_Conf;
- cl_mem m_UsedLines;
- unsigned int m_BufferSize;
- float m_DelayMultiplicatorRaw;
- char m_IsPAImage;
- size_t m_ChunkSize[3];
- };
-}
-#endif
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h b/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h
deleted file mode 100644
index 2fbe81bf48..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h
+++ /dev/null
@@ -1,80 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef _MITKPHOTOACOUSTICSOCLUSEDLINESCALCULATION_H_
-#define _MITKPHOTOACOUSTICSOCLUSEDLINESCALCULATION_H_
-
-#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN
-
-#include "mitkOclDataSetToDataSetFilter.h"
-#include <itkObject.h>
-#include "mitkBeamformingSettings.h"
-
-namespace mitk
-{
- /*!
- * \brief Class implementing a mitk::OclDataSetToDataSetFilter to calculate which lines each sample should use when beamforming.
- *
- * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::OCLDelayCalculation::SetConfig(BeamformingSettings conf)
- */
-
- class OCLUsedLinesCalculation : public OclDataSetToDataSetFilter, public itk::Object
- {
- public:
- mitkClassMacroItkParent(OCLUsedLinesCalculation, itk::Object);
- mitkNewMacro1Param(Self, mitk::BeamformingSettings::Pointer);
-
- void Update();
-
- void SetElementHeightsBuffer(cl_mem elementHeightsBuffer);
- void SetElementPositionsBuffer(cl_mem elementPositionsBuffer);
-
- protected:
-
- /** Constructor */
- OCLUsedLinesCalculation(mitk::BeamformingSettings::Pointer settings);
-
- /** Destructor */
- virtual ~OCLUsedLinesCalculation();
-
- /** Initialize the filter */
- bool Initialize();
-
- void Execute();
-
- mitk::PixelType GetOutputType()
- {
- return mitk::MakeScalarPixelType<unsigned short>();
- }
-
- int GetBytesPerElem()
- {
- return sizeof(unsigned short);
- }
-
- virtual us::Module* GetModule();
-
- int m_sizeThis;
-
- private:
- /** The OpenCL kernel for the filter */
- cl_kernel m_PixelCalculation;
-
- BeamformingSettings::Pointer m_Conf;
- float m_part;
- size_t m_ChunkSize[3];
- cl_mem m_ElementHeightsBuffer;
- cl_mem m_ElementPositionsBuffer;
- };
-}
-#endif
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkBandpassFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkBandpassFilter.h
deleted file mode 100644
index a3f990736a..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkBandpassFilter.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITK_BANDPASS_FILTER
-#define MITK_BANDPASS_FILTER
-
-#include "mitkImageToImageFilter.h"
-#include "MitkPhotoacousticsAlgorithmsExports.h"
-#include "mitkPhotoacousticFilterService.h"
-
-namespace mitk {
- /*!
- * \brief Class implementing an mitk::ImageToImageFilter for casting any mitk image to a float image
- */
-
- class MITKPHOTOACOUSTICSALGORITHMS_EXPORT BandpassFilter : public ImageToImageFilter
- {
- public:
- mitkClassMacro(BandpassFilter, ImageToImageFilter);
-
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- itkSetMacro(HighPass, float);
- itkSetMacro(LowPass, float);
- itkSetMacro(HighPassAlpha, float);
- itkSetMacro(LowPassAlpha, float);
- itkSetMacro(SpeedOfSound, float);
- itkSetMacro(TimeSpacing, float);
- itkSetMacro(IsBFImage, bool);
-
- protected:
- BandpassFilter();
-
- ~BandpassFilter() override;
-
- void SanityCheckPreconditions();
-
- float m_SpeedOfSound;
- float m_TimeSpacing;
- bool m_IsBFImage;
- float m_HighPass;
- float m_LowPass;
- float m_HighPassAlpha;
- float m_LowPassAlpha;
- mitk::PhotoacousticFilterService::Pointer m_FilterService;
-
- void GenerateData() override;
- };
-} // namespace mitk
-
-#endif //MITK_CAST_TO_FLOAT_IMAGE_FILTER
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h
deleted file mode 100644
index 8828ed1d29..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingFilter.h
+++ /dev/null
@@ -1,86 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER
-#define MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER
-
-#include "mitkImageToImageFilter.h"
-#include <functional>
-#include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h"
-#include "mitkBeamformingSettings.h"
-#include "mitkBeamformingUtils.h"
-#include "MitkPhotoacousticsAlgorithmsExports.h"
-
-namespace mitk {
- /*!
- * \brief Class implementing an mitk::ImageToImageFilter for beamforming on both CPU and GPU
- *
- * The class must be given a configuration class instance of mitk::BeamformingSettings for beamforming parameters through mitk::BeamformingFilter::Configure(BeamformingSettings settings)
- * Whether the GPU is used can be set in the configuration.
- * For significant problems or important messages a string is written, which can be accessed via GetMessageString().
- */
-
- class MITKPHOTOACOUSTICSALGORITHMS_EXPORT BeamformingFilter : public ImageToImageFilter
- {
- public:
- mitkClassMacro(BeamformingFilter, ImageToImageFilter);
-
- mitkNewMacro1Param(Self, mitk::BeamformingSettings::Pointer);
- itkCloneMacro(Self);
-
- /** \brief Sets a callback for progress checking
- *
- * An std::function<void(int, std::string)> can be set, through which progress of the currently updating filter is reported.
- * The integer argument is a number between 0 an 100 to indicate how far completion has been achieved, the std::string argument indicates what the filter is currently doing.
- */
- void SetProgressHandle(std::function<void(int, std::string)> progressHandle);
-
- protected:
- BeamformingFilter(mitk::BeamformingSettings::Pointer settings);
-
- ~BeamformingFilter() override;
-
- void GenerateInputRequestedRegion() override;
-
- void GenerateOutputInformation() override;
-
- void GenerateData() override;
-
- //##Description
- //## @brief Time when Header was last initialized
- itk::TimeStamp m_TimeOfHeaderInitialization;
-
- /** \brief The std::function<void(int, std::string)>, through which progress of the currently updating filter is reported.
- */
- std::function<void(int, std::string)> m_ProgressHandle;
-
- float* m_OutputData;
- float* m_InputData;
- float* m_InputDataPuffer;
- unsigned short* m_MinMaxLines;
-
- /** \brief Current configuration set
- */
- BeamformingSettings::Pointer m_Conf;
-
- /**
- * The size of the apodization array when it last changed.
- */
- int m_LastApodizationArraySize;
-
- /** \brief Pointer to the GPU beamforming filter class; for performance reasons the filter is initialized within the constructor and kept for all later computations.
- */
- mitk::PhotoacousticOCLBeamformingFilter::Pointer m_BeamformingOclFilter;
- };
-} // namespace mitk
-
-#endif //MITK_PHOTOACOUSTICS_BEAMFORMING_FILTER
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h
deleted file mode 100644
index dbb6c4f129..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingSettings.h
+++ /dev/null
@@ -1,244 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITK_BEAMFORMING_SETTINGS
-#define MITK_BEAMFORMING_SETTINGS
-
-#include <itkObject.h>
-#include <itkMacro.h>
-#include <mitkCommon.h>
-#include <MitkPhotoacousticsAlgorithmsExports.h>
-
-namespace mitk {
- /*!
- * \brief Class holding the configuration data for the beamforming filters mitk::BeamformingFilter and mitk::PhotoacousticOCLBeamformingFilter
- *
- * A detailed description can be seen below. All parameters should be set manually for successfull beamforming.
- */
-
- class MITKPHOTOACOUSTICSALGORITHMS_EXPORT BeamformingSettings : public itk::Object
- {
- public:
- mitkClassMacroItkParent(BeamformingSettings, itk::Object);
- itkCloneMacro(Self);
-
- /** \brief Available apodization functions:
- * - Hamming function.
- * - Von-Hann function.
- * - Box function.
- */
- enum Apodization { Hamm, Hann, Box };
-
- /** \brief Available beamforming algorithms:
- * - DAS (Delay and sum).
- * - DMAS (Delay multiply and sum).
- */
- enum BeamformingAlgorithm { DMAS, DAS, sDMAS };
-
- /** \brief Available geometries for Probes:
- * - Linear
- * - Concave
- */
- enum ProbeGeometry { Linear, Concave};
-
- itkGetConstMacro(PitchInMeters, float);
- itkGetConstMacro(SpeedOfSound, float);
- itkGetConstMacro(TimeSpacing, float);
- itkGetConstMacro(Angle, float);
- itkGetConstMacro(IsPhotoacousticImage, bool);
- itkGetConstMacro(TransducerElements, unsigned int);
- itkGetConstMacro(SamplesPerLine, unsigned int);
- itkGetConstMacro(ReconstructionLines, unsigned int);
- itkGetConstMacro(InputDim, const unsigned int*);
- itkGetConstMacro(UseGPU, bool);
- itkGetConstMacro(GPUBatchSize, unsigned int);
- itkGetConstMacro(ApodizationFunction, const float*);
- itkGetConstMacro(Apod, Apodization);
- itkGetConstMacro(ApodizationArraySize, int);
- itkGetConstMacro(Algorithm, BeamformingAlgorithm);
- itkGetConstMacro(ReconstructionDepth, float);
- itkGetConstMacro(Geometry, ProbeGeometry);
- itkGetConstMacro(ProbeRadius, float);
- itkGetConstMacro(ElementHeights, float*);
- itkGetConstMacro(ElementPositions, float*);
- itkGetConstMacro(HorizontalExtent, float);
-
- /** \brief function for mitk::PhotoacousticOCLBeamformingFilter to check whether buffers need to be updated
- * this method only checks parameters relevant for the openCL implementation
- */
- static bool SettingsChangedOpenCL(const BeamformingSettings::Pointer lhs, const BeamformingSettings::Pointer rhs)
- {
- return !((std::abs(lhs->GetAngle() - rhs->GetAngle()) < 0.01f) && // 0.01 degree error margin
- (lhs->GetApod() == rhs->GetApod()) &&
- (lhs->GetGeometry() == rhs->GetGeometry()) &&
- (std::abs(lhs->GetProbeRadius() - rhs->GetProbeRadius()) < 0.001f) &&
- (lhs->GetIsPhotoacousticImage() == rhs->GetIsPhotoacousticImage()) &&
- (std::abs(lhs->GetPitchInMeters() - rhs->GetPitchInMeters()) < 0.000001f) && // 0.0001 mm error margin
- (lhs->GetReconstructionLines() == rhs->GetReconstructionLines()) &&
- (lhs->GetSamplesPerLine() == rhs->GetSamplesPerLine()) &&
- (lhs->GetReconstructionDepth() == rhs->GetReconstructionDepth()) &&
- (std::abs(lhs->GetSpeedOfSound() - rhs->GetSpeedOfSound()) < 0.01f) &&
- (std::abs(lhs->GetTimeSpacing() - rhs->GetTimeSpacing()) < 0.00000000001f) && //0.01 ns error margin
- (lhs->GetTransducerElements() == rhs->GetTransducerElements()));
- }
-
- static Pointer New(float pitchInMeters,
- float speedOfSound,
- float timeSpacing,
- float angle,
- bool isPhotoacousticImage,
- unsigned int samplesPerLine,
- unsigned int reconstructionLines,
- unsigned int* inputDim,
- float reconstructionDepth,
- bool useGPU,
- unsigned int GPUBatchSize,
- Apodization apod,
- unsigned int apodizationArraySize,
- BeamformingAlgorithm algorithm,
- ProbeGeometry geometry,
- float probeRadius)
- {
- Pointer smartPtr = new BeamformingSettings(pitchInMeters,
- speedOfSound,
- timeSpacing,
- angle,
- isPhotoacousticImage,
- samplesPerLine,
- reconstructionLines,
- inputDim,
- reconstructionDepth,
- useGPU,
- GPUBatchSize,
- apod,
- apodizationArraySize,
- algorithm,
- geometry,
- probeRadius);
- smartPtr->UnRegister();
- return smartPtr;
- }
-
- unsigned short* GetMinMaxLines();
-
- protected:
-
- /**
- */
- BeamformingSettings(float pitchInMeters,
- float speedOfSound,
- float timeSpacing,
- float angle,
- bool isPhotoacousticImage,
- unsigned int samplesPerLine,
- unsigned int reconstructionLines,
- unsigned int* inputDim,
- float reconstructionDepth,
- bool useGPU,
- unsigned int GPUBatchSize,
- Apodization apod,
- unsigned int apodizationArraySize,
- BeamformingAlgorithm algorithm,
- ProbeGeometry geometry,
- float probeRadius
- );
-
- ~BeamformingSettings() override;
-
- /** \brief Pitch of the used transducer in [m].
- */
- float m_PitchInMeters;
-
- /** \brief Speed of sound in the used medium in [m/s].
- */
- float m_SpeedOfSound;
-
- /** \brief The time spacing of the input image
- */
- float m_TimeSpacing; // [s]
-
- /** \brief The angle of the transducer elements
- */
- float m_Angle;
-
- /** \brief Flag whether processed image is a photoacoustic image or an ultrasound image
- */
- bool m_IsPhotoacousticImage;
-
- /** \brief How many transducer elements the used transducer had.
- */
- unsigned int m_TransducerElements;
-
- /** \brief How many vertical samples should be used in the final image.
- */
- unsigned int m_SamplesPerLine;
-
- /** \brief How many lines should be reconstructed in the final image.
- */
- unsigned int m_ReconstructionLines;
-
- /** \brief Sets the dimensions of the inputImage.
- */
- const unsigned int* m_InputDim;
-
- /** \brief The Depth up to which the filter should reconstruct the image [m]
- */
- float m_ReconstructionDepth;
-
- /** \brief Decides whether GPU computing should be used
- */
- bool m_UseGPU;
-
- unsigned int m_GPUBatchSize;
- /** \brief Sets the amount of image slices in batches when GPU is used
- */
-
- const float* m_ApodizationFunction;
-
- /** \brief Sets the used apodization function.
- */
- Apodization m_Apod;
-
- /** \brief Sets the resolution of the apodization array (must be greater than 0).
- */
- int m_ApodizationArraySize;
-
- /** \brief Sets the used beamforming algorithm.
- */
- BeamformingAlgorithm m_Algorithm;
-
- /** \brief Sets the used probe geometry
- */
- ProbeGeometry m_Geometry;
-
- /** \brief Sets the radius of the curved probe [m]
- */
- float m_ProbeRadius;
-
- /**
- */
- float *m_ElementHeights;
-
- /**
- */
- float *m_ElementPositions;
-
- /**
- */
- float m_HorizontalExtent;
-
- /**
- */
- unsigned short* m_MinMaxLines;
- };
-}
-#endif //MITK_BEAMFORMING_SETTINGS
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h b/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h
deleted file mode 100644
index 5a53157e44..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkBeamformingUtils.h
+++ /dev/null
@@ -1,68 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITK_BEAMFORMING_FILTER_UTILS
-#define MITK_BEAMFORMING_FILTER_UTILS
-
-#include "mitkImageToImageFilter.h"
-#include <functional>
-#include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h"
-#include "mitkBeamformingSettings.h"
-
-namespace mitk {
- /*!
- * \brief Class implementing util functionality for beamforming on CPU
- *
- */
- class BeamformingUtils final
- {
- public:
-
- /** \brief Function to perform beamforming on CPU for a single line, using DAS and spherical delay
- */
- static void DASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config);
-
- /** \brief Function to perform beamforming on CPU for a single line, using DMAS and spherical delay
- */
- static void DMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config);
-
- /** \brief Function to perform beamforming on CPU for a single line, using signed DMAS and spherical delay
- */
- static void sDMASSphericalLine(float* input, float* output, float inputDim[2], float outputDim[2], const short& line, const mitk::BeamformingSettings::Pointer config);
-
- /** \brief Pointer holding the Von-Hann apodization window for beamforming
- * @param samples the resolution at which the window is created
- */
- static float* VonHannFunction(int samples);
-
- /** \brief Function to create a Hamming apodization window
- * @param samples the resolution at which the window is created
- */
- static float* HammFunction(int samples);
-
- /** \brief Function to create a Box apodization window
- * @param samples the resolution at which the window is created
- */
- static float* BoxFunction(int samples);
-
- /** \brief
- */
- static unsigned short* MinMaxLines(const mitk::BeamformingSettings::Pointer config);
-
- protected:
- BeamformingUtils();
-
- ~BeamformingUtils();
- };
-} // namespace mitk
-
-#endif //MITK_BEAMFORMING_FILTER_UTILS
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkCastToFloatImageFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkCastToFloatImageFilter.h
deleted file mode 100644
index 94a49f3e7e..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkCastToFloatImageFilter.h
+++ /dev/null
@@ -1,41 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITK_CAST_TO_FLOAT_IMAGE_FILTER
-#define MITK_CAST_TO_FLOAT_IMAGE_FILTER
-
-#include "mitkImageToImageFilter.h"
-#include "MitkPhotoacousticsAlgorithmsExports.h"
-
-namespace mitk {
- /*!
- * \brief Class implementing an mitk::ImageToImageFilter for casting any mitk image to a float image
- */
-
- class MITKPHOTOACOUSTICSALGORITHMS_EXPORT CastToFloatImageFilter : public ImageToImageFilter
- {
- public:
- mitkClassMacro(CastToFloatImageFilter, ImageToImageFilter);
-
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- protected:
- CastToFloatImageFilter();
-
- ~CastToFloatImageFilter() override;
-
- void GenerateData() override;
- };
-} // namespace mitk
-
-#endif //MITK_CAST_TO_FLOAT_IMAGE_FILTER
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkCropImageFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkCropImageFilter.h
deleted file mode 100644
index 3316865d0b..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkCropImageFilter.h
+++ /dev/null
@@ -1,65 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITK_CROP_IMAGE_FILTER
-#define MITK_CROP_IMAGE_FILTER
-
-#include <MitkPhotoacousticsAlgorithmsExports.h>
-#include "mitkImageToImageFilter.h"
-#include "itkMacro.h"
-
-namespace mitk {
- /*!
- * \brief Class implementing an mitk::ImageToImageFilter for casting any mitk image to a float image
- */
-
- class MITKPHOTOACOUSTICSALGORITHMS_EXPORT CropImageFilter : public ImageToImageFilter
- {
- public:
- mitkClassMacro(CropImageFilter, ImageToImageFilter);
-
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- itkGetMacro(XPixelsCropStart, unsigned int);
- itkSetMacro(XPixelsCropStart, unsigned int);
- itkGetMacro(YPixelsCropStart, unsigned int);
- itkSetMacro(YPixelsCropStart, unsigned int);
- itkGetMacro(ZPixelsCropStart, unsigned int);
- itkSetMacro(ZPixelsCropStart, unsigned int);
-
- itkGetMacro(XPixelsCropEnd, unsigned int);
- itkSetMacro(XPixelsCropEnd, unsigned int);
- itkGetMacro(YPixelsCropEnd, unsigned int);
- itkSetMacro(YPixelsCropEnd, unsigned int);
- itkGetMacro(ZPixelsCropEnd, unsigned int);
- itkSetMacro(ZPixelsCropEnd, unsigned int);
-
- protected:
- CropImageFilter();
-
- ~CropImageFilter() override;
-
- void GenerateData() override;
-
- void SanityCheckPreconditions();
-
- unsigned int m_XPixelsCropStart;
- unsigned int m_YPixelsCropStart;
- unsigned int m_ZPixelsCropStart;
- unsigned int m_XPixelsCropEnd;
- unsigned int m_YPixelsCropEnd;
- unsigned int m_ZPixelsCropEnd;
- };
-} // namespace mitk
-
-#endif //MITK_CROP_IMAGE_FILTER
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkImageSliceSelectionFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkImageSliceSelectionFilter.h
deleted file mode 100644
index 4e7aaa59cc..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkImageSliceSelectionFilter.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITK_IMAGE_SLICE_SELECTION_FILTER
-#define MITK_IMAGE_SLICE_SELECTION_FILTER
-
-#include "mitkImageToImageFilter.h"
-
-namespace mitk {
- /*!
- * \brief Class implementing an mitk::ImageToImageFilter for casting any mitk image to a float image
- */
-
- class ImageSliceSelectionFilter : public ImageToImageFilter
- {
- public:
- mitkClassMacro(ImageSliceSelectionFilter, ImageToImageFilter);
-
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- protected:
- ImageSliceSelectionFilter();
-
- ~ImageSliceSelectionFilter() override;
-
- void GenerateData() override;
- };
-} // namespace mitk
-
-#endif //MITK_IMAGE_SLICE_SELECTION_FILTER
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h
deleted file mode 100644
index 4bc3447162..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticFilterService.h
+++ /dev/null
@@ -1,129 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef mitkPhotoacousticFilterService_H_HEADER_INCLUDED
-#define mitkPhotoacousticFilterService_H_HEADER_INCLUDED
-
-#include "itkObject.h"
-#include "mitkCommon.h"
-#include "mitkImage.h"
-#include <functional>
-
-#include "mitkBeamformingSettings.h"
-#include "mitkBeamformingFilter.h"
-#include "MitkPhotoacousticsAlgorithmsExports.h"
-
-namespace mitk {
- /*!
- * \brief Class holding methods to apply all Filters within the Photoacoustics Algorithms Module
- *
- * Implemented are:
- * - A B-Mode Filter
- * - A Resampling Filter
- * - Beamforming on GPU and CPU
- * - A Bandpass Filter
- */
-
- class MITKPHOTOACOUSTICSALGORITHMS_EXPORT PhotoacousticFilterService : public itk::Object
- {
- public:
- mitkClassMacroItkParent(mitk::PhotoacousticFilterService, itk::Object);
- itkFactorylessNewMacro(Self);
-
- /** \brief Defines the methods for the B-Mode filter
- * Currently implemented are an Envelope Detection filter and a simple Absolute filter.
- */
- enum BModeMethod { EnvelopeDetection, Abs };
-
- /** \brief Applies a B-Mode Filter
- *
- * Applies a B-Mode filter using the given parameters.
- * @param inputImage The image to be processed.
- * @param method The kind of B-Mode Filter to be used.
- * @param UseLogFilter Setting this to true will apply a simple logarithm to the image after the B-Mode Filter has been applied.
- * @return The processed image is returned after the filter has finished.
- */
- mitk::Image::Pointer ApplyBmodeFilter(mitk::Image::Pointer inputImage,
- BModeMethod method = BModeMethod::Abs,
- bool UseLogFilter = false);
-
- /** \brief Resamples the given image
- *
- * Resamples an image using the given parameters.
- * @param inputImage The image to be processed.
- * @param outputSpacing An array of dimensions the image should be resampled to.
- * @return The processed image is returned after the filter has finished.
- */
- mitk::Image::Pointer ApplyResampling(mitk::Image::Pointer inputImage, double* outputSpacing);
-
- mitk::Image::Pointer ApplyResamplingToDim(mitk::Image::Pointer inputImage, double* outputDimension);
-
- /** \brief Beamforms the given image
- *
- * Resamples an image using the given parameters.
- * @param inputImage The image to be processed.
- * @param config The configuration set to be used for beamforming.
- * @param progressHandle An std::function<void(int, std::string)>, through which progress of the currently updating filter is reported.
- * The integer argument is a number between 0 an 100 to indicate how far completion has been achieved, the std::string argument indicates what the filter is currently doing.
- * @return The processed image is returned after the filter has finished.
- */
- mitk::Image::Pointer ApplyBeamforming(mitk::Image::Pointer inputImage, BeamformingSettings::Pointer config, std::function<void(int, std::string)> progressHandle = [](int, std::string) {});
-
- /** \brief Crops the given image
- *
- * Crops an image in 3 dimension using the given parameters.
- * @param inputImage The image to be processed.
- * @param above How many voxels will be cut from the top of the image.
- * @param below How many voxels will be cut from the bottom of the image.
- * @param right How many voxels will be cut from the right side of the image.
- * @param left How many voxels will be cut from the left side of the image.
- * @param minSlice The first slice to be present in the resulting volume.
- * @param maxSlice How many slices are cut off from the end of the volume.
- * @param errCode
- * @return The processed image is returned after the filter has finished. For the purposes of this module, the returned image is always of type float.
- */
- mitk::Image::Pointer ApplyCropping(mitk::Image::Pointer inputImage, int above, int below, int right, int left, int minSlice, int maxSlice, int* errCode);
-
- mitk::Image::Pointer ExtendImage(mitk::Image::Pointer inputImage, float pixelColor, unsigned int outputDimensionY);
-
- /** \brief Applies a Bandpass filter to the given image
- *
- * Applies a bandpass filter to the given image using the given parameters.
- * @param data The image to be processed.
- * @param BPHighPass The position at which Lower frequencies are completely cut off in Hz.
- * @param BPLowPass The position at which Higher frequencies are completely cut off in Hz.
- * @param alphaHighPass The high pass tukey window parameter to control the shape of the bandpass filter: 0 will make it a Box function, 1 a Hann function. alpha can be set between those two bounds.
- * @param alphaLowPass The low passtukey window parameter to control the shape of the bandpass filter: 0 will make it a Box function, 1 a Hann function. alpha can be set between those two bounds.
- * @param timeSpacing
- * @param SpeedOfSound
- * @param IsBFImage
- * @return The processed image is returned after the filter has finished.
- */
- mitk::Image::Pointer ApplyBandpassFilter(mitk::Image::Pointer data,
- float BPHighPass, float BPLowPass,
- float alphaHighPass, float alphaLowPass,
- float timeSpacing, float SpeedOfSound, bool IsBFImage);
-
- protected:
- PhotoacousticFilterService();
- ~PhotoacousticFilterService() override;
-
- /** \brief
- For performance reasons, an instance of the Beamforming filter is initialized as soon as possible and kept for all further uses.
- */
- mitk::BeamformingFilter::Pointer m_BeamformingFilter;
-
- mitk::Image::Pointer ConvertToFloat(mitk::Image::Pointer);
- };
-} // namespace mitk
-
-#endif /* mitkPhotoacousticFilterService_H_HEADER_INCLUDED */
diff --git a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticMotionCorrectionFilter.h b/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticMotionCorrectionFilter.h
deleted file mode 100644
index de4d9124dc..0000000000
--- a/Modules/PhotoacousticsAlgorithms/include/mitkPhotoacousticMotionCorrectionFilter.h
+++ /dev/null
@@ -1,307 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef _MITKPHOTOACOUSTICSMOTIONCORRECTIONFILTER_H_
-#define _MITKPHOTOACOUSTICSMOTIONCORRECTIONFILTER_H_
-
-#include "mitkImageToImageFilter.h"
-#include <itkObject.h>
-
-#include "opencv2/imgproc.hpp"
-// TODO: Find out why build fails with this option or replace with something
-// else
-/* #include "opencv2/opencv.hpp" */
-#include "opencv2/video/tracking.hpp"
-
-#include "itkOpenCVImageBridge.h"
-
-#include <MitkPhotoacousticsAlgorithmsExports.h>
-
-#include "mitkImageCast.h"
-#include <mitkImageToOpenCVImageFilter.h>
-#include <mitkOpenCVToMitkImageFilter.h>
-#include <mitkImageStatisticsHolder.h>
-
-#define IMAGE_DIMENSION 3 /*!< All images need to have dimension 3*/
-#define MAX_MATRIX 255.0 /*!< Rescaling constant to maximum character*/
-
-namespace mitk
-{
- /*!
- * \brief Class implementing a mitk::ImageToImageFilter for PAUS motion
- * correction.
- *
- * The filter takes a stack of PA and US images. It then computes the optical
- * flow
- * within the US image and compensates the PA and US images for the flow.
- * Afterwards it
- * returns the stack of PA and US images.
- *
- * @see
- * https://docs.opencv.org/3.0-beta/modules/video/doc/motion_analysis_and_object_tracking.html#calcopticalflowfarneback
- */
- class MITKPHOTOACOUSTICSALGORITHMS_EXPORT PhotoacousticMotionCorrectionFilter : public ImageToImageFilter
- {
- public:
- mitkClassMacro(PhotoacousticMotionCorrectionFilter, ImageToImageFilter);
-
- itkFactorylessNewMacro(Self);
-
- // Setters and Getters for the class variables
- itkSetMacro(BatchSize, unsigned int);
- itkSetMacro(PyrScale, double);
- itkSetMacro(Levels, unsigned int);
- itkSetMacro(WinSize, unsigned int);
- itkSetMacro(Iterations, unsigned int);
- itkSetMacro(PolyN, unsigned int);
- itkSetMacro(PolySigma, double);
- itkSetMacro(Flags, unsigned int);
- itkGetConstMacro(BatchSize, unsigned int);
- itkGetConstMacro(PyrScale, double);
- itkGetConstMacro(Levels, unsigned int);
- itkGetConstMacro(WinSize, unsigned int);
- itkGetConstMacro(Iterations, unsigned int);
- itkGetConstMacro(PolyN, unsigned int);
- itkGetConstMacro(PolySigma, double);
- itkGetConstMacro(Flags, unsigned int);
-
- // Wrapper for SetInput, GetInput and GetOutput
- /*!
- * \brief Wrapper which sets the photoacoustic image as the correct input
- *
- * This method is a wrapper around the @c SetInput method. It is implemented
- * for convenience such that you do not have to remember which input is for
- * which image.
- *
- * @param input The photoacoustic image
- */
- void SetPaInput(mitk::Image::Pointer input);
- /*!
- * \brief Wrapper which gets the photoacoustic image out of the correct input
- *
- * This method is a wrapper around the @c GetInput method. It is implemented
- * for convenience such that you do not have to remember which input is for
- * which image.
- *
- * @return The photoacoustic image
- */
- mitk::Image::Pointer GetPaInput();
- /*!
- * \brief Wrapper which sets the ultrasonic image as the correct input
- *
- * This method is a wrapper around the @c SetInput method. It is implemented
- * for convenience such that you do not have to remember which input is for
- * which image.
- *
- * @param input The ultrasonic image
- */
- void SetUsInput(mitk::Image::Pointer input);
- /*!
- * \brief Wrapper which gets the ultrasonic image out of the correct input
- *
- * This method is a wrapper around the @c GetInput method. It is implemented
- * for convenience such that you do not have to remember which input is for
- * which image.
- *
- * @return The ultrasonic image
- */
- mitk::Image::Pointer GetUsInput();
- /*!
- * \brief Wrapper which gets the photoacoustic image out of the correct output
- *
- * This method is a wrapper around the @c GetOutput method. It is implemented
- * for convenience such that you do not have to remember which output is for
- * which image.
- *
- * @return The photoacoustic image
- */
- mitk::Image::Pointer GetPaOutput();
- /*!
- * \brief Wrapper which gets the ultrasonic image out of the correct output
- *
- * This method is a wrapper around the @c GetOutput method. It is implemented
- * for convenience such that you do not have to remember which output is for
- * which image.
- *
- * @return The ultrasonic image
- */
- mitk::Image::Pointer GetUsOutput();
-
- protected:
- PhotoacousticMotionCorrectionFilter();
-
- ~PhotoacousticMotionCorrectionFilter() override;
-
- /*!
- * \brief Apply OpenCV algorithm to compensate motion in a 2d image time
- * series
- *
- * This method uses two 3d mitk images. Both will be interpreted as time
- * series of 2d images. @c GetInput(0) should be a photoacoustic image whereas
- * @c GetInput(1) should be an ultrasound image. The input will be validated
- * and then converted to OpenCV matrices. In the end the Farneback algorithm
- * will be used to compute the optical flow in consecutive images and
- * compensate for this flow. The Output will be two 3d mitk images of the same
- * dimensions as the input containing the compensated data.
- *
- * @warning The input images need to be 3-dimensional (with the same size in
- * each dimension). Otherwise, an @c invalid_argument exception will be
- * thrown.
- * @throws invalid_argument
- */
- void GenerateData() override;
- /*!
- * \brief Validate the input images
- *
- * The input images have to be non-empty, 3d and have to coincide in the
- * length in each dimension. If any of these conditions are violated, the
- * method will throw an @c invalid_argument exception.
- *
- * @param paImage A mitk image
- * @param usImage A mitk image
- * @warning If the two images are not 3d and do not coincide in the length in
- * each dimension, this method will throw an @c invalid_argument exception.
- * @throws invalid_argument
- */
- void CheckInput(mitk::Image::Pointer paImage, mitk::Image::Pointer usImage);
- /*!
- * \brief Assure that the output images have the same dimensions as the input
- * images.
- *
- * The output images need to have the same dimensions as the input images.
- * This will be checked here. If the dimensions do not match, the output will
- * be reinitialized and the image data from the input images will be copied to
- * the output images (in order to make sure that they have a valid data
- * pointer).
- *
- * @param paInput Pointer to the photoacoustic input image
- * @param usInput Pointer to the ultrasonic input image
- * @param paOutput Pointer to the photoacoustic output image
- * @param usOutput Pointer to the ultrasonic output image
- */
- void InitializeOutputIfNecessary(mitk::Image::Pointer paInput,
- mitk::Image::Pointer usInput,
- mitk::Image::Pointer paOutput,
- mitk::Image::Pointer usOutput);
- /*!
- * \brief Copy the image data from the input image to the output image
- *
- * This method copys the image data from @p input to @p output. This method
- * assumes that the dimensions of the two images match and will not test this.
- *
- * @param input A mitk image
- * @param output A mitk image
- */
- void InitializeOutput(mitk::Image::Pointer input, mitk::Image::Pointer output);
- /*!
- * \brief This method performs the actual motion compensation.
- *
- * This method uses the ultrasonic input image @p usInput to compute the
- * optical flow in the time series of 2d images. Then it compensates both the
- * @p usInput and @p paInput for it and saves the result in @p usOutput and @p
- * paOutput respectively. In the background the OpenCV Farneback algorithm is
- * used for the flow determination.
- *
- * @param paInput The photoacoustic input image
- * @param usInput The ultrasonic input image
- * @param paOutput The photoacoustic output image
- * @param usOutput The ultrasonic output image
- */
- void PerformCorrection(mitk::Image::Pointer paInput,
- mitk::Image::Pointer usInput,
- mitk::Image::Pointer paOutput,
- mitk::Image::Pointer usOutput);
- /*!
- * \brief Extract a 2d slice as OpenCV matrix.
- *
- * This method extracts slice @p i from the 3-dimensional image @p input and
- * converts it to a OpenCV matrix. Internally, the
- * mitkImageToOpenCVImageFilter is used.
- *
- * @param input A 3d image from which a slice is extracted as a 2d OpenCV
- * matrix.
- * @param i Determines the slice to be extracted.
- * @return returns a OpenCV matrix containing the 2d slice.
- */
- cv::Mat GetMatrix(const mitk::Image::Pointer input, unsigned int i);
-
- /*!
- * \brief Rescale matrix such that the values lie between 0 and 255
- *
- * This method rescales the matrix such that its values lie between 0 and 255. In order to do that it uses the maximum and the minimum of the input ultrasonic image.
- *
- * @warning This is a specialized method which does not perform the operation in general, but only if the matrix stems from the right ultrasonic image. Therefore, the method should only be called internally.
- *
- * @param mat The OpenCV matrix to be rescaled
- * @return The rescaled OpenCV matrix
- */
- cv::Mat FitMatrixToChar(cv::Mat mat);
-
- /*!
- * \brief Insert a OpenCV matrix as a slice into an image
- *
- * This method converts the 2d OpenCV matrix @p mat into an mitk image using
- * the mitkOpenCVToMitkImageFilter. Afterwards it inserts the image as slice
- * @p i into the 3d mitk image @p output.
- *
- * @param mat The matrix to be inserted as a slice
- * @param output The 3d image the matrix is inserted into
- * @param i The index of the slice to be replaced.
- */
- void InsertMatrixAsSlice(cv::Mat mat, mitk::Image::Pointer output, unsigned int i);
-
- /*!
- * \brief Compute the remapping map from an optical flow
- *
- * The optical flow cannot be used directly to compensate an image. Instead we have to generate an appropriate map.
- *
- * @param flow The optical flow which is the base for the remapping.
- * @return The remapping map.
- */
- cv::Mat ComputeFlowMap(cv::Mat flow);
-
- private:
- // Parameters
- double m_PyrScale; /*!< See @c pyr_scale in @c cv::calcOpticalFlowFarneback
- */
- double m_PolySigma; /*!< See @c poly_sigma in @c cv::calcOpticalFlowFarneback
- */
- unsigned int m_Levels; /*!< See @c levels in @c cv::calcOpticalFlowFarneback */
- unsigned int m_WinSize; /*!< See @c winsize in @c cv::calcOpticalFlowFarneback */
- unsigned int m_Iterations; /*!< See @c iterations in @c cv::calcOpticalFlowFarneback */
- unsigned int m_PolyN; /*!< See @c poly_n in @c cv::calcOpticalFlowFarneback */
- unsigned int m_Flags; /*!< See @c flags in @c cv::calcOpticalFlowFarneback */
- unsigned int m_BatchSize; /*!< Determines how many slices belong together and will be
- motion compensated with regard to the first image in the
- batch. If the variable is set to 0, the whole time series will
- be processed as one batch. */
- float m_MaxValue; /*!< The maximum of the ultrasonic image*/
- float m_MinValue; /*!< The minimum of the ultrasonic image*/
-
- // Stuff that OpenCV needs
- cv::Mat m_UsRef; /*!< Contains the reference ultrasonic image to which the
- motion compensation is compared to.*/
- cv::Mat m_Flow; /*!< Contains the optical flow between @c m_UsRef and @c m_UsMat*/
- cv::Mat m_PaRes; /*!< Contains the motion compensated photoacoustic image*/
- cv::Mat m_UsRes; /*!< Contains the motion compensated ultrasonic image*/
- cv::Mat m_PaMat; /*!< Contains the latest photoacoustic image to be motion compensated*/
- cv::Mat m_UsMat; /*!< Contains the latest ultrasonic image on which the
- optical flow is to be computed */
- cv::Mat m_Map; /*!< Contains the remapping map */
-
- mitk::OpenCVToMitkImageFilter::Pointer m_OpenCVToImageFilter =
- mitk::OpenCVToMitkImageFilter::New(); /*!< Filter which converts an OpenCV matrix to a mitk image */
- mitk::ImageToOpenCVImageFilter::Pointer m_ImageToOpenCVFilter =
- mitk::ImageToOpenCVImageFilter::New(); /*!< Filter which converts a mitk image to an OpenCV matrix */
- };
-}
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp
deleted file mode 100644
index 785100fe4a..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticBModeFilter.cpp
+++ /dev/null
@@ -1,87 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "./OpenCLFilter/mitkPhotoacousticBModeFilter.h"
-#include "usServiceReference.h"
-#include <mitkImageReadAccessor.h>
-
-mitk::PhotoacousticBModeFilter::PhotoacousticBModeFilter() : m_UseLogFilter(false)
-{
- this->SetNumberOfIndexedInputs(1);
- this->SetNumberOfRequiredInputs(1);
-}
-
-mitk::PhotoacousticBModeFilter::~PhotoacousticBModeFilter()
-{
-}
-
-void mitk::PhotoacousticBModeFilter::GenerateInputRequestedRegion()
-{
- Superclass::GenerateInputRequestedRegion();
-
- mitk::Image::Pointer output = this->GetOutput();
- mitk::Image::Pointer input = this->GetInput();
-
- if (!output->IsInitialized())
- return;
-
- input->SetRequestedRegionToLargestPossibleRegion();
-}
-
-void mitk::PhotoacousticBModeFilter::GenerateOutputInformation()
-{
- mitk::Image::ConstPointer input = this->GetInput();
- mitk::Image::Pointer output = this->GetOutput();
-
- if ((output->IsInitialized()) && (this->GetMTime() <= m_TimeOfHeaderInitialization.GetMTime()))
- return;
-
- output->Initialize(input->GetPixelType(), input->GetDimension(), input->GetDimensions());
- output->GetGeometry()->SetSpacing(input->GetGeometry()->GetSpacing());
- output->GetGeometry()->Modified();
- output->SetPropertyList(input->GetPropertyList()->Clone());
-
- m_TimeOfHeaderInitialization.Modified();
-}
-
-void mitk::PhotoacousticBModeFilter::GenerateData()
-{
- GenerateOutputInformation();
- mitk::Image::Pointer input = this->GetInput();
- mitk::Image::Pointer output = this->GetOutput();
-
- if (!output->IsInitialized())
- return;
-
- mitk::ImageReadAccessor reader(input);
-
- unsigned int size = output->GetDimension(0) * output->GetDimension(1) * output->GetDimension(2);
-
- const float* InputData = (const float*)(reader.GetData());
- float* OutputData = new float[size];
- if (!m_UseLogFilter)
- for (unsigned int i = 0; i < size; ++i)
- {
- OutputData[i] = std::abs(InputData[i]);
- }
- else
- {
- for (unsigned int i = 0; i < size; ++i)
- {
- OutputData[i] = log(std::abs(InputData[i]));
- }
- }
-
- output->SetImportVolume(OutputData, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
- delete[] OutputData;
- m_TimeOfHeaderInitialization.Modified();
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp
deleted file mode 100644
index 4dcd2933d5..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.cpp
+++ /dev/null
@@ -1,321 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN
-
-#include "./OpenCLFilter/mitkPhotoacousticOCLBeamformingFilter.h"
-#include "usServiceReference.h"
-
-mitk::PhotoacousticOCLBeamformingFilter::PhotoacousticOCLBeamformingFilter(BeamformingSettings::Pointer settings) :
- m_PixelCalculation(NULL),
- m_inputSlices(1),
- m_Conf(settings),
- m_InputImage(mitk::Image::New()),
- m_ApodizationBuffer(nullptr),
- m_DelaysBuffer(nullptr),
- m_UsedLinesBuffer(nullptr),
- m_ElementHeightsBuffer(nullptr),
- m_ElementPositionsBuffer(nullptr)
-{
- MITK_INFO << "Instantiating OCL beamforming Filter...";
- this->AddSourceFile("DAS.cl");
- this->AddSourceFile("DMAS.cl");
- this->AddSourceFile("sDMAS.cl");
- this->m_FilterID = "OpenCLBeamformingFilter";
-
- this->Initialize();
-
- unsigned int dim[] = { 128, 2048, 2 };
-
- m_InputImage->Initialize(mitk::MakeScalarPixelType<float>(), 3, dim);
-
- m_ChunkSize[0] = 128;
- m_ChunkSize[1] = 128;
- m_ChunkSize[2] = 8;
-
- m_UsedLinesCalculation = mitk::OCLUsedLinesCalculation::New(m_Conf);
- m_DelayCalculation = mitk::OCLDelayCalculation::New(m_Conf);
- MITK_INFO << "Instantiating OCL beamforming Filter...[Done]";
-}
-
-mitk::PhotoacousticOCLBeamformingFilter::~PhotoacousticOCLBeamformingFilter()
-{
- if (this->m_PixelCalculation)
- {
- clReleaseKernel(m_PixelCalculation);
- }
-
- if (m_ApodizationBuffer) clReleaseMemObject(m_ApodizationBuffer);
- if (m_ElementHeightsBuffer) clReleaseMemObject(m_ElementHeightsBuffer);
- if (m_ElementPositionsBuffer) clReleaseMemObject(m_ElementPositionsBuffer);
-}
-
-void mitk::PhotoacousticOCLBeamformingFilter::Update()
-{
- //Check if context & program available
- if (!this->Initialize())
- {
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- // clean-up also the resources
- resources->InvalidateStorage();
- mitkThrow() << "Filter is not initialized. Cannot update.";
- }
- else {
- // Execute
- this->Execute();
- }
-}
-
-void mitk::PhotoacousticOCLBeamformingFilter::UpdateDataBuffers()
-{
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
- cl_context gpuContext = resources->GetContext();
-
- //Initialize the Output
- try
- {
- size_t outputSize = (size_t)m_Conf->GetReconstructionLines() * (size_t)m_Conf->GetSamplesPerLine() *
- (size_t)m_inputSlices;
- m_OutputDim[0] = m_Conf->GetReconstructionLines();
- m_OutputDim[1] = m_Conf->GetSamplesPerLine();
- m_OutputDim[2] = m_inputSlices;
- this->InitExec(this->m_PixelCalculation, m_OutputDim, outputSize, sizeof(float));
- }
- catch (const mitk::Exception& e)
- {
- MITK_ERROR << "Caught exception while initializing filter: " << e.what();
- return;
- }
-
- cl_int clErr = 0;
- MITK_DEBUG << "Updating GPU Buffers for new configuration";
-
- // create the apodisation buffer
- if (m_Apodisation == nullptr)
- {
- MITK_INFO << "No apodisation function set; Beamforming will be done without any apodisation.";
- m_Apodisation = new float[1]{ 1 };
- m_ApodArraySize = 1;
- }
-
- if (m_ApodizationBuffer) clReleaseMemObject(m_ApodizationBuffer);
-
- this->m_ApodizationBuffer = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * m_ApodArraySize, const_cast<float*>(m_Apodisation), &clErr);
- CHECK_OCL_ERR(clErr);
-
- if (m_ElementHeightsBuffer) clReleaseMemObject(m_ElementHeightsBuffer);
- this->m_ElementHeightsBuffer = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * m_Conf->GetTransducerElements(), const_cast<float*>(m_Conf->GetElementHeights()), &clErr);
- CHECK_OCL_ERR(clErr);
-
- if (m_ElementPositionsBuffer) clReleaseMemObject(m_ElementPositionsBuffer);
- this->m_ElementPositionsBuffer = clCreateBuffer(gpuContext, CL_MEM_READ_ONLY | CL_MEM_USE_HOST_PTR, sizeof(float) * m_Conf->GetTransducerElements(), const_cast<float*>(m_Conf->GetElementPositions()), &clErr);
- CHECK_OCL_ERR(clErr);
- // calculate used lines
-
- m_UsedLinesCalculation->SetElementPositionsBuffer(m_ElementPositionsBuffer);
- m_UsedLinesCalculation->SetElementHeightsBuffer(m_ElementHeightsBuffer);
- m_UsedLinesCalculation->Update();
- m_UsedLinesBuffer = m_UsedLinesCalculation->GetGPUOutput()->GetGPUBuffer();
-
- // calculate the Delays
- m_DelayCalculation->SetInputs(m_UsedLinesBuffer);
- m_DelayCalculation->Update();
-
- m_DelaysBuffer = m_DelayCalculation->GetGPUOutput()->GetGPUBuffer();
-}
-
-void mitk::PhotoacousticOCLBeamformingFilter::Execute()
-{
- cl_int clErr = 0;
- UpdateDataBuffers();
- if (m_Conf->GetGeometry() == mitk::BeamformingSettings::ProbeGeometry::Linear)
- {
- unsigned int reconstructionLines = this->m_Conf->GetReconstructionLines();
- unsigned int samplesPerLine = this->m_Conf->GetSamplesPerLine();
-
- clErr = clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_mem), &(this->m_UsedLinesBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_mem), &(this->m_DelaysBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_mem), &(this->m_ApodizationBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_ushort), &(this->m_ApodArraySize));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 7, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 8, sizeof(cl_uint), &(m_inputSlices));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 9, sizeof(cl_uint), &(reconstructionLines));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 10, sizeof(cl_uint), &(samplesPerLine));
- }
- else
- {
- int reconstructionLines = this->m_Conf->GetReconstructionLines();
- int samplesPerLine = this->m_Conf->GetSamplesPerLine();
- float totalSamples_i = (float)(m_Conf->GetReconstructionDepth()) / (float)(m_Conf->GetSpeedOfSound() * m_Conf->GetTimeSpacing());
- totalSamples_i = totalSamples_i <= m_Conf->GetInputDim()[1] ? totalSamples_i : m_Conf->GetInputDim()[1];
- float horizontalExtent = m_Conf->GetHorizontalExtent();
- float mult = 1 / (this->m_Conf->GetTimeSpacing() * this->m_Conf->GetSpeedOfSound());
- char isPAImage = (char)m_Conf->GetIsPhotoacousticImage();
-
- clErr = clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_mem), &(this->m_ElementHeightsBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_mem), &(this->m_ElementPositionsBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_mem), &(this->m_ApodizationBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_ushort), &(this->m_ApodArraySize));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 7, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 8, sizeof(cl_int), &(m_inputSlices));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 9, sizeof(cl_int), &(reconstructionLines));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 10, sizeof(cl_int), &(samplesPerLine));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 11, sizeof(cl_float), &(totalSamples_i));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 12, sizeof(cl_float), &(horizontalExtent));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 13, sizeof(cl_float), &(mult));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 14, sizeof(cl_char), &(isPAImage));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 15, sizeof(cl_mem), &(this->m_UsedLinesBuffer));
- }
- // execute the filter on a 2D/3D NDRange
- if (m_OutputDim[2] == 1 || m_ChunkSize[2] == 1)
- {
- if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 2, m_ChunkSize, m_inputSlices, 50))
- mitkThrow() << "openCL Error when executing Kernel";
- }
- else
- {
- if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 3, m_ChunkSize, m_inputSlices, 50))
- mitkThrow() << "openCL Error when executing Kernel";
- }
-
- // signalize the GPU-side data changed
- m_Output->Modified(GPU_DATA);
-}
-
-us::Module *mitk::PhotoacousticOCLBeamformingFilter::GetModule()
-{
- return us::GetModuleContext()->GetModule();
-}
-
-bool mitk::PhotoacousticOCLBeamformingFilter::Initialize()
-{
- bool buildErr = true;
- cl_int clErr = 0;
-
- if (OclFilter::Initialize())
- {
- if (m_Conf->GetGeometry() == mitk::BeamformingSettings::ProbeGeometry::Linear)
- {
- switch (m_Conf->GetAlgorithm())
- {
- case BeamformingSettings::BeamformingAlgorithm::DAS:
- {
- MITK_INFO << "DAS bf";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS", &clErr);
- break;
- }
- case BeamformingSettings::BeamformingAlgorithm::DMAS:
- {
- MITK_INFO << "DMAS bf";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDMAS", &clErr);
- break;
- }
- case BeamformingSettings::BeamformingAlgorithm::sDMAS:
- {
- MITK_INFO << "sDMAS bf";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "cksDMAS", &clErr);
- break;
- }
- default:
- {
- MITK_INFO << "No beamforming algorithm specified, setting to DAS";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS", &clErr);
- break;
- }
- }
- }
- else
- {
- switch (m_Conf->GetAlgorithm())
- {
- case BeamformingSettings::BeamformingAlgorithm::DAS:
- {
- MITK_INFO << "DAS bf";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS_g", &clErr);
- break;
- }
- case BeamformingSettings::BeamformingAlgorithm::DMAS:
- {
- MITK_INFO << "DMAS bf";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDMAS_g", &clErr);
- break;
- }
- case BeamformingSettings::BeamformingAlgorithm::sDMAS:
- {
- MITK_INFO << "sDMAS bf";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "cksDMAS_g", &clErr);
- break;
- }
- default:
- {
- MITK_INFO << "No beamforming algorithm specified, setting to DAS";
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDAS_g", &clErr);
- break;
- }
- }
- }
- buildErr |= CHECK_OCL_ERR(clErr);
- }
-
- CHECK_OCL_ERR(clErr);
-
- return (OclFilter::IsInitialized() && buildErr);
-}
-
-void mitk::PhotoacousticOCLBeamformingFilter::SetInput(mitk::Image::Pointer image)
-{
- OclDataSetToDataSetFilter::SetInput(image);
- m_InputImage = image;
- m_inputSlices = image->GetDimension(2);
-}
-
-void mitk::PhotoacousticOCLBeamformingFilter::SetInput(void* data, unsigned int* dimensions, unsigned int BpE)
-{
- OclDataSetToDataSetFilter::SetInput(data, dimensions[0] * dimensions[1] * dimensions[2], BpE);
-}
-
-mitk::Image::Pointer mitk::PhotoacousticOCLBeamformingFilter::GetOutputAsImage()
-{
- mitk::Image::Pointer outputImage = mitk::Image::New();
-
- if (m_Output->IsModified(GPU_DATA))
- {
- void* pData = m_Output->TransferDataToCPU(m_CommandQue);
-
- const unsigned int dimension = 3;
- unsigned int dimensions[3] = { (unsigned int)m_OutputDim[0], (unsigned int)m_OutputDim[1], (unsigned int)m_OutputDim[2] };
-
- const mitk::SlicedGeometry3D::Pointer p_slg = m_InputImage->GetSlicedGeometry();
-
- MITK_DEBUG << "Creating new MITK Image.";
-
- outputImage->Initialize(this->GetOutputType(), dimension, dimensions);
- outputImage->SetSpacing(p_slg->GetSpacing());
- outputImage->SetImportVolume(pData, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
- free(pData);
- }
-
- MITK_DEBUG << "Image Initialized.";
-
- return outputImage;
-}
-
-void* mitk::PhotoacousticOCLBeamformingFilter::GetOutput()
-{
- return OclDataSetToDataSetFilter::GetOutput();
-}
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp
deleted file mode 100644
index fb777ce6a1..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.cpp
+++ /dev/null
@@ -1,124 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#define _USE_MATH_DEFINES
-
-#include <cmath>
-#include "./OpenCLFilter/mitkPhotoacousticOCLDelayCalculation.h"
-#include "usServiceReference.h"
-#include "mitkImageReadAccessor.h"
-
-mitk::OCLDelayCalculation::OCLDelayCalculation(mitk::BeamformingSettings::Pointer settings)
- : m_PixelCalculation(NULL),
- m_Conf(settings)
-{
- this->AddSourceFile("DelayCalculation.cl");
- this->m_FilterID = "DelayCalculation";
-
- m_ChunkSize[0] = 128;
- m_ChunkSize[1] = 128;
- m_ChunkSize[2] = 8;
-
- this->Initialize();
-}
-
-mitk::OCLDelayCalculation::~OCLDelayCalculation()
-{
- if (this->m_PixelCalculation)
- {
- clReleaseKernel(m_PixelCalculation);
- }
-}
-
-void mitk::OCLDelayCalculation::Update()
-{
- //Check if context & program available
- if (!this->Initialize())
- {
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- // clean-up also the resources
- resources->InvalidateStorage();
- mitkThrow() << "Filter is not initialized. Cannot update.";
- }
- else {
- // Execute
- this->Execute();
- }
-}
-
-void mitk::OCLDelayCalculation::Execute()
-{
- cl_int clErr = 0;
-
- unsigned int gridDim[3] = { m_Conf->GetReconstructionLines() / 2, m_Conf->GetSamplesPerLine(), 1 };
- m_BufferSize = gridDim[0] * gridDim[1] * 1;
-
- try
- {
- this->InitExecNoInput(this->m_PixelCalculation, gridDim, m_BufferSize, sizeof(unsigned short));
- }
- catch (const mitk::Exception& e)
- {
- MITK_ERROR << "Caught exception while initializing Delay Calculation filter: " << e.what();
- return;
- }
-
- // This calculation is the same for all kernels, so for performance reasons simply perform it here instead of within the kernels
- m_DelayMultiplicatorRaw = 1 / (m_Conf->GetTimeSpacing()*m_Conf->GetSpeedOfSound()) *
- (m_Conf->GetPitchInMeters()*(float)m_Conf->GetTransducerElements());
-
- // as openCL does not support bool as a kernel argument, we need to buffer this value in a char...
- m_IsPAImage = m_Conf->GetIsPhotoacousticImage();
-
- unsigned int reconstructionLines = this->m_Conf->GetReconstructionLines();
- unsigned int samplesperLine = this->m_Conf->GetSamplesPerLine();
-
- float totalSamples_i = (float)(m_Conf->GetReconstructionDepth()) / (float)(m_Conf->GetSpeedOfSound() * m_Conf->GetTimeSpacing());
- totalSamples_i = totalSamples_i <= m_Conf->GetInputDim()[1] ? totalSamples_i : m_Conf->GetInputDim()[1];
-
- clErr = clSetKernelArg(this->m_PixelCalculation, 1, sizeof(cl_mem), &(this->m_UsedLines));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_uint), &(reconstructionLines));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_uint), &(samplesperLine));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_char), &(this->m_IsPAImage));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 7, sizeof(cl_float), &(this->m_DelayMultiplicatorRaw));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 8, sizeof(cl_float), &(totalSamples_i));
-
- CHECK_OCL_ERR(clErr);
-
- // execute the filter on a 3D NDRange
- if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 2, m_ChunkSize, 16, 50))
- mitkThrow() << "openCL Error when executing Kernel";
- // signalize the GPU-side data changed
- m_Output->Modified(GPU_DATA);
-}
-
-us::Module *mitk::OCLDelayCalculation::GetModule()
-{
- return us::GetModuleContext()->GetModule();
-}
-
-bool mitk::OCLDelayCalculation::Initialize()
-{
- bool buildErr = true;
- cl_int clErr = 0;
-
- if (OclFilter::Initialize())
- {
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckDelayCalculationSphe", &clErr);
- buildErr |= CHECK_OCL_ERR(clErr);
- }
- return (OclFilter::IsInitialized() && buildErr);
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp b/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp
deleted file mode 100644
index e7ef79294c..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.cpp
+++ /dev/null
@@ -1,161 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN
-
-#include "./OpenCLFilter/mitkPhotoacousticOCLUsedLinesCalculation.h"
-#include "usServiceReference.h"
-#include "mitkImageReadAccessor.h"
-
-mitk::OCLUsedLinesCalculation::OCLUsedLinesCalculation(mitk::BeamformingSettings::Pointer settings)
- : m_PixelCalculation(NULL),
- m_Conf(settings)
-{
- this->AddSourceFile("UsedLinesCalculation.cl");
- this->m_FilterID = "UsedLinesCalculation";
-
- m_ChunkSize[0] = 128;
- m_ChunkSize[1] = 128;
- m_ChunkSize[2] = 8;
-
- this->Initialize();
-}
-
-mitk::OCLUsedLinesCalculation::~OCLUsedLinesCalculation()
-{
- if (this->m_PixelCalculation)
- {
- clReleaseKernel(m_PixelCalculation);
- }
-}
-
-void mitk::OCLUsedLinesCalculation::SetElementHeightsBuffer(cl_mem elementHeightsBuffer)
-{
- m_ElementHeightsBuffer = elementHeightsBuffer;
-}
-
-void mitk::OCLUsedLinesCalculation::SetElementPositionsBuffer(cl_mem elementPositionsBuffer)
-{
- m_ElementPositionsBuffer = elementPositionsBuffer;
-}
-
-void mitk::OCLUsedLinesCalculation::Update()
-{
- //Check if context & program available
- if (!this->Initialize())
- {
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- // clean-up also the resources
- resources->InvalidateStorage();
- mitkThrow() << "Filter is not initialized. Cannot update.";
- }
- else {
- // Execute
- this->Execute();
- }
-}
-
-void mitk::OCLUsedLinesCalculation::Execute()
-{
- cl_int clErr = 0;
-
- unsigned int gridDim[3] = { m_Conf->GetReconstructionLines(), m_Conf->GetSamplesPerLine(), 1 };
- size_t outputSize = gridDim[0] * gridDim[1] * 3;
-
- try
- {
- this->InitExecNoInput(this->m_PixelCalculation, gridDim, outputSize, sizeof(unsigned short));
- }
- catch (const mitk::Exception& e)
- {
- MITK_ERROR << "Caught exception while initializing UsedLines filter: " << e.what();
- return;
- }
-
- if (m_Conf->GetGeometry() == mitk::BeamformingSettings::ProbeGeometry::Linear)
- {
- // This calculation is the same for all kernels, so for performance reasons simply perform it here instead of within the kernels
- m_part = (tan(m_Conf->GetAngle() / 360 * 2 * itk::Math::pi) *
- ((m_Conf->GetSpeedOfSound() * m_Conf->GetTimeSpacing())) /
- (m_Conf->GetPitchInMeters() * m_Conf->GetTransducerElements())) * m_Conf->GetInputDim()[0];
- unsigned int reconLines = this->m_Conf->GetReconstructionLines();
- unsigned int samplesPerLine = this->m_Conf->GetSamplesPerLine();
-
- float totalSamples_i = (float)(m_Conf->GetReconstructionDepth()) / (float)(m_Conf->GetSpeedOfSound() * m_Conf->GetTimeSpacing());
- totalSamples_i = totalSamples_i <= m_Conf->GetInputDim()[1] ? totalSamples_i : m_Conf->GetInputDim()[1];
- clErr = clSetKernelArg(this->m_PixelCalculation, 1, sizeof(cl_float), &(this->m_part));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_uint), &(reconLines));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_uint), &(samplesPerLine));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_float), &(totalSamples_i));
- }
- else
- {
- unsigned int reconLines = this->m_Conf->GetReconstructionLines();
- unsigned int samplesPerLine = this->m_Conf->GetSamplesPerLine();
-
- float probeRadius = m_Conf->GetProbeRadius();
- float sin_deg = std::sin(m_Conf->GetAngle() / 360 * 2 * itk::Math::pi);
-
- float horizontalExtent = m_Conf->GetHorizontalExtent();
- float verticalExtent = m_Conf->GetReconstructionDepth();
-
- clErr = clSetKernelArg(this->m_PixelCalculation, 1, sizeof(cl_mem), &(this->m_ElementHeightsBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 2, sizeof(cl_mem), &(this->m_ElementPositionsBuffer));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 3, sizeof(cl_float), &(sin_deg));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 4, sizeof(cl_float), &(probeRadius));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 5, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[0]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 6, sizeof(cl_uint), &(this->m_Conf->GetInputDim()[1]));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 7, sizeof(cl_uint), &(reconLines));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 8, sizeof(cl_uint), &(samplesPerLine));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 9, sizeof(cl_float), &(horizontalExtent));
- clErr |= clSetKernelArg(this->m_PixelCalculation, 10, sizeof(cl_float), &(verticalExtent));
- }
-
- CHECK_OCL_ERR(clErr);
-
- // execute the filter on a 2D NDRange
- if (!this->ExecuteKernelChunksInBatches(m_PixelCalculation, 2, m_ChunkSize, 16, 50))
- mitkThrow() << "openCL Error when executing Kernel";
-
- // signalize the GPU-side data changed
- m_Output->Modified(GPU_DATA);
-}
-
-us::Module *mitk::OCLUsedLinesCalculation::GetModule()
-{
- return us::GetModuleContext()->GetModule();
-}
-
-bool mitk::OCLUsedLinesCalculation::Initialize()
-{
- bool buildErr = true;
- cl_int clErr = 0;
-
- if (OclFilter::Initialize())
- {
- if (m_Conf->GetGeometry() == mitk::BeamformingSettings::ProbeGeometry::Linear)
- {
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckUsedLines", &clErr);
- buildErr |= CHECK_OCL_ERR(clErr);
- }
- else
- {
- this->m_PixelCalculation = clCreateKernel(this->m_ClProgram, "ckUsedLines_g", &clErr);
- buildErr |= CHECK_OCL_ERR(clErr);
- }
- }
- return (OclFilter::IsInitialized() && buildErr);
-}
-#endif
diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBandpassFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBandpassFilter.cpp
deleted file mode 100644
index eecd2270e4..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBandpassFilter.cpp
+++ /dev/null
@@ -1,260 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#define _USE_MATH_DEFINES
-#include <cmath>
-
-#include "mitkBandpassFilter.h"
-
-#include "../ITKFilter/ITKUltrasound/itkFFT1DComplexConjugateToRealImageFilter.h"
-#include "../ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h"
-#include "itkComplexToModulusImageFilter.h"
-#include "itkMultiplyImageFilter.h"
-#include "mitkIOUtil.h"
-#include "mitkITKImageImport.h"
-#include "mitkImageCast.h"
-
-mitk::BandpassFilter::BandpassFilter()
- : m_HighPass(0),
- m_LowPass(50),
- m_HighPassAlpha(1),
- m_LowPassAlpha(1),
- m_FilterService(mitk::PhotoacousticFilterService::New())
-{
- MITK_INFO << "Instantiating BandpassFilter...";
- SetNumberOfIndexedInputs(1);
- SetNumberOfIndexedOutputs(1);
- MITK_INFO << "Instantiating BandpassFilter...[Done]";
-}
-
-mitk::BandpassFilter::~BandpassFilter()
-{
- MITK_INFO << "Destructed BandpassFilter.";
-}
-
-void mitk::BandpassFilter::SanityCheckPreconditions()
-{
- auto input = GetInput();
-
- std::string type = input->GetPixelType().GetTypeAsString();
- if (!(type == "scalar (float)" || type == " (float)"))
- {
- MITK_ERROR << "This filter can currently only handle float type images.";
- mitkThrow() << "This filter can currently only handle float type images.";
- }
- if (m_HighPass > m_LowPass)
- {
- MITK_ERROR << "High Pass is higher than Low Pass; aborting.";
- mitkThrow() << "High Pass is higher than Low Pass; aborting.";
- }
-}
-
-itk::Image<float, 3U>::Pointer BPFunction(mitk::Image::Pointer reference,
- float cutoffFrequencyPixelHighPass,
- float cutoffFrequencyPixelLowPass,
- float alphaHighPass,
- float alphaLowPass)
-{
- float *imageData = new float[reference->GetDimension(0) * reference->GetDimension(1)];
-
- float width = cutoffFrequencyPixelLowPass - cutoffFrequencyPixelHighPass;
- float center = cutoffFrequencyPixelHighPass + width / 2.f;
-
- for (unsigned int n = 0; n < reference->GetDimension(1); ++n)
- {
- imageData[reference->GetDimension(0) * n] = 0;
- }
- for (int n = 0; n < width; ++n)
- {
- imageData[reference->GetDimension(0) * (int)(n + center - (width / 2.f))] = 1;
- if (n <= (alphaHighPass * (width - 1)) / 2.f)
- {
- if (alphaHighPass > 0.00001f)
- {
- imageData[reference->GetDimension(0) * (int)(n + center - (width / 2.f))] =
- (1 + cos(itk::Math::pi * (2 * n / (alphaHighPass * (width - 1)) - 1))) / 2;
- }
- else
- {
- imageData[reference->GetDimension(0) * (int)(n + center - (width / 2.f))] = 1;
- }
- }
- else if (n >= (width - 1) * (1 - alphaLowPass / 2.f))
- {
- if (alphaLowPass > 0.00001f)
- {
- imageData[reference->GetDimension(0) * (int)(n + center - (width / 2.f))] =
- (1 + cos(itk::Math::pi * (2 * n / (alphaLowPass * (width - 1)) + 1 - 2 / alphaLowPass))) / 2;
- }
- else
- {
- imageData[reference->GetDimension(0) * (int)(n + center - (width / 2.f))] = 1;
- }
- }
- }
-
- for (unsigned int n = reference->GetDimension(1) / 2; n < reference->GetDimension(1); ++n)
- {
- imageData[reference->GetDimension(0) * n] =
- imageData[(reference->GetDimension(1) - (n + 1)) * reference->GetDimension(0)];
- }
-
- for (unsigned int line = 1; line < reference->GetDimension(0); ++line)
- {
- for (unsigned int sample = 0; sample < reference->GetDimension(1); ++sample)
- {
- imageData[reference->GetDimension(0) * sample + line] = imageData[reference->GetDimension(0) * sample];
- }
- }
-
- typedef itk::Image<float, 3U> ImageType;
- ImageType::RegionType region;
- ImageType::IndexType start;
- start.Fill(0);
-
- region.SetIndex(start);
-
- ImageType::SizeType size;
- size[0] = reference->GetDimension(0);
- size[1] = reference->GetDimension(1);
- size[2] = reference->GetDimension(2);
-
- region.SetSize(size);
-
- ImageType::SpacingType SpacingItk;
- SpacingItk[0] = reference->GetGeometry()->GetSpacing()[0];
- SpacingItk[1] = reference->GetGeometry()->GetSpacing()[1];
- SpacingItk[2] = reference->GetGeometry()->GetSpacing()[2];
-
- ImageType::Pointer image = ImageType::New();
- image->SetRegions(region);
- image->Allocate();
- image->FillBuffer(itk::NumericTraits<float>::Zero);
- image->SetSpacing(SpacingItk);
-
- ImageType::IndexType pixelIndex;
-
- for (unsigned int slice = 0; slice < reference->GetDimension(2); ++slice)
- {
- for (unsigned int line = 0; line < reference->GetDimension(0); ++line)
- {
- for (unsigned int sample = 0; sample < reference->GetDimension(1); ++sample)
- {
- pixelIndex[0] = line;
- pixelIndex[1] = sample;
- pixelIndex[2] = slice;
-
- image->SetPixel(pixelIndex, imageData[line + sample * reference->GetDimension(0)]);
- }
- }
- }
-
- delete[] imageData;
-
- return image;
-}
-
-void mitk::BandpassFilter::GenerateData()
-{
- SanityCheckPreconditions();
- auto input = GetInput();
- auto output = GetOutput();
- mitk::Image::Pointer resampledInput = input;
-
- double powerOfTwo = std::log2(input->GetDimension(1));
- int finalSize = 0;
- double spacingResize = 1;
-
- // check if this is a power of two by checking that log2 is int
- if (std::fmod(powerOfTwo, 1.0) >= std::numeric_limits<double>::epsilon())
- {
- finalSize = (int)pow(2, std::ceil(powerOfTwo));
- double dim[2] = {(double)input->GetDimension(0), (double)finalSize };
- resampledInput = m_FilterService->ApplyResamplingToDim(input, dim);
- spacingResize = (double)input->GetDimension(1) / finalSize;
- }
-
- // do a fourier transform, multiply with an appropriate window for the filter, and transform back
- typedef itk::Image<float, 3> RealImageType;
- RealImageType::Pointer image;
- mitk::CastToItkImage(resampledInput, image);
- typedef itk::FFT1DRealToComplexConjugateImageFilter<RealImageType> ForwardFFTFilterType;
- typedef ForwardFFTFilterType::OutputImageType ComplexImageType;
- ForwardFFTFilterType::Pointer forwardFFTFilter = ForwardFFTFilterType::New();
- forwardFFTFilter->SetInput(image);
- forwardFFTFilter->SetDirection(1);
-
- try
- {
- forwardFFTFilter->UpdateOutputInformation();
- }
- catch (itk::ExceptionObject &error)
- {
- std::cerr << "Error: " << error << std::endl;
- MITK_ERROR << "Bandpass could not be applied";
- mitkThrow() << "bandpass error";
- }
-
- if (m_HighPass > m_LowPass)
- mitkThrow() << "High pass frequency higher than low pass frequency, abort";
-
- float singleVoxel = spacingResize / (m_TimeSpacing * resampledInput->GetDimension(1)); // [Hz]
- if(m_IsBFImage)
- singleVoxel = spacingResize / (resampledInput->GetGeometry()->GetSpacing()[1] / 1e3 / m_SpeedOfSound * resampledInput->GetDimension(1)); // [Hz]
- float cutoffPixelHighPass = std::min((m_HighPass / singleVoxel), (float)resampledInput->GetDimension(1) / 2.0f);
- float cutoffPixelLowPass = std::min((m_LowPass / singleVoxel), (float)resampledInput->GetDimension(1) / 2.0f);
-
- MITK_INFO << "SingleVoxel: " << singleVoxel;
- MITK_INFO << "HighPass: " << m_HighPass;
- MITK_INFO << "LowPass: " << m_LowPass;
-
- MITK_INFO << "cutoffPixelHighPass: " << cutoffPixelHighPass;
- MITK_INFO << "cutoffPixelLowPass: " << cutoffPixelLowPass;
-
- RealImageType::Pointer fftMultiplicator =
- BPFunction(resampledInput, cutoffPixelHighPass, cutoffPixelLowPass, m_HighPassAlpha, m_LowPassAlpha);
-
- typedef itk::MultiplyImageFilter<ComplexImageType, RealImageType, ComplexImageType> MultiplyFilterType;
- MultiplyFilterType::Pointer multiplyFilter = MultiplyFilterType::New();
- multiplyFilter->SetInput1(forwardFFTFilter->GetOutput());
- multiplyFilter->SetInput2(fftMultiplicator);
-
- /*
- GrabItkImageMemory(fftMultiplicator, output);
- mitk::IOUtil::Save(output, "D:/fftImage.nrrd");
-
- typedef itk::ComplexToModulusImageFilter< ComplexImageType, RealImageType > modulusType;
- modulusType::Pointer modul = modulusType::New();
-
- modul->SetInput(multiplyFilter->GetOutput());
- GrabItkImageMemory(modul->GetOutput(), output);
- mitk::IOUtil::Save(output, "D:/fftout.nrrd");
-
- modul->SetInput(forwardFFTFilter->GetOutput());
- GrabItkImageMemory(modul->GetOutput(), output);
- mitk::IOUtil::Save(output, "D:/fftin.nrrd");*/
-
- typedef itk::FFT1DComplexConjugateToRealImageFilter<ComplexImageType, RealImageType> InverseFilterType;
- InverseFilterType::Pointer inverseFFTFilter = InverseFilterType::New();
- inverseFFTFilter->SetInput(multiplyFilter->GetOutput());
- inverseFFTFilter->SetDirection(1);
-
- GrabItkImageMemory(inverseFFTFilter->GetOutput(), output);
-
- double dim[2] = { (double)input->GetDimension(0), (double)input->GetDimension(1) };
- auto resampledOutput = m_FilterService->ApplyResamplingToDim(output, dim);
-
- output->Initialize(mitk::MakeScalarPixelType<float>(), 3, input->GetDimensions());
- output->SetSpacing(resampledOutput->GetGeometry()->GetSpacing());
- ImageReadAccessor copy(resampledOutput);
- output->SetImportVolume(copy.GetData());
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp
deleted file mode 100644
index fdd45dd679..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingFilter.cpp
+++ /dev/null
@@ -1,261 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkProperties.h"
-#include "mitkImageReadAccessor.h"
-#include <algorithm>
-#include <itkImageIOBase.h>
-#include <chrono>
-#include <thread>
-#include <itkImageIOBase.h>
-#include "mitkImageCast.h"
-#include "mitkBeamformingFilter.h"
-#include "mitkBeamformingUtils.h"
-
-mitk::BeamformingFilter::BeamformingFilter(mitk::BeamformingSettings::Pointer settings) :
- m_OutputData(nullptr),
- m_InputData(nullptr),
- m_Conf(settings)
-{
- MITK_INFO << "Instantiating BeamformingFilter...";
- this->SetNumberOfIndexedInputs(1);
- this->SetNumberOfRequiredInputs(1);
-
- m_ProgressHandle = [](int, std::string) {};
-#if defined(PHOTOACOUSTICS_USE_GPU)
- m_BeamformingOclFilter = mitk::PhotoacousticOCLBeamformingFilter::New(m_Conf);
-#else
- m_BeamformingOclFilter = mitk::PhotoacousticOCLBeamformingFilter::New();
-#endif
-
- MITK_INFO << "Instantiating BeamformingFilter...[Done]";
-}
-
-void mitk::BeamformingFilter::SetProgressHandle(std::function<void(int, std::string)> progressHandle)
-{
- m_ProgressHandle = progressHandle;
-}
-
-mitk::BeamformingFilter::~BeamformingFilter()
-{
- MITK_INFO << "Destructed BeamformingFilter";
-}
-
-void mitk::BeamformingFilter::GenerateInputRequestedRegion()
-{
- Superclass::GenerateInputRequestedRegion();
-
- mitk::Image* output = this->GetOutput();
- mitk::Image* input = const_cast<mitk::Image *> (this->GetInput());
- if (!output->IsInitialized())
- {
- return;
- }
-
- input->SetRequestedRegionToLargestPossibleRegion();
-}
-
-void mitk::BeamformingFilter::GenerateOutputInformation()
-{
- mitk::Image::ConstPointer input = this->GetInput();
- mitk::Image::Pointer output = this->GetOutput();
-
- if ((output->IsInitialized()) && (this->GetMTime() <= m_TimeOfHeaderInitialization.GetMTime()))
- return;
-
- mitk::Vector3D spacing;
- spacing[0] = m_Conf->GetHorizontalExtent() / m_Conf->GetReconstructionLines() * 1000;
- float desiredYSpacing = m_Conf->GetReconstructionDepth() * 1000 / m_Conf->GetSamplesPerLine();
- float maxYSpacing = m_Conf->GetSpeedOfSound() * m_Conf->GetTimeSpacing() * input->GetDimension(1) / m_Conf->GetSamplesPerLine() * 1000;
- spacing[1] = desiredYSpacing < maxYSpacing ? desiredYSpacing : maxYSpacing;
- spacing[2] = 1;
-
- unsigned int dim[] = { m_Conf->GetReconstructionLines(), m_Conf->GetSamplesPerLine(), input->GetDimension(2)};
- output->Initialize(mitk::MakeScalarPixelType<float>(), 3, dim);
- output->GetGeometry()->SetSpacing(spacing);
- output->GetGeometry()->Modified();
- output->SetPropertyList(input->GetPropertyList()->Clone());
-
- m_TimeOfHeaderInitialization.Modified();
-}
-
-void mitk::BeamformingFilter::GenerateData()
-{
- mitk::Image::Pointer input = this->GetInput();
- if (!(input->GetPixelType().GetTypeAsString() == "scalar (float)" || input->GetPixelType().GetTypeAsString() == " (float)"))
- {
- MITK_ERROR << "Pixel type of input needs to be float for this filter to work.";
- mitkThrow() << "Pixel type of input needs to be float for this filter to work.";
- }
-
- GenerateOutputInformation();
- mitk::Image::Pointer output = this->GetOutput();
-
- if (!output->IsInitialized())
- return;
-
- auto begin = std::chrono::high_resolution_clock::now(); // debbuging the performance...
-
- if (!m_Conf->GetUseGPU())
- {
- int progInterval = output->GetDimension(2) / 20 > 1 ? output->GetDimension(2) / 20 : 1;
- // the interval at which we update the gui progress bar
-
- float inputDim[2] = { (float)input->GetDimension(0), (float)input->GetDimension(1) };
- float outputDim[2] = { (float)output->GetDimension(0), (float)output->GetDimension(1) };
-
- for (unsigned int i = 0; i < output->GetDimension(2); ++i) // seperate Slices should get Beamforming seperately applied
- {
- mitk::ImageReadAccessor inputReadAccessor(input, input->GetSliceData(i));
- m_InputData = (float*)inputReadAccessor.GetData();
-
- m_OutputData = new float[m_Conf->GetReconstructionLines()*m_Conf->GetSamplesPerLine()];
-
- // fill the image with zeros
- for (int l = 0; l < outputDim[0]; ++l)
- {
- for (int s = 0; s < outputDim[1]; ++s)
- {
- m_OutputData[l*(short)outputDim[1] + s] = 0;
- }
- }
-
- std::thread *threads = new std::thread[(short)outputDim[0]];
-
- // every line will be beamformed in a seperate thread
- if (m_Conf->GetAlgorithm() == BeamformingSettings::BeamformingAlgorithm::DAS)
- {
- for (short line = 0; line < outputDim[0]; ++line)
- {
- threads[line] = std::thread(&BeamformingUtils::DASSphericalLine, m_InputData,
- m_OutputData, inputDim, outputDim, line, m_Conf);
- }
- }
- else if (m_Conf->GetAlgorithm() == BeamformingSettings::BeamformingAlgorithm::DMAS)
- {
- for (short line = 0; line < outputDim[0]; ++line)
- {
- threads[line] = std::thread(&BeamformingUtils::DMASSphericalLine, m_InputData,
- m_OutputData, inputDim, outputDim, line, m_Conf);
- }
- }
- else if (m_Conf->GetAlgorithm() == BeamformingSettings::BeamformingAlgorithm::sDMAS)
- {
- for (short line = 0; line < outputDim[0]; ++line)
- {
- threads[line] = std::thread(&BeamformingUtils::sDMASSphericalLine, m_InputData,
- m_OutputData, inputDim, outputDim, line, m_Conf);
- }
- }
- // wait for all lines to finish
- for (short line = 0; line < outputDim[0]; ++line)
- {
- threads[line].join();
- }
-
- output->SetSlice(m_OutputData, i);
-
- if (i % progInterval == 0)
- m_ProgressHandle((int)((i + 1) / (float)output->GetDimension(2) * 100), "performing reconstruction");
-
- delete[] m_OutputData;
- m_OutputData = nullptr;
- m_InputData = nullptr;
- }
- }
-#if defined(PHOTOACOUSTICS_USE_GPU) || DOXYGEN
- else
- {
- try
- {
- // first, we check whether the data is float, other formats are unsupported
- if (!(input->GetPixelType().GetTypeAsString() == "scalar (float)" || input->GetPixelType().GetTypeAsString() == " (float)"))
- {
- MITK_ERROR << "Pixel type is not float, abort";
- mitkThrow() << "Pixel type is not float, abort";
- }
-
- unsigned long availableMemory = m_BeamformingOclFilter->GetDeviceMemory();
-
- unsigned int batchSize = m_Conf->GetGPUBatchSize();
- unsigned int batches = (unsigned int)((float)input->GetDimension(2) / batchSize) + (input->GetDimension(2) % batchSize > 0);
-
- unsigned int batchDim[] = { input->GetDimension(0), input->GetDimension(1), batchSize };
- unsigned int batchDimLast[] = { input->GetDimension(0), input->GetDimension(1), input->GetDimension(2) % batchSize };
-
- // the following safeguard is probably only needed for absurdly small GPU memory
- if((unsigned long)batchSize *
- ((unsigned long)(batchDim[0] * batchDim[1]) * 4 + // single input image (float)
- (unsigned long)(m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine()) * 4) // single output image (float)
- > availableMemory -
- (unsigned long)(m_Conf->GetReconstructionLines() / 2 * m_Conf->GetSamplesPerLine()) * 2 - // Delays buffer (unsigned short)
- (unsigned long)(m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine()) * 3 * 2 - // UsedLines buffer (unsigned short)
- 50 * 1024 * 1024)// 50 MB buffer for local data, system purposes etc
- {
- MITK_ERROR << "device memory too small for GPU beamforming; try decreasing the batch size";
- return;
- }
-
- mitk::ImageReadAccessor copy(input);
-
- for (unsigned int i = 0; i < batches; ++i)
- {
- m_ProgressHandle(100.f * (float)i / (float)batches, "performing reconstruction");
-
- mitk::Image::Pointer inputBatch = mitk::Image::New();
- unsigned int num_Slices = 1;
- if (i == batches - 1 && (input->GetDimension(2) % batchSize > 0))
- {
- inputBatch->Initialize(mitk::MakeScalarPixelType<float>(), 3, batchDimLast);
- num_Slices = batchDimLast[2];
- }
- else
- {
- inputBatch->Initialize(mitk::MakeScalarPixelType<float>(), 3, batchDim);
- num_Slices = batchDim[2];
- }
-
- inputBatch->SetSpacing(input->GetGeometry()->GetSpacing());
-
- inputBatch->SetImportVolume(&(((float*)copy.GetData())[input->GetDimension(0) * input->GetDimension(1) * batchSize * i]));
-
- m_BeamformingOclFilter->SetApodisation(m_Conf->GetApodizationFunction(), m_Conf->GetApodizationArraySize());
- m_BeamformingOclFilter->SetInput(inputBatch);
- m_BeamformingOclFilter->Update();
-
- void* out = m_BeamformingOclFilter->GetOutput();
-
- for (unsigned int slice = 0; slice < num_Slices; ++slice)
- {
- output->SetImportSlice(
- &(((float*)out)[m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine() * slice]),
- batchSize * i + slice, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
- }
- free(out);
- }
- }
- catch (mitk::Exception &e)
- {
- std::string errorMessage = "Caught unexpected exception ";
- errorMessage.append(e.what());
- MITK_ERROR << errorMessage;
-
- float* dummyData = new float[m_Conf->GetReconstructionLines() * m_Conf->GetSamplesPerLine() * m_Conf->GetInputDim()[2]];
- output->SetImportVolume(dummyData, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
- }
- }
-#endif
- m_TimeOfHeaderInitialization.Modified();
-
- auto end = std::chrono::high_resolution_clock::now();
- MITK_INFO << "Beamforming of " << output->GetDimension(2) << " Images completed in " << ((float)std::chrono::duration_cast<std::chrono::nanoseconds>(end - begin).count()) / 1000000 << "ms" << std::endl;
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingSettings.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingSettings.cpp
deleted file mode 100644
index 7afe9eb327..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkBeamformingSettings.cpp
+++ /dev/null
@@ -1,137 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkBeamformingSettings.h"
-#include "mitkBeamformingUtils.h"
-#include "itkMutexLock.h"
-
-mitk::BeamformingSettings::BeamformingSettings(float pitchInMeters,
- float speedOfSound,
- float timeSpacing,
- float angle,
- bool isPhotoacousticImage,
- unsigned int samplesPerLine,
- unsigned int reconstructionLines,
- unsigned int* inputDim,
- float reconstructionDepth,
- bool useGPU,
- unsigned int GPUBatchSize,
- Apodization apod,
- unsigned int apodizationArraySize,
- BeamformingAlgorithm algorithm,
- ProbeGeometry geometry,
- float probeRadius
-) :
- m_PitchInMeters(pitchInMeters),
- m_SpeedOfSound(speedOfSound),
- m_TimeSpacing(timeSpacing),
- m_Angle(angle),
- m_IsPhotoacousticImage(isPhotoacousticImage),
- m_SamplesPerLine(samplesPerLine),
- m_ReconstructionLines(reconstructionLines),
- m_ReconstructionDepth(reconstructionDepth),
- m_UseGPU(useGPU),
- m_GPUBatchSize(GPUBatchSize),
- m_Apod(apod),
- m_ApodizationArraySize(apodizationArraySize),
- m_Algorithm(algorithm),
- m_Geometry(geometry),
- m_ProbeRadius(probeRadius),
- m_MinMaxLines(nullptr)
-{
- if (inputDim == nullptr)
- {
- MITK_ERROR << "No input dimension given.";
- mitkThrow() << "No input dimension given.";
- }
-
- switch (GetApod())
- {
- case BeamformingSettings::Apodization::Hann:
- m_ApodizationFunction = mitk::BeamformingUtils::VonHannFunction(GetApodizationArraySize());
- break;
- case BeamformingSettings::Apodization::Hamm:
- m_ApodizationFunction = mitk::BeamformingUtils::HammFunction(GetApodizationArraySize());
- break;
- case BeamformingSettings::Apodization::Box:
- default:
- m_ApodizationFunction = mitk::BeamformingUtils::BoxFunction(GetApodizationArraySize());
- break;
- }
- m_InputDim = new unsigned int[3]{ inputDim[0], inputDim[1], inputDim[2] };
- m_TransducerElements = m_InputDim[0];
-
- m_ElementHeights = new float[m_TransducerElements];
- m_ElementPositions = new float[m_TransducerElements];
-
- if (m_Geometry == ProbeGeometry::Concave)
- {
- float openingAngle = (m_TransducerElements * m_PitchInMeters) / (probeRadius * 2 * itk::Math::pi) * 2 * itk::Math::pi;
- m_HorizontalExtent = std::sin(openingAngle / 2.f) * probeRadius * 2.f;
-
- float elementAngle = 0;
-
- for (unsigned int i = 0; i < m_TransducerElements; ++i)
- {
- elementAngle = ((i- m_TransducerElements /2.f) * m_PitchInMeters) / (probeRadius * 2 * itk::Math::pi) * 2 * itk::Math::pi;
- m_ElementHeights[i] = probeRadius - std::cos(elementAngle) * probeRadius;
- m_ElementPositions[i] = m_HorizontalExtent/2.f + std::sin(elementAngle) * probeRadius;
- }
- }
- else
- {
- m_HorizontalExtent = m_PitchInMeters * m_TransducerElements;
- for (unsigned int i = 0; i < m_TransducerElements; ++i)
- {
- m_ElementHeights[i] = 0;
- m_ElementPositions[i] = i * m_PitchInMeters;
- }
- }
-}
-
-mitk::BeamformingSettings::~BeamformingSettings()
-{
- MITK_INFO << "Destructing beamforming settings...";
- //Free memory
- if (m_ApodizationFunction != nullptr)
- {
- MITK_INFO << "Deleting apodization function...";
- delete[] m_ApodizationFunction;
- MITK_INFO << "Deleting apodization function...[Done]";
- }
-
- if (m_InputDim != nullptr)
- {
- MITK_INFO << "Deleting input dim...";
- delete[] m_InputDim;
- MITK_INFO << "Deleting input dim...[Done]";
- }
- if (m_ElementHeights != nullptr || m_ElementPositions != nullptr)
- {
- MITK_INFO << "Deleting element geometry...";
- if (m_ElementHeights != nullptr)
- delete[] m_ElementHeights;
-
- if (m_ElementPositions != nullptr)
- delete[] m_ElementPositions;
- MITK_INFO << "Destructing beamforming settings...[Done]";
- }
- if (m_MinMaxLines)
- delete[] m_MinMaxLines;
-}
-
-unsigned short* mitk::BeamformingSettings::GetMinMaxLines()
-{
- if (!m_MinMaxLines)
- m_MinMaxLines = mitk::BeamformingUtils::MinMaxLines(this);
- return m_MinMaxLines;
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp
deleted file mode 100644
index ae7a162d83..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCastToFloatImageFilter.cpp
+++ /dev/null
@@ -1,88 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkCastToFloatImageFilter.h"
-#include "mitkImageReadAccessor.h"
-#include "mitkImageWriteAccessor.h"
-
-mitk::CastToFloatImageFilter::CastToFloatImageFilter()
-{
- MITK_INFO << "Instantiating CastToFloatImageFilter...";
- SetNumberOfIndexedInputs(1);
- SetNumberOfIndexedOutputs(1);
- MITK_INFO << "Instantiating CastToFloatImageFilter...[Done]";
-}
-
-mitk::CastToFloatImageFilter::~CastToFloatImageFilter()
-{
- MITK_INFO << "Destructed CastToFloatImageFilter.";
-}
-
-template<class TPixelType>
-float* CastData(const void* inputArray, unsigned long length)
-{
- float* outputArray = new float[length];
- for (unsigned long i = 0; i < length; ++i)
- {
- outputArray[i] = (float)((TPixelType*)inputArray)[i];
- }
- return outputArray;
-}
-
-void mitk::CastToFloatImageFilter::GenerateData()
-{
- mitk::Image::Pointer inputImage = GetInput();
- mitk::Image::Pointer outputImage = GetOutput();
-
- std::string type = inputImage->GetPixelType().GetTypeAsString();
-
- if (type == "scalar (float)" || type == " (float)")
- {
- outputImage->Initialize(mitk::MakeScalarPixelType<float>(), inputImage->GetDimension(), inputImage->GetDimensions());
- outputImage->SetSpacing(inputImage->GetGeometry()->GetSpacing());
- outputImage->SetImportVolume(mitk::ImageWriteAccessor(inputImage).GetData(), 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
- MITK_INFO << "Input is already float type. Nothing to do here.";
- return;
- }
- if (outputImage.IsNull())
- {
- outputImage = mitk::Image::New();
- }
-
- unsigned long length = 1;
- for (unsigned int i = 0, limit = inputImage->GetDimension(); i < limit; ++i)
- length *= inputImage->GetDimensions()[i];
-
- float* outputData;
-
- mitk::ImageReadAccessor readAccess(inputImage);
-
- if (type == "scalar (short)" || type == " (short)")
- outputData = CastData<short>(readAccess.GetData(), length);
- else if (type == "scalar (unsigned short)" || type == " (unsigned short)" || type == " (unsigned_short)" || type == "scalar (unsigned_short)")
- outputData = CastData<unsigned short>(readAccess.GetData(), length);
- else if (type == "scalar (int)" || type == " (int)")
- outputData = CastData<int>(readAccess.GetData(), length);
- else if (type == "scalar (unsigned int)" || type == " (unsigned int)" || type == " (unsigned_int)" || type == "scalar (unsigned_int)")
- outputData = CastData<unsigned int>(readAccess.GetData(), length);
- else if (type == "scalar (double)" || type == " (double)")
- outputData = CastData<double>(readAccess.GetData(), length);
- else if (type == "scalar (long)" || type == " (long)")
- outputData = CastData<long>(readAccess.GetData(), length);
- else
- mitkThrow() << "The given image has a datatype that is not yet supported. Given datatype: " << type;
-
- outputImage->Initialize(mitk::MakeScalarPixelType<float>(), inputImage->GetDimension(), inputImage->GetDimensions());
- outputImage->SetSpacing(inputImage->GetGeometry()->GetSpacing());
- outputImage->SetImportVolume(outputData, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
- delete[] outputData;
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp
deleted file mode 100644
index 2ad7cc6ee7..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkCropImageFilter.cpp
+++ /dev/null
@@ -1,116 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkCropImageFilter.h"
-#include <mitkImageReadAccessor.h>
-#include <mitkImageWriteAccessor.h>
-
-mitk::CropImageFilter::CropImageFilter() :
- m_XPixelsCropStart(0),
- m_YPixelsCropStart(0),
- m_ZPixelsCropStart(0),
- m_XPixelsCropEnd(0),
- m_YPixelsCropEnd(0),
- m_ZPixelsCropEnd(0)
-{
- MITK_INFO << "Instantiating CropImageFilter...";
- SetNumberOfIndexedInputs(1);
- SetNumberOfIndexedOutputs(1);
- MITK_INFO << "Instantiating CropImageFilter...[Done]";
-}
-
-mitk::CropImageFilter::~CropImageFilter()
-{
- MITK_INFO << "Destructed CastToFloatImageFilter.";
-}
-
-void mitk::CropImageFilter::SanityCheckPreconditions()
-{
- mitk::Image::Pointer inputImage = GetInput();
-
- std::string type = inputImage->GetPixelType().GetTypeAsString();
- if (!(type == "scalar (float)" || type == " (float)"))
- {
- MITK_ERROR << "This filter can currently only handle float type images.";
- mitkThrow() << "This filter can currently only handle float type images.";
- }
-
- if (m_XPixelsCropStart + m_XPixelsCropEnd >= inputImage->GetDimension(0))
- {
- MITK_ERROR << "X Crop area too large for selected input image";
- mitkThrow() << "X Crop area too large for selected input image";
- }
- if (m_YPixelsCropStart + m_YPixelsCropEnd >= inputImage->GetDimension(1))
- {
- MITK_ERROR << "Y Crop area too large for selected input image";
- mitkThrow() << "Y Crop area too large for selected input image";
- }
-
- if (inputImage->GetDimension() == 3)
- {
- if (m_ZPixelsCropStart + m_ZPixelsCropEnd >= inputImage->GetDimension(2))
- {
- MITK_INFO << m_ZPixelsCropStart + m_ZPixelsCropEnd << "vs" << inputImage->GetDimension(2);
- MITK_ERROR << "Z Crop area too large for selected input image";
- mitkThrow() << "Z Crop area too large for selected input image";
- }
- }
- else
- {
- if (m_ZPixelsCropStart + m_ZPixelsCropEnd > 0)
- {
- mitkThrow() << "Z Crop area too large for selected input image";
- }
- }
-}
-
-void mitk::CropImageFilter::GenerateData()
-{
- mitk::Image::Pointer inputImage = GetInput();
- mitk::Image::Pointer outputImage = GetOutput();
-
- SanityCheckPreconditions();
- unsigned int* outputDim;
- unsigned int* inputDim = inputImage->GetDimensions();
- if (inputImage->GetDimension() == 2)
- outputDim = new unsigned int[2]{ inputImage->GetDimension(0) - m_XPixelsCropStart - m_XPixelsCropEnd,
- inputImage->GetDimension(1) - m_YPixelsCropStart - m_YPixelsCropEnd };
- else
- outputDim = new unsigned int[3]{ inputImage->GetDimension(0) - m_XPixelsCropStart - m_XPixelsCropEnd,
- inputImage->GetDimension(1) - m_YPixelsCropStart - m_YPixelsCropEnd,
- inputImage->GetDimension(2) - m_ZPixelsCropStart - m_ZPixelsCropEnd };
-
- outputImage->Initialize(mitk::MakeScalarPixelType<float>(), inputImage->GetDimension(), outputDim);
- outputImage->SetSpacing(inputImage->GetGeometry()->GetSpacing());
-
- ImageReadAccessor accR(inputImage);
- const float* inputData = (const float*)(accR.GetData());
-
- ImageWriteAccessor accW(outputImage);
- float* outputData = (float*)(accW.GetData());
-
- unsigned int zLength = inputImage->GetDimension() == 3 ? outputDim[2] : 1;
-
- for (unsigned int sl = 0; sl < zLength; ++sl)
- {
- for (unsigned int l = 0; l < outputDim[0]; ++l)
- {
- for (unsigned int s = 0; s < outputDim[1]; ++s)
- {
- outputData[l + s*outputDim[0] + sl*outputDim[0] * outputDim[1]] =
- inputData[(l + m_XPixelsCropStart) + (s + m_YPixelsCropStart)*inputDim[0] +
- (sl + m_ZPixelsCropStart)*inputDim[0] * inputDim[1]];
- }
- }
- }
- delete[] outputDim;
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/filters/mitkImageSliceSelectionFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/filters/mitkImageSliceSelectionFilter.cpp
deleted file mode 100644
index 6c609828e5..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/filters/mitkImageSliceSelectionFilter.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkImageSliceSelectionFilter.h"
-
-mitk::ImageSliceSelectionFilter::ImageSliceSelectionFilter()
-{
- MITK_INFO << "Instantiating CropImageFilter...";
- SetNumberOfIndexedInputs(1);
- SetNumberOfIndexedOutputs(1);
- MITK_INFO << "Instantiating CropImageFilter...[Done]";
-}
-
-mitk::ImageSliceSelectionFilter::~ImageSliceSelectionFilter()
-{
- MITK_INFO << "Destructed CastToFloatImageFilter.";
-}
-
-void mitk::ImageSliceSelectionFilter::GenerateData()
-{
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticMotionCorrectionFilter.cpp b/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticMotionCorrectionFilter.cpp
deleted file mode 100644
index 3899b0617f..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/mitkPhotoacousticMotionCorrectionFilter.cpp
+++ /dev/null
@@ -1,234 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "./mitkPhotoacousticMotionCorrectionFilter.h"
-#include <mitkImageReadAccessor.h>
-
-mitk::PhotoacousticMotionCorrectionFilter::
- PhotoacousticMotionCorrectionFilter() {
- // Set the defaults for the OpticalFlowFarneback algorithm
- // The values are taken directly out of Thomas's
- // US-CV-Based-Optical-Flow-Carotis.ipyn
- m_BatchSize = 5;
- m_PyrScale = 0.5;
- m_Levels = 1;
- m_WinSize = 40;
- m_Iterations = 2;
- m_PolyN = 7;
- m_PolySigma = 1.5;
- m_Flags = 0;
-
- m_MaxValue = 255.0;
- m_MinValue = 0.0;
-
- this->SetNumberOfIndexedInputs(2);
- this->SetNumberOfIndexedOutputs(2);
- this->SetNthOutput(0, mitk::Image::New());
- this->SetNthOutput(1, mitk::Image::New());
-}
-
-mitk::PhotoacousticMotionCorrectionFilter::
- ~PhotoacousticMotionCorrectionFilter() {}
-
-void mitk::PhotoacousticMotionCorrectionFilter::SetPaInput(
- mitk::Image::Pointer input) {
- this->SetInput(0, input);
-}
-
-mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetPaInput() {
- return this->GetInput(0);
-}
-
-void mitk::PhotoacousticMotionCorrectionFilter::SetUsInput(
- mitk::Image::Pointer input) {
- this->SetInput(1, input);
-}
-
-mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetUsInput() {
- return this->GetInput(1);
-}
-
-mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetPaOutput() {
- return this->GetOutput(0);
-}
-
-mitk::Image::Pointer mitk::PhotoacousticMotionCorrectionFilter::GetUsOutput() {
- return this->GetOutput(1);
-}
-
-void mitk::PhotoacousticMotionCorrectionFilter::CheckInput(
- mitk::Image::Pointer paImage, mitk::Image::Pointer usImage) {
- // Check that we actually got some images
- if (!paImage || !usImage) {
- MITK_ERROR << "We did not get two images!";
- throw std::invalid_argument("One of the images was NULL.");
- }
-
- // Check that the image dimensions are the same
- if (paImage->GetDimension() != IMAGE_DIMENSION || usImage->GetDimension() != IMAGE_DIMENSION) {
- MITK_ERROR << "Mismatching image dimensions detected in the motion "
- "compensation filter.";
- throw std::invalid_argument("Both images must have dimension 3.");
- }
-
- // Check that each dimension has the same size
- for (unsigned int i = 0; i < paImage->GetDimension(); ++i) {
- if (paImage->GetDimensions()[i] != usImage->GetDimensions()[i]) {
- MITK_ERROR << "Mismatching image dimensions detected in the motion "
- "compensation filter.";
- throw std::invalid_argument(
- "Both images must have the same length in each dimension.");
- }
- }
-}
-
-void mitk::PhotoacousticMotionCorrectionFilter::InitializeOutputIfNecessary(
- mitk::Image::Pointer paInput, mitk::Image::Pointer usInput,
- mitk::Image::Pointer paOutput, mitk::Image::Pointer usOutput) {
- if (paOutput->GetDimension() != IMAGE_DIMENSION) {
- this->InitializeOutput(paInput, paOutput);
- this->InitializeOutput(usInput, usOutput);
- }
-
- for (unsigned int i = 0; i < usOutput->GetDimension(); ++i) {
- if (usOutput->GetDimensions()[i] != usInput->GetDimensions()[i]) {
- this->InitializeOutput(paInput, paOutput);
- this->InitializeOutput(usInput, usOutput);
- break;
- }
- }
-}
-
-void mitk::PhotoacousticMotionCorrectionFilter::InitializeOutput(
- mitk::Image::Pointer input, mitk::Image::Pointer output) {
- output->Initialize(input);
- mitk::ImageReadAccessor accessor(input);
- output->SetImportVolume(accessor.GetData());
-}
-
-void mitk::PhotoacousticMotionCorrectionFilter::PerformCorrection(
- mitk::Image::Pointer paInput, mitk::Image::Pointer usInput,
- mitk::Image::Pointer paOutput, mitk::Image::Pointer usOutput) {
-
- // If batch size was set to 0, use one single batch for the whole data set.
- unsigned int batch;
- if (m_BatchSize == 0) {
- batch = paInput->GetDimensions()[IMAGE_DIMENSION - 1];
- } else {
- batch = m_BatchSize;
- }
-
- for (unsigned int i = 0; i < paInput->GetDimensions()[IMAGE_DIMENSION - 1]; ++i) {
-
- // Get the 2d matrix from slice at i
- m_PaMat = this->GetMatrix(paInput, i);
- m_UsMat = this->GetMatrix(usInput, i);
-
- // At the beginning of a batch we set the new reference image and directly
- // write the result images
- if (i % batch == 0) {
- // Rescale reference to full char resolution
- m_UsRef = this->FitMatrixToChar(m_UsMat);
- m_UsRes = m_UsMat.clone();
- m_PaRes = m_PaMat.clone();
- } else {
- cv::Mat UsMatRescaled = this->FitMatrixToChar(m_UsMat);
- cv::calcOpticalFlowFarneback(m_UsRef, UsMatRescaled, m_Flow, m_PyrScale,
- m_Levels, m_WinSize, m_Iterations, m_PolyN,
- m_PolySigma, m_Flags);
-
- m_Map = this->ComputeFlowMap(m_Flow);
-
- // Apply the flow to the matrices
- cv::remap(m_PaMat, m_PaRes, m_Map, cv::noArray(), cv::INTER_LINEAR);
- cv::remap(m_UsMat, m_UsRes, m_Map, cv::noArray(), cv::INTER_LINEAR);
- }
-
- // Enter the matrix as a slice at position i into output
- this->InsertMatrixAsSlice(m_PaRes, paOutput, i);
- this->InsertMatrixAsSlice(m_UsRes, usOutput, i);
- }
-}
-
-// Copied from https://stackoverflow.com/questions/17459584/opencv-warping-image-based-on-calcopticalflowfarneback
-cv::Mat mitk::PhotoacousticMotionCorrectionFilter::ComputeFlowMap(cv::Mat flow) {
- cv::Mat map(flow.size(), flow.type());
-
- for (int y = 0; y < map.rows; ++y) {
- for(int x = 0; x < map.cols; ++x) {
- cv::Point2f f = flow.at<cv::Point2f>(y,x);
- map.at<cv::Point2f>(y,x) = cv::Point2f(x + f.x, y + f.y);
- }
- }
-
- return map;
-}
-
-cv::Mat mitk::PhotoacousticMotionCorrectionFilter::FitMatrixToChar(cv::Mat mat) {
-
- if (m_MaxValue == m_MinValue) {
-
- return mat.clone();
- }
-
- return MAX_MATRIX*(mat.clone() - m_MinValue) / (m_MaxValue - m_MinValue);
-}
-
-cv::Mat mitk::PhotoacousticMotionCorrectionFilter::GetMatrix(
- const mitk::Image::Pointer input, unsigned int i) {
-
- // Access slice i of image input
- mitk::ImageReadAccessor accessor(input, input->GetSliceData(i));
- mitk::Image::Pointer slice = mitk::Image::New();
- slice->Initialize(input->GetPixelType(), IMAGE_DIMENSION - 1, input->GetDimensions());
- slice->SetVolume(accessor.GetData());
-
- // Transform the slice to matrix
- m_ImageToOpenCVFilter->SetImage(slice);
- return m_ImageToOpenCVFilter->GetOpenCVMat();
-}
-
-void mitk::PhotoacousticMotionCorrectionFilter::InsertMatrixAsSlice(
- cv::Mat mat, mitk::Image::Pointer output, unsigned int i) {
-
- m_OpenCVToImageFilter->SetOpenCVMat(mat);
- m_OpenCVToImageFilter->Update();
- mitk::Image::Pointer slice = m_OpenCVToImageFilter->GetOutput();
-
- mitk::ImageReadAccessor accessor(slice);
- output->SetSlice(accessor.GetData(), i);
-}
-
-// TODO: remove debug messages
-void mitk::PhotoacousticMotionCorrectionFilter::GenerateData() {
- MITK_INFO << "Start motion compensation.";
-
- mitk::Image::Pointer paInput = this->GetInput(0);
- mitk::Image::Pointer usInput = this->GetInput(1);
- mitk::Image::Pointer paOutput = this->GetOutput(0);
- mitk::Image::Pointer usOutput = this->GetOutput(1);
-
- // Check that we have two input images with agreeing dimensions
- this->CheckInput(paInput, usInput);
-
- // Check the output images and (re-)initialize, if necessary.
- this->InitializeOutputIfNecessary(paInput, usInput, paOutput, usOutput);
-
- // Set Max and Min of ultrasonic image
- this->m_MaxValue = usInput->GetStatistics()->GetScalarValueMax();
- this->m_MinValue = usInput->GetStatistics()->GetScalarValueMin();
-
- // m_ImageToOpenCVFilter->SetImage(paInput);
- this->PerformCorrection(paInput, usInput, paOutput, usOutput);
-
- MITK_INFO << "Motion compensation accomplished.";
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp b/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp
deleted file mode 100644
index 30c197f9e3..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/utils/mitkBeamformingUtils.cpp
+++ /dev/null
@@ -1,408 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkProperties.h"
-#include "mitkImageReadAccessor.h"
-#include <algorithm>
-#include <itkImageIOBase.h>
-#include <chrono>
-#include <thread>
-#include <itkImageIOBase.h>
-#include "mitkImageCast.h"
-#include "mitkBeamformingUtils.h"
-
-mitk::BeamformingUtils::BeamformingUtils()
-{
-}
-
-mitk::BeamformingUtils::~BeamformingUtils()
-{
-}
-
-float* mitk::BeamformingUtils::VonHannFunction(int samples)
-{
- float* ApodWindow = new float[samples];
-
- for (int n = 0; n < samples; ++n)
- {
- ApodWindow[n] = (1 - cos(2 * itk::Math::pi * n / (samples - 1))) / 2;
- }
-
- return ApodWindow;
-}
-
-float* mitk::BeamformingUtils::HammFunction(int samples)
-{
- float* ApodWindow = new float[samples];
-
- for (int n = 0; n < samples; ++n)
- {
- ApodWindow[n] = 0.54 - 0.46*cos(2 * itk::Math::pi*n / (samples - 1));
- }
-
- return ApodWindow;
-}
-
-float* mitk::BeamformingUtils::BoxFunction(int samples)
-{
- float* ApodWindow = new float[samples];
-
- for (int n = 0; n < samples; ++n)
- {
- ApodWindow[n] = 1;
- }
-
- return ApodWindow;
-}
-
-unsigned short* mitk::BeamformingUtils::MinMaxLines(const mitk::BeamformingSettings::Pointer config)
-{
- unsigned int outputL = (unsigned int)config->GetReconstructionLines();
- unsigned int outputS = (unsigned int)config->GetSamplesPerLine();
-
- unsigned short* dDest = new unsigned short[outputL * outputS * 2];
-
- unsigned int inputL = (unsigned int)config->GetInputDim()[0];
-
- float horizontalExtent = config->GetHorizontalExtent();
- float verticalExtent = config->GetReconstructionDepth();
-
- float partMult = (tan(config->GetAngle() / 360 * 2 * itk::Math::pi) *
- ((config->GetSpeedOfSound() * config->GetTimeSpacing())) /
- (config->GetPitchInMeters() * config->GetTransducerElements())) * inputL;
- float totalSamples_i = (float)(config->GetReconstructionDepth()) / (float)(config->GetSpeedOfSound() * config->GetTimeSpacing());
-
- totalSamples_i = totalSamples_i <= config->GetInputDim()[1] ? totalSamples_i : config->GetInputDim()[1];
-
- if ((int)config->GetGeometry() == 0) // if this is raw data from a linear probe geometry
- {
- for (unsigned int x = 0; x < outputL; ++x)
- {
- for (unsigned int y = 0; y < outputS; ++y)
- {
- float l_i = (float)x / outputL * inputL;
- float s_i = (float)y / (float)outputS * totalSamples_i;
-
- float part = partMult * s_i;
- if (part < 1)
- part = 1;
- unsigned short maxLine = std::min((l_i + part) + 1, (float)inputL);
- unsigned short minLine = std::max((l_i - part), 0.0f);
-
- dDest[y * 2 * outputL + 2 * x] = (unsigned short)minLine; //minLine
- dDest[y * 2 * outputL + 2 * x + 1] = (unsigned short)maxLine; //maxLine
- }
- }
-
- }
- else // if this is *not* raw data from a linear probe geometry (currently meaning its a concave geometry)
- {
- float probeRadius = config->GetProbeRadius();
- float* elementHeights = config->GetElementHeights();
- float* elementPositions = config->GetElementPositions();
-
- float sin_deg = std::sin(config->GetAngle() / 360 * 2 * itk::Math::pi);
-
- float x_center_pos = horizontalExtent / 2.0;
- float y_center_pos = probeRadius;
-
- for (unsigned int x = 0; x < outputL; ++x)
- {
- for (unsigned int y = 0; y < outputS; ++y)
- {
- float x_cm = (float)x / outputL * horizontalExtent; // x*Xspacing
- float y_cm = (float)y / (float)outputS * verticalExtent; // y*Yspacing
-
- unsigned int maxLine = inputL;
- unsigned int minLine = 0;
-
- for (unsigned int l_s = minLine; l_s <= inputL; l_s += 1)
- {
- float x_sensor_pos = elementPositions[l_s];
- float y_sensor_pos = elementHeights[l_s];
-
- float distance_sensor_target = sqrt((x_cm - x_sensor_pos)*(x_cm - x_sensor_pos)
- + (y_cm - y_sensor_pos)*(y_cm - y_sensor_pos));
-
- // solving line equation
- float center_to_sensor_a = y_sensor_pos - y_center_pos;
- float center_to_sensor_b = x_center_pos - x_sensor_pos;
- float center_to_sensor_c = -(center_to_sensor_a * x_center_pos + center_to_sensor_b * y_center_pos);
- float distance_to_sensor_direction = std::fabs((center_to_sensor_a * x_cm
- + center_to_sensor_b * y_cm
- + center_to_sensor_c)) /
- (sqrt(center_to_sensor_a*center_to_sensor_a + center_to_sensor_b*center_to_sensor_b));
-
- if (distance_to_sensor_direction < sin_deg*distance_sensor_target)
- {
- minLine = l_s;
- break;
- }
- }
-
- for (unsigned int l_s = maxLine - 1; l_s > minLine; l_s -= 1) // start with maxline-1 otherwise elementPositions[] will go out of range
- {
- float x_sensor_pos = elementPositions[l_s];
- float y_sensor_pos = elementHeights[l_s];
-
- float distance_sensor_target = sqrt((x_cm - x_sensor_pos)*(x_cm - x_sensor_pos)
- + (y_cm - y_sensor_pos)*(y_cm - y_sensor_pos));
-
- // solving line equation
- float center_to_sensor_a = y_sensor_pos - y_center_pos;
- float center_to_sensor_b = x_center_pos - x_sensor_pos;
- float center_to_sensor_c = -(center_to_sensor_a * x_center_pos + center_to_sensor_b * y_center_pos);
- float distance_to_sensor_direction = std::fabs((center_to_sensor_a * x_cm
- + center_to_sensor_b * y_cm
- + center_to_sensor_c)) /
- (sqrt(center_to_sensor_a*center_to_sensor_a + center_to_sensor_b*center_to_sensor_b));
-
- if (distance_to_sensor_direction < sin_deg*distance_sensor_target)
- {
- maxLine = l_s;
- break;
- }
- }
- dDest[y * 2 * outputL + 2 * x] = (unsigned short)minLine; //minLine
- dDest[y * 2 * outputL + 2 * x + 1] = (unsigned short)maxLine; //maxLine
- }
- }
- }
- return dDest;
-}
-
-void mitk::BeamformingUtils::DASSphericalLine(
- float* input, float* output, float inputDim[2], float outputDim[2],
- const short& line, const mitk::BeamformingSettings::Pointer config)
-{
- const float* apodisation = config->GetApodizationFunction();
- const short apodArraySize = config->GetApodizationArraySize();
-
- const float* elementHeights = config->GetElementHeights();
- const float* elementPositions = config->GetElementPositions();
-
- float& inputS = inputDim[1];
- float& inputL = inputDim[0];
-
- float& outputS = outputDim[1];
- float& outputL = outputDim[0];
-
- short AddSample = 0;
- short maxLine = 0;
- short minLine = 0;
- float l_p = 0;
- float s_i = 0;
-
- float apod_mult = 1;
-
- short usedLines = (maxLine - minLine);
-
- float totalSamples_i = (float)(config->GetReconstructionDepth()) / (float)(config->GetSpeedOfSound() * config->GetTimeSpacing());
- totalSamples_i = totalSamples_i <= inputS ? totalSamples_i : inputS;
-
- l_p = (float)line / outputL * config->GetHorizontalExtent();
-
- for (short sample = 0; sample < outputS; ++sample)
- {
- s_i = (float)sample / outputS * totalSamples_i;
-
- minLine = config->GetMinMaxLines()[2*sample*(short)outputL + 2*line];
- maxLine = config->GetMinMaxLines()[2*sample*(short)outputL + 2*line + 1];
- usedLines = (maxLine - minLine);
-
- apod_mult = (float)apodArraySize / (float)usedLines;
-
- for (short l_s = minLine; l_s < maxLine; ++l_s)
- {
- AddSample = (int)sqrt(
- pow(s_i-elementHeights[l_s]/(config->GetSpeedOfSound()*config->GetTimeSpacing()), 2)
- +
- pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound())) * (l_p - elementPositions[l_s]), 2)
- ) + (1 - config->GetIsPhotoacousticImage())*s_i;
- if (AddSample < inputS && AddSample >= 0)
- output[sample*(short)outputL + line] += input[l_s + AddSample*(short)inputL] *
- apodisation[(short)((l_s - minLine)*apod_mult)];
- else
- --usedLines;
- }
- output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / usedLines;
- }
-}
-
-void mitk::BeamformingUtils::DMASSphericalLine(
- float* input, float* output, float inputDim[2], float outputDim[2],
- const short& line, const mitk::BeamformingSettings::Pointer config)
-{
- const float* apodisation = config->GetApodizationFunction();
- const short apodArraySize = config->GetApodizationArraySize();
-
- const float* elementHeights = config->GetElementHeights();
- const float* elementPositions = config->GetElementPositions();
-
- float& inputS = inputDim[1];
- float& inputL = inputDim[0];
-
- float& outputS = outputDim[1];
- float& outputL = outputDim[0];
-
- short maxLine = 0;
- short minLine = 0;
- float l_p = 0;
- float s_i = 0;
-
- float apod_mult = 1;
-
- float mult = 0;
-
- short usedLines = (maxLine - minLine);
-
- float totalSamples_i = (float)(config->GetReconstructionDepth()) /
- (float)(config->GetSpeedOfSound() * config->GetTimeSpacing());
- totalSamples_i = totalSamples_i <= inputS ? totalSamples_i : inputS;
-
- l_p = (float)line / outputL * config->GetHorizontalExtent();
-
- for (short sample = 0; sample < outputS; ++sample)
- {
- s_i = (float)sample / outputS * totalSamples_i;
-
- minLine = config->GetMinMaxLines()[2 * sample*(short)outputL + 2 * line];
- maxLine = config->GetMinMaxLines()[2 * sample*(short)outputL + 2 * line + 1];
- usedLines = (maxLine - minLine);
-
- apod_mult = (float)apodArraySize / (float)usedLines;
-
- //calculate the AddSamples beforehand to save some time
- short* AddSample = new short[maxLine - minLine];
- for (short l_s = 0; l_s < maxLine - minLine; ++l_s)
- {
- AddSample[l_s] = (int)sqrt(
- pow(s_i - elementHeights[l_s + minLine] / (config->GetSpeedOfSound()*config->GetTimeSpacing()), 2)
- +
- pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound())) * (l_p - elementPositions[l_s + minLine]), 2)
- ) + (1 - config->GetIsPhotoacousticImage())*s_i;
- }
-
- float s_1 = 0;
- float s_2 = 0;
-
- for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1)
- {
- if (AddSample[l_s1 - minLine] < inputS && AddSample[l_s1 - minLine] >= 0)
- {
- for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2)
- {
- if (AddSample[l_s2 - minLine] < inputS && AddSample[l_s2 - minLine] >= 0)
- {
- s_2 = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL];
- s_1 = input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL];
-
- mult = s_2 * apodisation[(int)((l_s2 - minLine)*apod_mult)] * s_1 * apodisation[(int)((l_s1 - minLine)*apod_mult)];
- output[sample*(short)outputL + line] += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0));
- }
- }
- }
- else
- --usedLines;
- }
-
- output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / (float)(pow(usedLines, 2) - (usedLines - 1));
-
- delete[] AddSample;
- }
-}
-
-void mitk::BeamformingUtils::sDMASSphericalLine(
- float* input, float* output, float inputDim[2], float outputDim[2],
- const short& line, const mitk::BeamformingSettings::Pointer config)
-{
- const float* apodisation = config->GetApodizationFunction();
- const short apodArraySize = config->GetApodizationArraySize();
-
- const float* elementHeights = config->GetElementHeights();
- const float* elementPositions = config->GetElementPositions();
-
- float& inputS = inputDim[1];
- float& inputL = inputDim[0];
-
- float& outputS = outputDim[1];
- float& outputL = outputDim[0];
-
- short maxLine = 0;
- short minLine = 0;
- float l_p = 0;
- float s_i = 0;
-
- float apod_mult = 1;
-
- float mult = 0;
-
- short usedLines = (maxLine - minLine);
-
- float totalSamples_i = (float)(config->GetReconstructionDepth()) /
- (float)(config->GetSpeedOfSound() * config->GetTimeSpacing());
- totalSamples_i = totalSamples_i <= inputS ? totalSamples_i : inputS;
-
- l_p = (float)line / outputL * config->GetHorizontalExtent();
-
- for (short sample = 0; sample < outputS; ++sample)
- {
- s_i = (float)sample / outputS * totalSamples_i;
-
- minLine = config->GetMinMaxLines()[2 * sample*(short)outputL + 2 * line];
- maxLine = config->GetMinMaxLines()[2 * sample*(short)outputL + 2 * line + 1];
- usedLines = (maxLine - minLine);
-
- apod_mult = (float)apodArraySize / (float)usedLines;
-
- //calculate the AddSamples beforehand to save some time
- short* AddSample = new short[maxLine - minLine];
- for (short l_s = 0; l_s < maxLine - minLine; ++l_s)
- {
- AddSample[l_s] = (int)sqrt(
- pow(s_i - elementHeights[l_s + minLine] / (config->GetSpeedOfSound()*config->GetTimeSpacing()), 2)
- +
- pow((1 / (config->GetTimeSpacing()*config->GetSpeedOfSound())) * (l_p - elementPositions[l_s + minLine]), 2)
- ) + (1 - config->GetIsPhotoacousticImage())*s_i;
- }
-
- float s_1 = 0;
- float s_2 = 0;
- float sign = 0;
-
- for (short l_s1 = minLine; l_s1 < maxLine - 1; ++l_s1)
- {
- if (AddSample[l_s1 - minLine] < inputS && AddSample[l_s1 - minLine] >= 0)
- {
- s_1 = input[l_s1 + AddSample[l_s1 - minLine] * (short)inputL];
- sign += s_1;
-
- for (short l_s2 = l_s1 + 1; l_s2 < maxLine; ++l_s2)
- {
- if (AddSample[l_s2 - minLine] < inputS && AddSample[l_s2 - minLine] >= 0)
- {
- s_2 = input[l_s2 + AddSample[l_s2 - minLine] * (short)inputL];
-
- mult = s_2 * apodisation[(int)((l_s2 - minLine)*apod_mult)] * s_1 * apodisation[(int)((l_s1 - minLine)*apod_mult)];
- output[sample*(short)outputL + line] += sqrt(fabs(mult)) * ((mult > 0) - (mult < 0));
- }
- }
- }
- else
- --usedLines;
- }
-
- output[sample*(short)outputL + line] = output[sample*(short)outputL + line] / (float)(pow(usedLines, 2) - (usedLines - 1)) * ((sign > 0) - (sign < 0));
-
- delete[] AddSample;
- }
-}
diff --git a/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp b/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp
deleted file mode 100644
index cd3f6749c5..0000000000
--- a/Modules/PhotoacousticsAlgorithms/source/utils/mitkPhotoacousticFilterService.cpp
+++ /dev/null
@@ -1,302 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPhotoacousticFilterService.h"
-
-#include "mitkITKImageImport.h"
-#include <chrono>
-#include <mitkCropImageFilter.h>
-#include "./OpenCLFilter/mitkPhotoacousticBModeFilter.h"
-#include "mitkConvert2Dto3DImageFilter.h"
-#include <mitkCastToFloatImageFilter.h>
-#include "../ITKFilter/ITKUltrasound/itkBModeImageFilter.h"
-#include "../ITKFilter/itkPhotoacousticBModeImageFilter.h"
-#include <mitkBandpassFilter.h>
-
-// itk dependencies
-#include "itkImage.h"
-#include "itkResampleImageFilter.h"
-#include "itkCastImageFilter.h"
-#include "itkCropImageFilter.h"
-#include "itkRescaleIntensityImageFilter.h"
-#include "itkIntensityWindowingImageFilter.h"
-#include <itkIndex.h>
-#include "itkBSplineInterpolateImageFunction.h"
-#include <mitkImageToItk.h>
-
-// needed itk image filters
-#include "mitkImageCast.h"
-
-mitk::PhotoacousticFilterService::PhotoacousticFilterService()
-{
- MITK_INFO << "[PhotoacousticFilterService] created filter service";
-}
-
-mitk::PhotoacousticFilterService::~PhotoacousticFilterService()
-{
- MITK_INFO << "[PhotoacousticFilterService] destructed filter service";
-}
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBmodeFilter(
- mitk::Image::Pointer inputImage,
- BModeMethod method, bool UseLogFilter)
-{
- // the image needs to be of floating point type for the envelope filter to work; the casting is done automatically by the CastToItkImage
- typedef itk::Image< float, 3 > itkFloatImageType;
-
- auto floatImage = ConvertToFloat(inputImage);
-
- if (method == BModeMethod::Abs)
- {
- PhotoacousticBModeFilter::Pointer filter = PhotoacousticBModeFilter::New();
- filter->UseLogFilter(UseLogFilter);
- filter->SetInput(floatImage);
- filter->Update();
- return filter->GetOutput();
- }
-
- typedef itk::BModeImageFilter < itkFloatImageType, itkFloatImageType > BModeFilterType;
- BModeFilterType::Pointer bModeFilter = BModeFilterType::New(); // LogFilter
-
- typedef itk::PhotoacousticBModeImageFilter < itkFloatImageType, itkFloatImageType > PhotoacousticBModeImageFilter;
- PhotoacousticBModeImageFilter::Pointer photoacousticBModeFilter = PhotoacousticBModeImageFilter::New(); // No LogFilter
-
- typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter;
- ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New();
-
- itkFloatImageType::Pointer itkImage;
-
- mitk::CastToItkImage(floatImage, itkImage);
-
- if (UseLogFilter)
- {
- bModeFilter->SetInput(itkImage);
- bModeFilter->SetDirection(1);
- itkImage = bModeFilter->GetOutput();
- }
- else
- {
- photoacousticBModeFilter->SetInput(itkImage);
- photoacousticBModeFilter->SetDirection(1);
- itkImage = photoacousticBModeFilter->GetOutput();
- }
-
- return mitk::GrabItkImageMemory(itkImage);
-}
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyResampling(
- mitk::Image::Pointer inputImage,
- double *outputSpacing)
-{
- typedef itk::Image< float, 3 > itkFloatImageType;
-
- auto floatImage = ConvertToFloat(inputImage);
-
- typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter;
- ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New();
-
- itkFloatImageType::Pointer itkImage;
-
- mitk::CastToItkImage(floatImage, itkImage);
-
- itkFloatImageType::SpacingType outputSpacingItk;
- itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize();
- itkFloatImageType::SizeType outputSizeItk = inputSizeItk;
-
- outputSpacingItk[0] = outputSpacing[0];
- outputSpacingItk[1] = outputSpacing[1];
- outputSpacingItk[2] = itkImage->GetSpacing()[2];
-
- outputSizeItk[0] = outputSizeItk[0] * (floatImage->GetGeometry()->GetSpacing()[0] / outputSpacing[0]);
- outputSizeItk[1] = outputSizeItk[1] * (floatImage->GetGeometry()->GetSpacing()[1] / outputSpacing[1]);
-
- resampleImageFilter->SetInput(itkImage);
- resampleImageFilter->SetSize(outputSizeItk);
- resampleImageFilter->SetOutputSpacing(outputSpacingItk);
-
- resampleImageFilter->UpdateLargestPossibleRegion();
- return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput());
-}
-
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyResamplingToDim(
- mitk::Image::Pointer inputImage,
- double *outputDimension)
-{
- typedef itk::Image< float, 3 > itkFloatImageType;
-
- auto floatImage = ConvertToFloat(inputImage);
-
- typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter;
- ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New();
-
- itkFloatImageType::Pointer itkImage;
-
- mitk::CastToItkImage(floatImage, itkImage);
-
- itkFloatImageType::SpacingType outputSpacingItk;
- itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize();
- itkFloatImageType::SizeType outputSizeItk = inputSizeItk;
-
- outputSizeItk[0] = outputDimension[0];
- outputSizeItk[1] = outputDimension[1];
-
- MITK_INFO << outputSizeItk[0] << " " << outputSizeItk[1];
-
- outputSpacingItk[0] = (double)inputSizeItk[0] / (double)outputSizeItk[0] * floatImage->GetGeometry()->GetSpacing()[0];
- outputSpacingItk[1] = (double)inputSizeItk[1] / (double)outputSizeItk[1] * floatImage->GetGeometry()->GetSpacing()[1];
- outputSpacingItk[2] = itkImage->GetSpacing()[2];
-
- MITK_INFO << outputSpacingItk[0] << " " << outputSpacingItk[1];
-
- resampleImageFilter->SetInput(itkImage);
- resampleImageFilter->SetSize(outputSizeItk);
- resampleImageFilter->SetOutputSpacing(outputSpacingItk);
-
- resampleImageFilter->UpdateLargestPossibleRegion();
- return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput());
-}
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyCropping(
- mitk::Image::Pointer inputImage,
- int above, int below,
- int right, int left,
- int zStart, int zEnd,
- int* errCode)
-{
- *errCode = 0;
- try
- {
- auto floatImage = ConvertToFloat(inputImage);
- mitk::CropImageFilter::Pointer cropImageFilter = mitk::CropImageFilter::New();
- cropImageFilter->SetInput(floatImage);
- cropImageFilter->SetXPixelsCropStart(left);
- cropImageFilter->SetXPixelsCropEnd(right);
- cropImageFilter->SetYPixelsCropStart(above);
- cropImageFilter->SetYPixelsCropEnd(below);
- cropImageFilter->SetZPixelsCropStart(zStart);
- cropImageFilter->SetZPixelsCropEnd(zEnd);
- cropImageFilter->Update();
- return cropImageFilter->GetOutput();
- }
- catch (mitk::Exception &e)
- {
- std::string errorMessage = "Caught unexpected exception ";
- errorMessage.append(e.what());
- MITK_ERROR << errorMessage;
- *errCode = -1;
- mitk::Image::Pointer ret = mitk::Image::New();
- unsigned int dim[3] = { 1,1,1 };
- ret->Initialize(MakeScalarPixelType<float>(), 3, dim);
-
- return ret;
- }
-}
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ExtendImage(mitk::Image::Pointer inputImage, float pixelColor, unsigned int outputDimensionY)
-{
- mitk::Image::Pointer outputImage = mitk::Image::New();
- unsigned int dim[] = {inputImage->GetDimension(0), outputDimensionY, inputImage->GetDimension(2)};
- outputImage->Initialize(inputImage->GetPixelType(), 3, dim);
-
- float *sliceData = new float[dim[0] * dim[1]];
-
- for (size_t i = inputImage->GetDimension(1) * dim[0]; i < dim[0] * dim[1]; ++i)
- {
- sliceData[i] = pixelColor;
- }
-
- for (unsigned int slice = 0; slice < dim[2]; ++slice)
- {
- mitk::ImageReadAccessor cpy(inputImage, inputImage->GetSliceData(slice));
- cpy.GetData();
- std::memcpy((void*)sliceData, cpy.GetData(), sizeof(float) * inputImage->GetDimension(1) * dim[0]);
- outputImage->SetSlice(sliceData, slice);
- }
-
- delete[] sliceData;
- return outputImage;
-}
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBeamforming(
- mitk::Image::Pointer inputImage,
- BeamformingSettings::Pointer config,
- std::function<void(int, std::string)> progressHandle)
-{
- Image::Pointer processedImage = mitk::Image::New();
-
- if (inputImage->GetDimension() != 3)
- {
- mitk::Convert2Dto3DImageFilter::Pointer dimensionImageFilter = mitk::Convert2Dto3DImageFilter::New();
- dimensionImageFilter->SetInput(inputImage);
- dimensionImageFilter->Update();
- processedImage = dimensionImageFilter->GetOutput();
- }
- else
- {
- processedImage = inputImage;
- }
-
- m_BeamformingFilter = mitk::BeamformingFilter::New(config);
- m_BeamformingFilter->SetInput(ConvertToFloat(processedImage));
- m_BeamformingFilter->SetProgressHandle(progressHandle);
- m_BeamformingFilter->UpdateLargestPossibleRegion();
-
- processedImage = m_BeamformingFilter->GetOutput();
-
- return processedImage;
-}
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ApplyBandpassFilter(
- mitk::Image::Pointer data,
- float BPHighPass, float BPLowPass,
- float alphaHighPass, float alphaLowPass,
- float TimeSpacing, float SpeedOfSound, bool IsBFImage)
-{
- try
- {
- auto floatData = ConvertToFloat(data);
- mitk::BandpassFilter::Pointer bandpassFilter = mitk::BandpassFilter::New();
- bandpassFilter->SetInput(floatData);
- bandpassFilter->SetHighPass(BPHighPass);
- bandpassFilter->SetLowPass(BPLowPass);
- bandpassFilter->SetHighPassAlpha(alphaHighPass);
- bandpassFilter->SetLowPassAlpha(alphaLowPass);
- bandpassFilter->SetSpeedOfSound(SpeedOfSound);
- bandpassFilter->SetTimeSpacing(TimeSpacing);
- bandpassFilter->SetIsBFImage(IsBFImage);
- bandpassFilter->Update();
- return bandpassFilter->GetOutput();
- }
- catch (mitk::Exception &e)
- {
- std::string errorMessage = "Caught unexpected exception ";
- errorMessage.append(e.what());
- MITK_ERROR << errorMessage;
-
- return data;
- }
-}
-
-mitk::Image::Pointer mitk::PhotoacousticFilterService::ConvertToFloat(mitk::Image::Pointer inputImage)
-{
- if ((inputImage->GetPixelType().GetTypeAsString() == "scalar (float)" ||
- inputImage->GetPixelType().GetTypeAsString() == " (float)"))
- {
- return inputImage;
- }
-
- mitk::CastToFloatImageFilter::Pointer castToFloatImageFilter = mitk::CastToFloatImageFilter::New();
- castToFloatImageFilter->SetInput(inputImage);
- castToFloatImageFilter->Update();
- return castToFloatImageFilter->GetOutput();
-}
diff --git a/Modules/PhotoacousticsAlgorithms/test/CMakeLists.txt b/Modules/PhotoacousticsAlgorithms/test/CMakeLists.txt
deleted file mode 100644
index 153cd81e2e..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/CMakeLists.txt
+++ /dev/null
@@ -1 +0,0 @@
-MITK_CREATE_MODULE_TESTS()
diff --git a/Modules/PhotoacousticsAlgorithms/test/files.cmake b/Modules/PhotoacousticsAlgorithms/test/files.cmake
deleted file mode 100644
index f3ac9a4454..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/files.cmake
+++ /dev/null
@@ -1,21 +0,0 @@
-set(MODULE_TESTS
- # IMPORTANT: If you plan to deactivate / comment out a test please write a bug number to the commented out line of code.
- #
- # Example: #mitkMyTest #this test is commented out because of bug 12345
- #
- # It is important that the bug is open and that the test will be activated again before the bug is closed. This assures that
- # no test is forgotten after it was commented out. If there is no bug for your current problem, please add a new one and
- # mark it as critical.
- ################## DISABLED TESTS #####################################################
-
- #mitkBandpassFilterTest.cpp #This test is disabled because of T25780
- #mitkBeamformingFilterTest.cpp #This test is disabled because of T25780
-
- ################# RUNNING TESTS #######################################################
-
- mitkPhotoacousticMotionCorrectionFilterTest.cpp
- mitkPAFilterServiceTest.cpp
- mitkCastToFloatImageFilterTest.cpp
- mitkCropImageFilterTest.cpp
- )
-set(RESOURCE_FILES)
diff --git a/Modules/PhotoacousticsAlgorithms/test/mitkBandpassFilterTest.cpp b/Modules/PhotoacousticsAlgorithms/test/mitkBandpassFilterTest.cpp
deleted file mode 100644
index 373435a6af..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/mitkBandpassFilterTest.cpp
+++ /dev/null
@@ -1,188 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#define _USE_MATH_DEFINES
-#include <cmath>
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-#include <mitkImage.h>
-#include <mitkImageReadAccessor.h>
-#include <mitkPhotoacousticFilterService.h>
-#include <random>
-#include <mitkIOUtil.h>
-
-#include "../ITKFilter/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h"
-#include "mitkImageCast.h"
-#include "mitkITKImageImport.h"
-#include "itkComplexToModulusImageFilter.h"
-
-class mitkBandpassFilterTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkBandpassFilterTestSuite);
- MITK_TEST(testHighPass);
- MITK_TEST(testLowPass);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::PhotoacousticFilterService::Pointer m_FilterService;
- const unsigned int NUM_ITERATIONS = 10;
- const unsigned int DATA_XY_DIM = 512;
- const unsigned int DATA_Z_DIM = 8;
- const float TIME_SPACING = 0.00625; // [us]
- float FREQUENCY_RESOLUTION = 1 / (TIME_SPACING / 1e6 * DATA_XY_DIM); // [Hz]
- const float MAX_FREQUENCY = FREQUENCY_RESOLUTION * DATA_XY_DIM / 2.f; // [Hz]
- const float HIGHPASS_FREQENCY = MAX_FREQUENCY * 0.8f; // [Hz]
- const float LOWPASS_FREQENCY = MAX_FREQUENCY * 0.1f; // [Hz]
- const float ALPHA = 0.01; // 0 = box, 1 = von Hann; changing this may make the test invalid
- const float EPSILON_FFT = 0.0001f;
-
-public:
-
- void setUp() override
- {
- m_FilterService = mitk::PhotoacousticFilterService::New();
- }
-
- void test(float HighPass, float LowPass, float HighPassAlpha, float LowPassAlpha, bool useLow, bool useHigh)
- {
- std::random_device r;
- std::default_random_engine randGen(r());
- std::uniform_real_distribution<float> randDistrHighPass(HighPass * 0.01f, HighPass * 0.2f);
- std::uniform_real_distribution<float> randDistrLowPass(LowPass * 1.5f, LowPass * 2.f);
- float* data = new float[DATA_XY_DIM*DATA_XY_DIM*DATA_Z_DIM];
-
- mitk::Image::Pointer inputImage = mitk::Image::New();
- unsigned int dimension[3]{ DATA_XY_DIM, DATA_XY_DIM, DATA_Z_DIM };
- inputImage->Initialize(mitk::MakeScalarPixelType<float>(), 3, dimension);
- mitk::Vector3D spacing;
- spacing[0] = 1;
- spacing[1] = TIME_SPACING;
- spacing[2] = 1;
- inputImage->SetSpacing(spacing);
-
- for (unsigned int iteration = 0; iteration < NUM_ITERATIONS; ++iteration)
- {
- // fill image with zeros
- for (unsigned int i = 0; i < DATA_XY_DIM*DATA_XY_DIM*DATA_Z_DIM; ++i)
- {
- data[i] = 0;
- }
-
- // write specific frequencies to the image
- if (useHigh)
- addFrequency(randDistrHighPass(randGen), TIME_SPACING, data, dimension);
- if (useLow)
- addFrequency(randDistrLowPass(randGen), TIME_SPACING, data, dimension);
-
- inputImage->SetImportVolume(data, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
-
- if (!useHigh)
- HighPass = 0;
-
- if (!useLow)
- LowPass = MAX_FREQUENCY;
-
- mitk::Image::Pointer outputImage = m_FilterService->ApplyBandpassFilter(inputImage, HighPass, LowPass, HighPassAlpha, LowPassAlpha, TIME_SPACING / 1e6, 0, false);
-
- // do a fourier transform, and check whether the part of the image that has been filtered is zero
- typedef itk::Image< float, 3 > RealImageType;
- RealImageType::Pointer image;
-
- mitk::CastToItkImage(outputImage, image);
-
- typedef itk::FFT1DRealToComplexConjugateImageFilter<RealImageType> ForwardFFTFilterType;
- // typedef ForwardFFTFilterType::OutputImageType ComplexImageType;
- ForwardFFTFilterType::Pointer forwardFFTFilter = ForwardFFTFilterType::New();
- forwardFFTFilter->SetInput(image);
- forwardFFTFilter->SetDirection(1);
- forwardFFTFilter->UpdateOutputInformation();
- forwardFFTFilter->Update();
-
- auto fftResult = forwardFFTFilter->GetOutput();
-
- /*
- std::string img = "D:/img" + std::to_string(iteration) + ".nrrd";
- mitk::IOUtil::Save(inputImage, img);
- std::string res = "D:/res" + std::to_string(iteration) + ".nrrd";
- mitk::IOUtil::Save(outputImage, res);*/
-
- // the resulting image should consist only of zeros, as we filtered the frequencies out
- for (unsigned int z = 0; z < DATA_Z_DIM; ++z)
- {
- for (unsigned int y = 0; y < DATA_XY_DIM / 2; ++y)
- {
- if (y < (unsigned int)std::floor(0.95 * HighPass / FREQUENCY_RESOLUTION) || y >(unsigned int)std::ceil(1.05 * LowPass / FREQUENCY_RESOLUTION))
- {
- for (unsigned int x = 0; x < DATA_XY_DIM; ++x)
- {
- // unsigned int outPos = x + y * DATA_XY_DIM + z * DATA_XY_DIM * DATA_XY_DIM;
- std::complex<float> value = fftResult->GetPixel({ x,y,z });
- CPPUNIT_ASSERT_MESSAGE(std::string("Expected 0, got (" + std::to_string(value.real()) + " + " + std::to_string(value.imag()) + "i) at " + std::to_string(x) + "-" + std::to_string(y) + "-" + std::to_string(z)),
- (value.real() < EPSILON_FFT) && (value.imag() < EPSILON_FFT));
- }
- }
- }
-
- for (unsigned int y = DATA_XY_DIM / 2; y < DATA_XY_DIM; ++y)
- {
- if (y > DATA_XY_DIM - (unsigned int)std::floor(HighPass / FREQUENCY_RESOLUTION) || y < DATA_XY_DIM - (unsigned int)std::ceil(LowPass / FREQUENCY_RESOLUTION))
- {
- for (unsigned int x = 0; x < DATA_XY_DIM; ++x)
- {
- // unsigned int outPos = x + y * DATA_XY_DIM + z * DATA_XY_DIM * DATA_XY_DIM;
- std::complex<float> value = fftResult->GetPixel({ x,y,z });
- CPPUNIT_ASSERT_MESSAGE(std::string("Expected 0, got (" + std::to_string(value.real()) + " + " + std::to_string(value.imag()) + "i) at " + std::to_string(x) + "-" + std::to_string(y) + "-" + std::to_string(z)),
- (value.real() < EPSILON_FFT) && (value.imag() < EPSILON_FFT));
- }
- }
- }
- }
- }
-
- delete[] data;
- }
-
- // write a fixed-frequency signal to the image
- void addFrequency(float freq, float timeSpacing, float* data, unsigned int* dim)
- {
- for (unsigned int z = 0; z < dim[2]; ++z)
- {
- for (unsigned int y = 0; y < dim[1]; ++y)
- {
- for (unsigned int x = 0; x < dim[0]; ++x)
- {
- data[x + y * dim[0] + z * dim[0] * dim[1]] += std::sin(freq * timeSpacing * y);
- }
- }
- }
- }
-
- void testHighPass()
- {
- MITK_INFO << "Performing HighPass test";
- test(HIGHPASS_FREQENCY, 0, ALPHA, ALPHA, false, true);
- }
-
- void testLowPass()
- {
- MITK_INFO << "Performing LowPass test";
- test(0, LOWPASS_FREQENCY, ALPHA, ALPHA, true, false);
- }
-
- void tearDown() override
- {
- m_FilterService = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkBandpassFilter)
diff --git a/Modules/PhotoacousticsAlgorithms/test/mitkBeamformingFilterTest.cpp b/Modules/PhotoacousticsAlgorithms/test/mitkBeamformingFilterTest.cpp
deleted file mode 100644
index b8867a6c62..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/mitkBeamformingFilterTest.cpp
+++ /dev/null
@@ -1,276 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-#include <mitkImage.h>
-#include <mitkImageReadAccessor.h>
-#include <mitkBeamformingFilter.h>
-#include <mitkIOUtil.h>
-#include <usModuleResource.h>
-#include <random>
-
-class SyntheticPAImageData
-{
-public:
- SyntheticPAImageData(float spacing_x, float spacing_y, unsigned int samples, unsigned int num_transducers, float speedOfSound)
- {
- m_Spacing_x = spacing_x;
- m_Spacing_y = spacing_y;
- m_TransducerElements = num_transducers;
- m_Samples = samples;
- m_SpeedOfSound = speedOfSound;
- m_Data = new float[m_Samples*m_TransducerElements];
-
- for (size_t i = 0; i < m_Samples * m_TransducerElements; ++i)
- {
- m_Data[i] = 0;
- }
- }
-
- ~SyntheticPAImageData()
- {
- delete[] m_Data;
- }
-
- void AddWave(float origin_depth, float origin_x, float base_value= 10000)
- {
- AddLine(origin_depth, origin_x, base_value);
- AddLine(origin_depth + 0.0001f, origin_x, -base_value);
- }
-
- const float* GetData()
- {
- return (const float*)m_Data;
- }
-
-private:
- void AddLine(float origin_depth, unsigned int origin_x, float base_value = 10000)
- {
- for (unsigned int x = 0; x < m_TransducerElements; ++x)
- {
- float distance = std::abs((int)x - (int)origin_x);
- float delay_in_seconds = std::sqrt(std::pow(origin_depth, 2) + std::pow(distance*m_Spacing_x, 2)) / m_SpeedOfSound;
- int pixels = std::round(delay_in_seconds / m_Spacing_y);
-
- for (int index = -4; index < 9; ++index)
- {
- if ((int)pixels + index < (int)m_Samples && (int)pixels + index > 0)
- {
- m_Data[(size_t)(x + (pixels + index)*m_TransducerElements)] += base_value / std::sqrt(distance + 1);
- }
- }
- }
- }
-
- float* m_Data;
- float m_Spacing_x;
- float m_Spacing_y;
- unsigned int m_TransducerElements;
- unsigned int m_Samples;
- float m_SpeedOfSound;
-};
-
-class mitkBeamformingFilterTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkBeamformingFilterTestSuite);
- MITK_TEST(testBeamformingCPU_DAS);
- MITK_TEST(testBeamformingGPU_DAS);
- MITK_TEST(testBeamformingCPU_DMAS);
- MITK_TEST(testBeamformingGPU_DMAS);
- MITK_TEST(testBeamformingCPU_sDMAS);
- MITK_TEST(testBeamformingGPU_sDMAS);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::BeamformingFilter::Pointer m_BeamformingFilter;
- const unsigned int NUM_ITERATIONS = 15;
- const unsigned int SAMPLES = 5000 * 2;
- const unsigned int RECONSTRUCTED_SAMPLES = 2048;
- const unsigned int ELEMENTS = 128;
- const unsigned int RECONSTRUCTED_LINES = 128;
- const float SPEED_OF_SOUND = 1540; // m/s
- const float SPACING_X = 0.3; // mm
- const float SPACING_Y = 0.00625 / 2; // us
- const unsigned int GPU_BATCH_SIZE = 16;
-
-public:
-
- void setUp() override
- {
-
- }
-
- void test()
- {
- std::random_device r;
- std::default_random_engine randGen(r());
- float maxDepthInMeters = SAMPLES * (SPACING_Y / 1000000) * SPEED_OF_SOUND / 2;
- std::uniform_real_distribution<float> randDistrDepth(maxDepthInMeters*0.1, maxDepthInMeters*0.8);
-
- for (unsigned int iteration = 0; iteration < NUM_ITERATIONS; ++iteration)
- {
- // create some synthetic input data
- float depth_in_meters1 = randDistrDepth(randGen);
- float depth_in_meters2 = randDistrDepth(randGen);
- float depth_in_meters3 = randDistrDepth(randGen);
-
- unsigned int element1 = 29;
- unsigned int element2 = 63;
- unsigned int element3 = 98;
-
- SyntheticPAImageData image(SPACING_X / 1000.f, SPACING_Y / 1000000.f, SAMPLES, ELEMENTS, SPEED_OF_SOUND);
- image.AddWave(depth_in_meters1, 29);
- image.AddWave(depth_in_meters2, 63);
- image.AddWave(depth_in_meters3, 98);
-
- mitk::Image::Pointer inputImage = mitk::Image::New();
- unsigned int dimension[3]{ ELEMENTS, SAMPLES, 1 };
- inputImage->Initialize(mitk::MakeScalarPixelType<float>(), 3, dimension);
- mitk::Vector3D spacing;
- spacing[0] = SPACING_X;
- spacing[1] = SPACING_Y;
- spacing[2] = 1;
- inputImage->SetSpacing(spacing);
- inputImage->SetImportVolume((const void*)image.GetData(), mitk::Image::CopyMemory);
-
- // setup the beamforming filter
- m_BeamformingFilter->SetInput(inputImage);
- m_BeamformingFilter->Update();
-
- mitk::Image::Pointer outputImage = m_BeamformingFilter->GetOutput();
- mitk::ImageReadAccessor readAccess(outputImage);
- const float* outputData = (const float*)readAccess.GetData();
-
- unsigned int pos1[3] = { element1, (unsigned int)std::round(depth_in_meters1 * 1000.f / outputImage->GetGeometry()->GetSpacing()[1]), 0 };
- unsigned int pos2[3] = { element2, (unsigned int)std::round(depth_in_meters2 * 1000.f / outputImage->GetGeometry()->GetSpacing()[1]), 0 };
- unsigned int pos3[3] = { element3, (unsigned int)std::round(depth_in_meters3 * 1000.f / outputImage->GetGeometry()->GetSpacing()[1]), 0 };
-
- double average = 0;
-
- for (unsigned int i = 0; i < RECONSTRUCTED_LINES*RECONSTRUCTED_SAMPLES; ++i)
- {
- average += outputData[i] / (RECONSTRUCTED_LINES*RECONSTRUCTED_SAMPLES);
- }
-
- CPPUNIT_ASSERT_MESSAGE(std::string("Iteration " + std::to_string(iteration) + ": first point source incorrectly reconstructed; should be > average*100, is " +
- std::to_string(abs(outputData[pos1[0] + pos1[1] * RECONSTRUCTED_LINES]))) + " < " + std::to_string(average) + "*100"
- , abs(outputData[pos1[0] + pos1[1]*RECONSTRUCTED_LINES] / average) > 100);
- CPPUNIT_ASSERT_MESSAGE(std::string("Iteration " + std::to_string(iteration) + ": second point source incorrectly reconstructed; should be > average*100, is " +
- std::to_string(abs(outputData[pos2[0] + pos2[1] * RECONSTRUCTED_LINES]))) + " < " + std::to_string(average) + "*100"
- , abs(outputData[pos2[0] + pos2[1] * RECONSTRUCTED_LINES] / average) > 100);
- CPPUNIT_ASSERT_MESSAGE(std::string("Iteration " + std::to_string(iteration) + ": third point source incorrectly reconstructed; should be > average*100, is " +
- std::to_string(abs(outputData[pos3[0] + pos3[1] * RECONSTRUCTED_LINES]))) + " < " + std::to_string(average) + "*100"
- , abs(outputData[pos3[0] + pos3[1] * RECONSTRUCTED_LINES] / average) > 100);
- }
- }
-
- mitk::BeamformingSettings::Pointer createConfig(bool UseGPU, unsigned int* inputDim, mitk::BeamformingSettings::BeamformingAlgorithm alg)
- {
- return mitk::BeamformingSettings::New(SPACING_X / 1000,
- SPEED_OF_SOUND,
- SPACING_Y / 1000000,
- 27.f,
- true,
- RECONSTRUCTED_SAMPLES,
- RECONSTRUCTED_LINES,
- inputDim,
- SPEED_OF_SOUND * (SPACING_Y / 1000000) * SAMPLES,
- UseGPU,
- GPU_BATCH_SIZE,
- mitk::BeamformingSettings::DelayCalc::Spherical,
- mitk::BeamformingSettings::Apodization::Box,
- ELEMENTS * 2,
- alg);
- }
-
- void testBeamformingCPU_DAS()
- {
- MITK_INFO << "Started DAS test on CPU";
- unsigned int* inputDim = new unsigned int[3];
- inputDim[0] = ELEMENTS;
- inputDim[1] = SAMPLES;
- inputDim[2] = 1;
- m_BeamformingFilter = mitk::BeamformingFilter::New(createConfig(false, inputDim, mitk::BeamformingSettings::BeamformingAlgorithm::DAS));
-
- test();
- delete[] inputDim;
- }
-
- void testBeamformingGPU_DAS()
- {
- MITK_INFO << "Started DAS test on GPU";
- unsigned int* inputDim = new unsigned int[3];
- inputDim[0] = ELEMENTS;
- inputDim[1] = SAMPLES;
- inputDim[2] = 1;
- m_BeamformingFilter = mitk::BeamformingFilter::New(createConfig(true, inputDim, mitk::BeamformingSettings::BeamformingAlgorithm::DAS));
-
- test();
- delete[] inputDim;
- }
-
- void testBeamformingCPU_sDMAS()
- {
- MITK_INFO << "Started sDMAS test on CPU";
- unsigned int* inputDim = new unsigned int[3];
- inputDim[0] = ELEMENTS;
- inputDim[1] = SAMPLES;
- inputDim[2] = 1;
- m_BeamformingFilter = mitk::BeamformingFilter::New(createConfig(false, inputDim, mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS));
-
- test();
- delete[] inputDim;
- }
-
- void testBeamformingGPU_sDMAS()
- {
- MITK_INFO << "Started sDMAS test on GPU";
- unsigned int* inputDim = new unsigned int[3];
- inputDim[0] = ELEMENTS;
- inputDim[1] = SAMPLES;
- inputDim[2] = 1;
- m_BeamformingFilter = mitk::BeamformingFilter::New(createConfig(true, inputDim, mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS));
-
- test();
- delete[] inputDim;
- }
-
- void testBeamformingCPU_DMAS()
- {
- MITK_INFO << "Started DMAS test on CPU";
- unsigned int* inputDim = new unsigned int[3];
- inputDim[0] = ELEMENTS;
- inputDim[1] = SAMPLES;
- inputDim[2] = 1;
- m_BeamformingFilter = mitk::BeamformingFilter::New(createConfig(false, inputDim, mitk::BeamformingSettings::BeamformingAlgorithm::DMAS));
-
- test();
- delete[] inputDim;
- }
-
- void testBeamformingGPU_DMAS()
- {
- MITK_INFO << "Started DMAS test on GPU";
- unsigned int* inputDim = new unsigned int[3];
- inputDim[0] = ELEMENTS;
- inputDim[1] = SAMPLES;
- inputDim[2] = 1;
- m_BeamformingFilter = mitk::BeamformingFilter::New(createConfig(true, inputDim, mitk::BeamformingSettings::BeamformingAlgorithm::DMAS));
-
- test();
- delete[] inputDim;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkBeamformingFilter)
diff --git a/Modules/PhotoacousticsAlgorithms/test/mitkCastToFloatImageFilterTest.cpp b/Modules/PhotoacousticsAlgorithms/test/mitkCastToFloatImageFilterTest.cpp
deleted file mode 100644
index 4cbb826971..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/mitkCastToFloatImageFilterTest.cpp
+++ /dev/null
@@ -1,104 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-#include <mitkImage.h>
-#include <mitkImageReadAccessor.h>
-#include <mitkCastToFloatImageFilter.h>
-
-class mitkCastToFloatImageFilterTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkCastToFloatImageFilterTestSuite);
- MITK_TEST(testShortConversion);
- MITK_TEST(testIntConversion);
- MITK_TEST(testLongConversion);
- MITK_TEST(testFloatConversion);
- MITK_TEST(testDoubleConversion);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::CastToFloatImageFilter::Pointer m_CastToFloatImageFilter;
- const unsigned int NUM_ITERATIONS = 15;
- const unsigned int DATA_DIM = 10;
-
-public:
-
- void setUp() override
- {
- m_CastToFloatImageFilter = mitk::CastToFloatImageFilter::New();
- }
-
- template<class TPixelType>
- void test()
- {
- TPixelType* data = new TPixelType[DATA_DIM*DATA_DIM*DATA_DIM];
-
- for (unsigned int i = 0; i < DATA_DIM*DATA_DIM*DATA_DIM; ++i)
- {
- data[i] = (TPixelType)i;
- }
-
- mitk::Image::Pointer inputImage = mitk::Image::New();
- unsigned int dimension[3]{ DATA_DIM, DATA_DIM, DATA_DIM };
- inputImage->Initialize(mitk::MakeScalarPixelType<TPixelType>(), 3, dimension);
- inputImage->SetImportVolume(data);
-
- for (unsigned int iteration = 0; iteration < NUM_ITERATIONS; ++iteration)
- {
- m_CastToFloatImageFilter->SetInput(inputImage);
- m_CastToFloatImageFilter->Update();
- mitk::Image::Pointer outputImage = m_CastToFloatImageFilter->GetOutput();
- mitk::ImageReadAccessor readAccess(outputImage);
- const float* outputData = (const float*)readAccess.GetData();
- for (unsigned int i = 0; i < DATA_DIM*DATA_DIM*DATA_DIM; ++i)
- {
- CPPUNIT_ASSERT_MESSAGE(std::string("expected " + std::to_string(data[i]) + " but was " + std::to_string(outputData[i])), std::abs(outputData[i] - data[i]) < mitk::eps);
- }
- }
- }
-
- void testFloatConversion()
- {
- test<float>();
- }
-
- void testShortConversion()
- {
- test<short>();
- test<unsigned short>();
- }
-
- void testIntConversion()
- {
- test<int>();
- test<unsigned int>();
- }
-
- void testDoubleConversion()
- {
- test<double>();
- }
-
- void testLongConversion()
- {
- test<long>();
- }
-
- void tearDown() override
- {
- m_CastToFloatImageFilter = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkCastToFloatImageFilter)
diff --git a/Modules/PhotoacousticsAlgorithms/test/mitkCropImageFilterTest.cpp b/Modules/PhotoacousticsAlgorithms/test/mitkCropImageFilterTest.cpp
deleted file mode 100644
index 1248d6231c..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/mitkCropImageFilterTest.cpp
+++ /dev/null
@@ -1,123 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-#include <mitkImage.h>
-#include <mitkImageReadAccessor.h>
-#include <mitkCropImageFilter.h>
-#include <random>
-
-class mitkCropImageFilterTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkCropImageFilterTestSuite);
- MITK_TEST(testCropImage);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::CropImageFilter::Pointer m_CropImageFilter;
- const unsigned int NUM_ITERATIONS = 5;
- const unsigned int DATA_DIM = 25;
-
-public:
-
- void setUp() override
- {
- m_CropImageFilter = mitk::CropImageFilter::New();
- }
-
- void test()
- {
- std::random_device r;
- std::default_random_engine randGen(r());
- std::uniform_int_distribution<int> randDistr(0, (DATA_DIM / 2) - 1);
-
- float* data = new float[DATA_DIM*DATA_DIM*DATA_DIM];
-
- for (unsigned int i = 0; i < DATA_DIM*DATA_DIM*DATA_DIM; ++i)
- {
- data[i] = (float)i;
- }
-
- mitk::Image::Pointer inputImage = mitk::Image::New();
- unsigned int dimension[3]{ DATA_DIM, DATA_DIM, DATA_DIM };
- inputImage->Initialize(mitk::MakeScalarPixelType<float>(), 3, dimension);
- inputImage->SetImportVolume(data, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
-
- for (unsigned int iteration = 0; iteration < NUM_ITERATIONS; ++iteration)
- {
- unsigned int XPixelsCropStart = randDistr(randGen);
- unsigned int YPixelsCropStart = randDistr(randGen);
- unsigned int ZPixelsCropStart = randDistr(randGen);
- unsigned int XPixelsCropEnd = randDistr(randGen);
- unsigned int YPixelsCropEnd = randDistr(randGen);
- unsigned int ZPixelsCropEnd = randDistr(randGen);
-
- unsigned int newXDim = DATA_DIM - XPixelsCropStart - XPixelsCropEnd;
- unsigned int newYDim = DATA_DIM - YPixelsCropStart - YPixelsCropEnd;
- unsigned int newZDim = DATA_DIM - ZPixelsCropStart - ZPixelsCropEnd;
-
- m_CropImageFilter->SetInput(inputImage);
-
- m_CropImageFilter->SetXPixelsCropStart(XPixelsCropStart);
- m_CropImageFilter->SetYPixelsCropStart(YPixelsCropStart);
- m_CropImageFilter->SetZPixelsCropStart(ZPixelsCropStart);
- m_CropImageFilter->SetXPixelsCropEnd(XPixelsCropEnd);
- m_CropImageFilter->SetYPixelsCropEnd(YPixelsCropEnd);
- m_CropImageFilter->SetZPixelsCropEnd(ZPixelsCropEnd);
-
- m_CropImageFilter->Update();
- mitk::Image::Pointer outputImage = m_CropImageFilter->GetOutput();
-
- mitk::ImageReadAccessor readAccess(outputImage);
- const float* outputData = (const float*)readAccess.GetData();
-
- CPPUNIT_ASSERT_MESSAGE(std::string("expected x size to be " + std::to_string(newXDim) + " but was " + std::to_string(outputImage->GetDimension(0))), newXDim == outputImage->GetDimension(0));
- CPPUNIT_ASSERT_MESSAGE(std::string("expected y size to be " + std::to_string(newYDim) + " but was " + std::to_string(outputImage->GetDimension(1))), newYDim == outputImage->GetDimension(1));
- CPPUNIT_ASSERT_MESSAGE(std::string("expected z size to be " + std::to_string(newZDim) + " but was " + std::to_string(outputImage->GetDimension(2))), newZDim == outputImage->GetDimension(2));
-
- for (unsigned int z = 0; z < newZDim; ++z)
- {
- for (unsigned int y = 0; y < newYDim; ++y)
- {
- for (unsigned int x = 0; x < newXDim; ++x)
- {
- unsigned int origPos = (x + XPixelsCropStart) + (y + YPixelsCropStart) * DATA_DIM + (z + ZPixelsCropStart) * DATA_DIM * DATA_DIM;
- unsigned int outPos = x + y * newXDim + z * newXDim * newYDim;
- CPPUNIT_ASSERT_MESSAGE(std::string("expected " + std::to_string(data[origPos])
- + " but was " + std::to_string(outputData[outPos])),
- std::abs((float)outputData[outPos] - (float)data[origPos]) < mitk::eps);
- }
- }
- }
- }
-
- delete[] data;
- }
-
- void testCropImage()
- {
- for (int repetition = 0; repetition < 20; ++repetition)
- {
- MITK_INFO << "[" << (repetition + 1) << "/20]";
- test();
- }
- }
-
- void tearDown() override
- {
- m_CropImageFilter = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkCropImageFilter)
diff --git a/Modules/PhotoacousticsAlgorithms/test/mitkPAFilterServiceTest.cpp b/Modules/PhotoacousticsAlgorithms/test/mitkPAFilterServiceTest.cpp
deleted file mode 100644
index d85d536145..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/mitkPAFilterServiceTest.cpp
+++ /dev/null
@@ -1,120 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPhotoacousticFilterService.h>
-#include <mitkImage.h>
-#include <mitkImageReadAccessor.h>
-#include <mitkBeamformingSettings.h>
-
-// us
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usGetModuleContext.h>
-#include <usModuleContext.h>
-#include <usModuleResourceStream.h>
-
-#include <random>
-#include <chrono>
-
-class mitkPAFilterServiceTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPAFilterServiceTestSuite);
- MITK_TEST(testRunning);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::PhotoacousticFilterService::Pointer m_PhotoacousticFilterService;
- mitk::BeamformingSettings::Pointer m_BeamformingSettings;
- unsigned int* inputDimensions;
- const int xDim = 16;
- const int yDim = 128;
- const int length = yDim * xDim;
-
-public:
-
- void setUp() override
- {
- m_PhotoacousticFilterService = mitk::PhotoacousticFilterService::New();
- m_BeamformingSettings = CreateBeamformingSettings();
- }
-
- mitk::BeamformingSettings::Pointer CreateBeamformingSettings()
- {
- inputDimensions = new unsigned int[length];
- inputDimensions[0] = yDim;
- inputDimensions[1] = xDim;
- mitk::BeamformingSettings::Pointer outputSettings = mitk::BeamformingSettings::New(
- (float)(0.3 / 1000),
- (float)(1500),
- (float)(0.0125 / 1000000),
- 27,
- true,
- 3000,
- 128,
- inputDimensions,
- yDim * (0.0125 / 1000000) * (1500),
- false,
- 16,
- mitk::BeamformingSettings::Apodization::Box,
- 128,
- mitk::BeamformingSettings::BeamformingAlgorithm::DAS,
- mitk::BeamformingSettings::ProbeGeometry::Linear,
- 0);
-
- return outputSettings;
- }
-
- void testRunning()
- {
- float* testArray = new float[length];
- for (int i = 0; i < length; ++i)
- {
- testArray[i] = 0;
- }
-
- mitk::PixelType pixelType = mitk::MakeScalarPixelType<float>();
- mitk::Image::Pointer testImage = mitk::Image::New();
- testImage->Initialize(pixelType, 2, inputDimensions);
- testImage->SetImportSlice(testArray, 0, 0, 0, mitk::Image::ImportMemoryManagementType::CopyMemory);
- delete[] testArray;
-
- mitk::ImageReadAccessor readAccessInput(testImage);
- const float* inputArray = (const float*)readAccessInput.GetData();
-
- for (int i = 0; i < length; ++i)
- {
- CPPUNIT_ASSERT_MESSAGE(std::string("Input array already not correct: " + std::to_string(inputArray[i])), std::abs(inputArray[i]) < 1e-5f);
- }
-
- auto output = m_PhotoacousticFilterService->ApplyBeamforming(testImage, m_BeamformingSettings);
-
- mitk::ImageReadAccessor readAccess(output);
- const float* outputArray = (const float*)readAccess.GetData();
-
- for (int i = 0; i < length; ++i)
- {
- CPPUNIT_ASSERT_MESSAGE(std::string("Output array not correct: " + std::to_string(std::abs(outputArray[i]))), std::abs(outputArray[i]) < 1e-5f);
- }
- }
-
- void tearDown() override
- {
- m_PhotoacousticFilterService = nullptr;
- delete[] inputDimensions;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPAFilterService)
diff --git a/Modules/PhotoacousticsAlgorithms/test/mitkPhotoacousticMotionCorrectionFilterTest.cpp b/Modules/PhotoacousticsAlgorithms/test/mitkPhotoacousticMotionCorrectionFilterTest.cpp
deleted file mode 100644
index d30aed5df2..0000000000
--- a/Modules/PhotoacousticsAlgorithms/test/mitkPhotoacousticMotionCorrectionFilterTest.cpp
+++ /dev/null
@@ -1,179 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPhotoacousticMotionCorrectionFilter.h>
-
-class mitkPhotoacousticMotionCorrectionFilterTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticMotionCorrectionFilterTestSuite);
- MITK_TEST(testSettingFirstInput);
- MITK_TEST(testSettingSecondInput);
- // MITK_TEST(testNoThirdInput);
- MITK_TEST(testGetFirstEmptyOutput);
- MITK_TEST(testGetSecondEmptyOutput);
- MITK_TEST(testSameInOutDimensions);
- MITK_TEST(testNo3DError);
- MITK_TEST(testSameInputDimension1);
- MITK_TEST(testSameInputDimension2);
- MITK_TEST(testNullPtr1);
- MITK_TEST(testNullPtr2);
- MITK_TEST(testNullPtr3);
- MITK_TEST(testSameInputDimensions);
- MITK_TEST(testStaticSliceCorrection);
- CPPUNIT_TEST_SUITE_END();
-
-
-private:
- mitk::PhotoacousticMotionCorrectionFilter::Pointer filter;
- mitk::Image::Pointer image, image4d, image2d, image3d1slice;
- float * data2d;
-
-public:
- void setUp() override {
- // get the filter I need
- filter = mitk::PhotoacousticMotionCorrectionFilter::New();
- // get a 3d mitk image
- image = mitk::Image::New();
- image2d = mitk::Image::New();
- image4d = mitk::Image::New();
- image3d1slice = mitk::Image::New();
- unsigned int * dimensions = new unsigned int[3] {2, 2, 2};
- unsigned int * dimensions2 = new unsigned int[3] {2, 2, 1};
- unsigned int * dim2 = new unsigned int[4] {2, 2, 2, 2};
- mitk::PixelType pt = mitk::MakeScalarPixelType<float>();
- float * data = new float[8] {0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
- float * data4d = new float[16];
- data2d = new float[4] {500.0, -500.5, 1000.0, 0.5};
- image->Initialize(pt, 3, dimensions);
- image->SetVolume(data);
- image4d->Initialize(pt, 4, dim2);
- image4d->SetVolume(data4d);
- image2d->Initialize(pt, 2, dimensions);
- image2d->SetVolume(data2d);
- image3d1slice->Initialize(pt, 3, dimensions2);
- image3d1slice->SetVolume(data);
- delete[] dimensions;
- delete[] dimensions2;
- delete[] data;
- delete[] data4d;
- delete[] dim2;
- }
-
- void tearDown() override {
- delete[] data2d;
- }
-
- void testSettingFirstInput() {
- filter->SetInput(0, image);
- mitk::Image::Pointer out = filter->GetInput(0);
- CPPUNIT_ASSERT_EQUAL(image, out);
- }
-
- void testSettingSecondInput() {
- filter->SetInput(1, image);
- mitk::Image::Pointer out = filter->GetInput(1);
- CPPUNIT_ASSERT_EQUAL(image, out);
- }
-
- // void testNoThirdInput() {
- // CPPUNIT_ASSERT_NO_THROW(filter->SetInput(2, image));
- // // CPPUNIT_ASSERT(true);
- // }
-
- void testGetFirstEmptyOutput() {
- mitk::Image::Pointer out = filter->GetOutput(0);
- unsigned int dim = 0;
- CPPUNIT_ASSERT_EQUAL(dim, out->GetDimension());
- }
-
- void testGetSecondEmptyOutput() {
- mitk::Image::Pointer out = filter->GetOutput(1);
- unsigned int dim = 0;
- CPPUNIT_ASSERT_EQUAL(dim, out->GetDimension());
- }
-
- void testSameInOutDimensions() {
- filter->SetInput(0, image);
- filter->SetInput(1, image);
- filter->Update();
- mitk::Image::Pointer out = filter->GetOutput(0);
- CPPUNIT_ASSERT_EQUAL(image->GetDimension(), out->GetDimension());
- out = filter->GetOutput(1);
- CPPUNIT_ASSERT_EQUAL(image->GetDimension(), out->GetDimension());
- }
-
- void testNo3DError() {
- filter->SetInput(0, image4d);
- filter->SetInput(1, image4d);
- CPPUNIT_ASSERT_THROW(filter->Update(), std::invalid_argument);
- }
-
- // I only test for dim input0 <= dim input1, because otherwise
- // itk will throw an error before the program even reaches the
- // parts I wrote.
- // Same for testSameInputDimension2
- void testSameInputDimension1() {
- filter->SetInput(0, image);
- filter->SetInput(1, image4d);
- CPPUNIT_ASSERT_THROW(filter->Update(), std::invalid_argument);
- }
-
- // See previous comment
- void testSameInputDimension2() {
- filter->SetInput(0, image2d);
- filter->SetInput(1, image);
- CPPUNIT_ASSERT_THROW(filter->Update(), std::invalid_argument);
- }
-
- // I tried to catch the error myself in the filter, but itk does some magic beforehand
- void testNullPtr1() {
- filter->SetInput(0, nullptr);
- filter->SetInput(1, image);
- CPPUNIT_ASSERT_THROW(filter->Update(), itk::ExceptionObject);
- }
-
- // Now I am allowed to catch it myself, because the first input is fine -.-
- void testNullPtr2() {
- filter->SetInput(0, image);
- filter->SetInput(1, nullptr);
- CPPUNIT_ASSERT_THROW(filter->Update(), std::invalid_argument);
- }
-
- void testNullPtr3() {
- filter->SetInput(0, nullptr);
- filter->SetInput(1, nullptr);
- CPPUNIT_ASSERT_THROW(filter->Update(), itk::ExceptionObject);
- }
-
- void testSameInputDimensions() {
- filter->SetInput(0, image3d1slice);
- filter->SetInput(1, image);
- CPPUNIT_ASSERT_THROW(filter->Update(), std::invalid_argument);
- }
-
- void testStaticSliceCorrection() {
- image->SetSlice(data2d, 0);
- image->SetSlice(data2d, 1);
- filter->SetInput(0, image);
- filter->SetInput(1, image);
- filter->Update();
- mitk::Image::Pointer out1 = filter->GetOutput(0);
- mitk::Image::Pointer out2 = filter->GetOutput(1);
- MITK_ASSERT_EQUAL(image, out1, "Check that static image does not get changed.");
- }
-
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticMotionCorrectionFilter)
diff --git a/Modules/PhotoacousticsHardware/CMakeLists.txt b/Modules/PhotoacousticsHardware/CMakeLists.txt
deleted file mode 100644
index 12ff4f08ad..0000000000
--- a/Modules/PhotoacousticsHardware/CMakeLists.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-if(WIN32)
-
- option(MITK_USE_GALIL_HARDWARE "Enable support for OPOTEK Lasers" OFF)
- option(MITK_USE_OPHIR_PYRO_HARDWARE "Enable support for Ophir Pyroelectrical Sensors" OFF)
-
- if(MITK_USE_OPHIR_PYRO_HARDWARE)
- set(MITK_OPHIR_API_PATH "" CACHE PATH "Path to Ophir API lib.")
- endif()
-
- if(MITK_USE_GALIL_HARDWARE)
- set(MITK_GALIL_API_PATH "" CACHE PATH "Path to Galil API header files.")
- MITK_CREATE_MODULE(
- DEPENDS MitkIGT
- INCLUDE_DIRS PUBLIC "${MITK_GALIL_API_PATH}/include" "${MITK_OPHIR_API_PATH}"
- INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
- ADDITIONAL_LIBS "${MITK_GALIL_API_PATH}/lib/dynamic/x64/gclib.lib" "${MITK_GALIL_API_PATH}/lib/dynamic/x64/gclibo.lib" tinyxml "${MITK_OPHIR_API_PATH}/OphirPyroWrapper.lib"
- PACKAGE_DEPENDS tinyxml
- )
- endif()
-endif()
diff --git a/Modules/PhotoacousticsHardware/OphirCppWrapper/ConsoleExample.cpp b/Modules/PhotoacousticsHardware/OphirCppWrapper/ConsoleExample.cpp
deleted file mode 100644
index a55a50fce9..0000000000
--- a/Modules/PhotoacousticsHardware/OphirCppWrapper/ConsoleExample.cpp
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <iostream>
-#include <windows.h>
-#include "OphirPyroWrapper.h"
-#include <vector>
-
-int main()
-{
- OphirPyroWrapper pyro;
-
- char* sn = pyro.ScanUSB();
- if (sn != 0)
- std::cout << "sn: " << sn << std::endl;
- else
- std::cout << "sn: NULL" << std::endl;
-
- int handle = pyro.OpenDevice(sn);
- std::cout << "handle: " << handle << std::endl;
-
- char* wl = pyro.GetWavelengths(handle);
- std::cout << "wl: " << wl << std::endl;
- char* gr = pyro.GetRanges(handle);
- std::cout << "gr: " << gr << std::endl;
-
- bool start = pyro.StartStream(handle);
- std::cout << "start: " << start << std::endl;
-
- std::vector<double> data;
- std::vector<double> timestamp;
- std::vector<int> status;
- Sleep(100);
- unsigned int gd = pyro.GetData(handle, &data, ×tamp, &status);
- std::cout << "gd: " << gd << std::endl;
- std::cout << "length: " << data.size() << std::endl;
- for(int i = 0; i<gd; i++)
- {
- std::cout << "data " << i << ": " << data[i] << " ts: " << timestamp[i] << " status: " << status[i] << std::endl;
- }
-
- Sleep(100);
- gd = pyro.GetData(handle, &data, ×tamp, &status);
- std::cout << "gd: " << gd << std::endl;
- std::cout << "length: " << data.size() << std::endl;
- for(int i = 0; i<gd; i++)
- {
- std::cout << "data " << i << ": " << data[i] << " ts: " << timestamp[i] << " status: " << status[i] << std::endl;
- }
-
-
- Sleep(100);
- gd = pyro.GetData(handle, &data, ×tamp, &status);
- std::cout << "gd: " << gd << std::endl;
- std::cout << "length: " << data.size() << std::endl;
- for(int i = 0; i<gd; i++)
- {
- std::cout << "data " << i << ": " << data[i] << " ts: " << timestamp[i] << " status: " << status[i] << std::endl;
- }
-
- Sleep(1000);
- gd = pyro.GetData(handle, &data, ×tamp, &status);
- std::cout << "gd: " << gd << std::endl;
- std::cout << "length: " << data.size() << std::endl;
- for(int i = 0; i<gd; i++)
- {
- std::cout << "data " << i << ": " << data[i] << " ts: " << timestamp[i] << " status: " << status[i] << std::endl;
- }
-
- bool stop = pyro.StopStream(handle);
- std::cout << "stop: " << stop << std::endl;
- bool closed = pyro.CloseDevice(handle);
- std::cout << "closed: " << closed << std::endl;
-}
diff --git a/Modules/PhotoacousticsHardware/OphirCppWrapper/OphirPyroWrapper.cpp b/Modules/PhotoacousticsHardware/OphirCppWrapper/OphirPyroWrapper.cpp
deleted file mode 100644
index 1bc08009cd..0000000000
--- a/Modules/PhotoacousticsHardware/OphirCppWrapper/OphirPyroWrapper.cpp
+++ /dev/null
@@ -1,137 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#using "Interop.OphirLMMeasurementLib.dll"
-#include <vector>
-#include <msclr\auto_gcroot.h>
-#include "OphirPyroWrapper.h"
-
-using namespace System::Runtime::InteropServices; // Marshal
-
-class OphirPyroWrapperPrivate
-{
- public: msclr::auto_gcroot<OphirLMMeasurementLib::CoLMMeasurement^> ophirAPI;
-};
-
-OphirPyroWrapper::OphirPyroWrapper()
-{
- _private = new OphirPyroWrapperPrivate();
- _private->ophirAPI = gcnew OphirLMMeasurementLib::CoLMMeasurement();
-}
-
-OphirPyroWrapper::~OphirPyroWrapper()
-{
- delete _private;
-}
-
-char* OphirPyroWrapper::ScanUSB()
-{
- char* foo;
- System::Object^ managedObject;
- _private->ophirAPI->ScanUSB(managedObject);
- array<System::String^>^ managedCapi = dynamic_cast<array<System::String^>^>(managedObject);
- if (managedCapi->Length != 0)
- return (char*)Marshal::StringToHGlobalAnsi(managedCapi[0]).ToPointer();
- else
- return 0;
-}
-
-int OphirPyroWrapper::OpenDevice(char* serialNumber)
-{
- int deviceHandle;
- _private->ophirAPI->OpenUSBDevice(gcnew System::String(serialNumber), deviceHandle);
-
- return deviceHandle;
-}
-
-char* OphirPyroWrapper::GetWavelengths(int deviceHandle)
-{
- int index;
- System::Object^ options;
- // Show wavelengths of channel 0
- _private->ophirAPI->GetWavelengths(deviceHandle, 0, index, options);
- array<System::String^>^ managedCapi = dynamic_cast<array<System::String^>^>(options);
- if (managedCapi->Length != 0)
- return (char*)Marshal::StringToHGlobalAnsi(managedCapi[index]).ToPointer();
- else
- return 0;
-}
-
-char* OphirPyroWrapper::GetRanges(int deviceHandle)
-{
- int index;
- System::Object^ options;
- // Show ranges of channel 0
- _private->ophirAPI->GetRanges(deviceHandle, 0, index, options);
- array<System::String^>^ managedCapi = dynamic_cast<array<System::String^>^>(options);
- if (managedCapi->Length != 0)
- return (char*)Marshal::StringToHGlobalAnsi(managedCapi[index]).ToPointer();
- else
- return 0;
-}
-
-bool OphirPyroWrapper::StartStream(int deviceHandle)
-{
- _private->ophirAPI->StartStream(deviceHandle, 0);
- return true;
-}
-
-bool OphirPyroWrapper::StopStream(int deviceHandle)
-{
- _private->ophirAPI->StopStream(deviceHandle, 0);
- return true;
-}
-
-bool OphirPyroWrapper::CloseDevice(int deviceHandle)
-{
- _private->ophirAPI->Close(deviceHandle);
- return true;
-}
-
-unsigned int OphirPyroWrapper::GetData(int deviceHandle, std::vector<double>* data, std::vector<double>* timestamp, std::vector<int>* status)
-{
- System::Object^ dataArray;
- System::Object^ timeStampArray;
- System::Object^ statusArray;
- array<double>^ managedDataArray;
- array<double>^ managedTimeStampArray;
- array<int>^ managedStatusArray;
- _private->ophirAPI->GetData(deviceHandle, 0, dataArray, timeStampArray, statusArray);
- managedDataArray = (array<double>^)dataArray;
- managedTimeStampArray = (array<double>^)timeStampArray;
- managedStatusArray = (array<int>^)statusArray;
- if (managedDataArray->Length > 0)
- {
- data->resize(managedDataArray->Length);
- timestamp->resize(managedDataArray->Length);
- status->resize(managedDataArray->Length);
- for(int i = 0; i<managedDataArray->Length; i++)
- {
- (*data)[i] = managedDataArray[i];
- (*timestamp)[i] = managedTimeStampArray[i];
- (*status)[i] = managedStatusArray[i];
- // DEBUG: std::cout << "managedDataArray " << i << ": " << managedDataArray[i] << " ts: " << managedTimeStampArray[i] << " status: " << managedStatusArray[i] << std::endl;
- }
- return managedDataArray->Length;
- }
- else
- {
- data->resize(1);
- timestamp->resize(1);
- status->resize(1);
- (*data)[0] = -1;
- (*timestamp)[0] = -1;
- (*status)[0] = -1;
- }
-
- return 0;
-}
diff --git a/Modules/PhotoacousticsHardware/OphirCppWrapper/OphirPyroWrapper.h b/Modules/PhotoacousticsHardware/OphirCppWrapper/OphirPyroWrapper.h
deleted file mode 100644
index dd3decfeb8..0000000000
--- a/Modules/PhotoacousticsHardware/OphirCppWrapper/OphirPyroWrapper.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <vector>
-
-class OphirPyroWrapperPrivate;
-
-class __declspec(dllexport) OphirPyroWrapper
-{
- private: OphirPyroWrapperPrivate* _private;
-
- public: OphirPyroWrapper();
-
- public: ~OphirPyroWrapper();
-
- public: char* ScanUSB();
-
- public: int OpenDevice(char* serialNumber);
-
- public: char* GetWavelengths(int deviceHandle);
-
- public: char* GetRanges(int deviceHandle);
-
- public: bool StartStream(int deviceHandle);
-
- public: bool StopStream(int deviceHandle);
-
- public: bool CloseDevice(int deviceHandle);
-
- public: unsigned int GetData(int deviceHandle, std::vector<double>* data, std::vector<double>* timestamp, std::vector<int>* status);
-};
diff --git a/Modules/PhotoacousticsHardware/OphirCppWrapper/readme.txt b/Modules/PhotoacousticsHardware/OphirCppWrapper/readme.txt
deleted file mode 100644
index 312e900b17..0000000000
--- a/Modules/PhotoacousticsHardware/OphirCppWrapper/readme.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-A C++/CLI Wrapper for Ophir Pyroelectrical Sensors
-
-compile release version of wapper via: cl /clr /LD OphirPyroWrapper.cpp
-compile debug version of wapper via: cl /clr /LDd OphirPyroWrapper.cpp
-you'll need: Interop.OphirLMMeasurementLib.dll
-
-compile shitty console example via: cl ConsoleExample.cpp OphirPyroWrapper.lib
-
-tested with:
-VS2015, Windows 10 + 8, Starlab 3.20
-
-todo:
-- write documentation
-
-thanks to:
-pragmateek for http://pragmateek.com/using-c-from-native-c-with-the-help-of-ccli-v2/
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/FTUNE.dmc b/Modules/PhotoacousticsHardware/Resources/FTUNE.dmc
deleted file mode 100644
index 454e5dacab..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/FTUNE.dmc
+++ /dev/null
@@ -1,57 +0,0 @@
-#AUTO
-#MAIN
-WT 1
-'AMP SETTINGS
-AU 0
-BR 1
-AG 0
-TM 1000
-TL 3
-TK 9.998
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-MT -1
-CE 0
-CN-1
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-'
-SHX
-WT 10
-JS#HOME
-WT 10
-JS#RESETP
-WT 10
-'
-SP 3000000
-AC 60000000
-DC 60000000
-count=0
-idx=0
-#MOVE
-II 1
-WT 5
-JP #MOVE
-EN
-#HOME
-OE 0
-JG -10000;BG
-#JOG;JP#JOG,@ABS[_TEX]<1000
-ST;AM
-OE 1
-WT 10
-EN
-#RESETP
-PR 32561;BG;AM
-DP*=0
-EN
-#ININT
-idx = count % points
-PA pos[idx];BG;AM;
-WT 10
-count = count + 1
-RI 1;
diff --git a/Modules/PhotoacousticsHardware/Resources/GHOME.dmc b/Modules/PhotoacousticsHardware/Resources/GHOME.dmc
deleted file mode 100644
index 7900469823..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/GHOME.dmc
+++ /dev/null
@@ -1,44 +0,0 @@
-#AUTO
-#MAIN
-#GHOME
-suc=99
-'AMP SETTINGS
-AU 0
-BR 1
-AG 0
-TM 1000
-TL 3
-TK 9.998
-suc=98
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-MT -1
-CE 0
-CN-1
-suc=97
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-suc=96
-SHX
-WT 10
-SP 3000000
-AC 60000000
-DC 60000000
-'
-suc=95
-OE 0
-JG -10000;BG
-#JOG;JP#JOG,@ABS[_TEX]<1000
-ST;AM
-suc=94
-OE 1
-WT10
-PR 32561;BG;AM
-suc=93
-DP*=0
-suc=1
-EN
diff --git a/Modules/PhotoacousticsHardware/Resources/OpotekPhocusMobile.xml b/Modules/PhotoacousticsHardware/Resources/OpotekPhocusMobile.xml
deleted file mode 100644
index 04f9701ac9..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/OpotekPhocusMobile.xml
+++ /dev/null
@@ -1,42 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<Motor>
- <Coefficients>
- <lambda0>-4.30076111e+07</lambda0>
- <lambda1>3.12495804e+05</lambda1>
- <lambda2>-9.43122022e+02</lambda2>
- <lambda3>1.51584088e+00</lambda3>
- <lambda4>-1.36913735e-03</lambda4>
- <lambda5>6.59021774e-07</lambda5>
- <lambda6>-1.32069448e-10</lambda6>
- <home>32561</home>
- </Coefficients>
- <Signal>
- <Signal-low>690.000</Signal-low>
- <Signal-default>750.000</Signal-default>
- <Signal-high>950.000</Signal-high>
- </Signal>
- <Seriell>
- <PortNumber>5</PortNumber>
- <Baud>115200</Baud>
- <DataBits>8</DataBits>
- <Parity>0</Parity>
- <StopBits>10</StopBits>
- </Seriell>
- <SpectralResponse>
- <Wavelength>690.0|695.2|700.4|705.6|710.8|716.0|721.2|726.4|731.6|736.8|742.0|747.2|752.4|757.6|762.8|768.0|773.2|778.4|783.6|788.8|794.0|799.2|804.4|809.6|814.8|820.0|825.2|830.4|835.6|840.8|846.0|851.2|856.4|861.6|866.8|872.0|877.2|882.4|887.6|892.8|898.0|903.2|908.4|913.6|918.8|924.0|929.2|934.4|939.6|944.8
- </Wavelength>
- <Amplitude>0.000727|0.000726|0.000764|0.000795|0.000824|0.000817|0.000832|0.000893|0.000898|0.000881|0.000870|0.000834|0.000849|0.000793|0.000778|0.000753|0.000755|0.000812|0.000843|0.000818|0.000843|0.000824|0.000829|0.000837|0.000832|0.000796|0.000808|0.000796|0.000774|0.000778|0.000760|0.000741|0.000724|0.000725|0.000703|0.000703|0.000695|0.000697|0.000671|0.000702|0.000679|0.000671|0.000676|0.000647|0.000660|0.000674|0.000686|0.000664|0.000658|0.000643
- </Amplitude>
- <Energy>0.042647|0.043251|0.045291|0.047462|0.048515|0.049305|0.049513|0.050434|0.049656|0.050895|0.048269|0.049129|0.050182|0.049334|0.046761|0.045675|0.045061|0.049129|0.050357|0.049206|0.050050|0.048745|0.048822|0.049041|0.048976|0.047813|0.047082|0.046980|0.046980|0.046442|0.045445|0.044063|0.043909|0.042451|0.041058|0.041760|0.042374|0.041683|0.040269|0.042374|0.041299|0.038996|0.041069|0.040736|0.039994|0.040839|0.040225|0.039994|0.038613|0.037692
- </Energy>
- </SpectralResponse>
-</Motor>
-<PumpLaser>
- <Seriell>
- <PortNumber>4</PortNumber>
- <Baud>115200</Baud>
- <DataBits>8</DataBits>
- <Parity>N</Parity>
- <StopBits>1</StopBits>
- </Seriell>
-</PumpLaser>
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/STUNE.dmc b/Modules/PhotoacousticsHardware/Resources/STUNE.dmc
deleted file mode 100644
index edc14db0ae..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/STUNE.dmc
+++ /dev/null
@@ -1,34 +0,0 @@
-#AUTO
-#STUNE
-suc=-1
-'*****************
-'AMP SETTINGS
-AU 0
-BR 1
-AG 0
-TM 1000
-TL 3
-TK 9.998
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-MT -1
-CE 0
-CN-1
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-'
-SHX
-WT 10
-SP 3000000
-AC 60000000
-DC 60000000
-'
-suc=-102
-WT 10
-PA pos;BG;AM
-suc=1
-EN
diff --git a/Modules/PhotoacousticsHardware/Resources/configFastTuneOPO.dmc b/Modules/PhotoacousticsHardware/Resources/configFastTuneOPO.dmc
deleted file mode 100644
index e60875bc93..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/configFastTuneOPO.dmc
+++ /dev/null
@@ -1,28 +0,0 @@
-#AUTO
-#MAIN
-rt=-1
-II1
-'AMP SETTINGS
-AU 0
-BR 1
-'AG 0
-TM 1000
-TL 3
-TK 9.998
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-'MT -1
-'CE 0
-CN-1
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-'
-SHX
-WT 250
-SP 3000000
-AC 120000000
-DC 120000000
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/configSlowTuneOPO.dmc b/Modules/PhotoacousticsHardware/Resources/configSlowTuneOPO.dmc
deleted file mode 100644
index 91b36d58b1..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/configSlowTuneOPO.dmc
+++ /dev/null
@@ -1,7 +0,0 @@
-#AUTO
-#MAIN
-rt=0
-'
-SP 150000
-AC 12000000
-DC 12000000
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/executeFastTuneOPO.dmc b/Modules/PhotoacousticsHardware/Resources/executeFastTuneOPO.dmc
deleted file mode 100644
index e616d85969..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/executeFastTuneOPO.dmc
+++ /dev/null
@@ -1,14 +0,0 @@
-points=pos[-1]
-#MOVE
-II 1
-WT 5
-rt=1
-JP #MOVE
-EN
-#ININT
-idx = count % points
-PA pos[idx];BG;AM;
-BG;AM;
-count = count + 1
-WT 1
-RI 1;
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/executeSlowTuneOPO.dmc b/Modules/PhotoacousticsHardware/Resources/executeSlowTuneOPO.dmc
deleted file mode 100644
index 741d78c64d..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/executeSlowTuneOPO.dmc
+++ /dev/null
@@ -1,5 +0,0 @@
-PA pos;BG;AM;
-BG;AM;
-WT 100
-rt = 1
-EN
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/fastTuneOPO.dmc b/Modules/PhotoacousticsHardware/Resources/fastTuneOPO.dmc
deleted file mode 100644
index e2d7463d93..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/fastTuneOPO.dmc
+++ /dev/null
@@ -1,55 +0,0 @@
-#AUTO
-#FTUNE
-rt=-1
-II1
-'AMP SETTINGS
-AU 0
-BR 1
-'AG 0
-TM 1000
-TL 3
-TK 9.998
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-'MT -1
-'CE 0
-CN-1
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-'
-SHX
-WT 250
-SP 3000000
-AC 120000000
-DC 120000000
-rt=-2
-count=0;idx=0;DM pos[2]
-rt=-3
-pos[0]=36459
-pos[1]=24577
-rt=-4
-points=pos[-1]
-rt=-5
-#MOVE
-rt=-6
-II 1
-WT 5
-rt=1
-JP #MOVE
-EN
-#ININT
-'MG "INSIDE INTERUPPT ROUTINE"
-rt=-7
-idx = count % points
-MG "idx = ", idx {F2.2}
-PA pos[idx];BG;AM;
-BG;AM;
-rt=-8
-count = count + 1
-WT 1
-RI 1; 'Return to the main program
-'and restore trip point
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/fastTuneOPO700to900.dmc b/Modules/PhotoacousticsHardware/Resources/fastTuneOPO700to900.dmc
deleted file mode 100644
index 10c65430d7..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/fastTuneOPO700to900.dmc
+++ /dev/null
@@ -1,48 +0,0 @@
-#AUTO
-#MAIN
-rt=-1
-II1
-'AMP SETTINGS
-AU 0
-BR 1
-'AG 0
-TM 1000
-TL 3
-TK 9.998
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-'MT -1
-'CE 0
-CN-1
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-'
-SHX
-WT 250
-SP 3000000
-AC 120000000
-DC 120000000
-count=0;idx=0;DM pos[2]
-pos[0]=36459
-pos[1]=24577
-points=pos[-1]
-#MOVE
-II 1
-WT 5
-rt=1
-JP #MOVE
-EN
-#ININT
-'MG "INSIDE INTERUPPT ROUTINE"
-idx = count % points
-MG "idx = ", idx {F2.2}
-PA pos[idx];BG;AM;
-BG;AM;
-count = count + 1
-WT 1
-RI 1; 'Return to the main program
-'and restore trip point
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/homeOPO.dmc b/Modules/PhotoacousticsHardware/Resources/homeOPO.dmc
deleted file mode 100644
index 80ef2aaaba..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/homeOPO.dmc
+++ /dev/null
@@ -1,35 +0,0 @@
-#AUTO
-#MAIN
-rh=-1
-'*****************
-'AMP SETTINGS
-AU 0
-BR 1
-'AG 0
-TM 1000
-TL 3
-TK 9.998
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-'MT -1
-'CE 0
-CN-1
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-'
-SHX
-WT 250
-'
-OE 0
-JG -10000;BG
-#JOG;JP#JOG,@ABS[_TEX]<1000
-ST;AM
-OE 1
-WT 100
-DP*=0
-rh=1
-EN
diff --git a/Modules/PhotoacousticsHardware/Resources/opotekPhocusMobileDkfz160907.ini b/Modules/PhotoacousticsHardware/Resources/opotekPhocusMobileDkfz160907.ini
deleted file mode 100644
index d2d84f4cfd..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/opotekPhocusMobileDkfz160907.ini
+++ /dev/null
@@ -1,747 +0,0 @@
-[Index]
-Motor Config Size=6
-Current Config=0
-Show Spectrometer=FALSE
-
-[Software Version]
-Software Version="1.3.2"
-
-[Motor Config 0]
-Double BL=1
-Name="SIGNAL"
-Default Wavelength=750.000000
-Motor 0 Equation=1
-Motor 0 Coeff="-10034351.9962601084000000000|66823.5712450537248000000|-182.2028426992165750000|0.2617740803347156640|-0.0002092387122824080|0.0000000881876090298|-0.0000000000152863918|146.4419507104903460000"
-Motor 0 Speed=150.000000
-Motor 0 Acceleration=10.000000
-Motor 0 Current=0.600000
-Motor 0 Home=0
-Motor 0 BL Size=0
-Motor 0 BL Dir=1
-Motor 0 Max Step=50000
-Motor 0 Min Step=0
-Motor 0 Mix WL=1064.000000
-Motor 0 Name="OPO"
-Motor 0 Park=0
-Motor 0 Ramp=150.000000
-Motor 0 Slope=10.000000
-Motor 0 First=0.600000
-Motor 1 Equation=0
-Motor 1 Coeff=""
-Motor 1 Speed=150.000000
-Motor 1 Acceleration=10.000000
-Motor 1 Current=0.600000
-Motor 1 Home=0
-Motor 1 BL Size=650
-Motor 1 BL Dir=1
-Motor 1 Max Step=69000
-Motor 1 Min Step=-200
-Motor 1 Mix WL=1064.000000
-Motor 1 Name="UV"
-Motor 1 Park=0
-Motor 1 Ramp=150.000000
-Motor 1 Slope=10.000000
-Motor 1 First=0.600000
-Motor 2 Equation=0
-Motor 2 Coeff=""
-Motor 2 Speed=150.000000
-Motor 2 Acceleration=10.000000
-Motor 2 Current=0.600000
-Motor 2 Home=0
-Motor 2 BL Size=650
-Motor 2 BL Dir=1
-Motor 2 Max Step=200000
-Motor 2 Min Step=-20000
-Motor 2 Mix WL=1064.000000
-Motor 2 Name="Beamguide"
-Motor 2 Park=0
-Motor 2 Ramp=150.000000
-Motor 2 Slope=10.000000
-Motor 2 First=0.600000
-Motor 3 Equation=0
-Motor 3 Coeff=""
-Motor 3 Speed=150.000000
-Motor 3 Acceleration=10.000000
-Motor 3 Current=0.600000
-Motor 3 Home=0
-Motor 3 BL Size=650
-Motor 3 BL Dir=1
-Motor 3 Max Step=69000
-Motor 3 Min Step=-200
-Motor 3 Mix WL=1064.000000
-Motor 3 Name="UV L2"
-Motor 3 Park=0
-Motor 3 Ramp=150.000000
-Motor 3 Slope=10.000000
-Motor 3 First=0.600000
-
-[Motor Config 1]
-Double BL=1
-Name="IDLER"
-Default Wavelength=1200.000000
-Motor 0 Equation=2
-Motor 0 Coeff="-10034351.9962601084000000000|66823.5712450537248000000|-182.2028426992165750000|0.2617740803347156640|-0.0002092387122824080|0.0000000881876090298|-0.0000000000152863918|146.4419507104903460000"
-Motor 0 Speed=150.000000
-Motor 0 Acceleration=10.000000
-Motor 0 Current=0.600000
-Motor 0 Home=0
-Motor 0 BL Size=0
-Motor 0 BL Dir=1
-Motor 0 Max Step=50000
-Motor 0 Min Step=0
-Motor 0 Mix WL=1064.000000
-Motor 0 Name="OPO"
-Motor 0 Park=0
-Motor 0 Ramp=150.000000
-Motor 0 Slope=10.000000
-Motor 0 First=0.600000
-Motor 1 Equation=0
-Motor 1 Coeff=""
-Motor 1 Speed=150.000000
-Motor 1 Acceleration=10.000000
-Motor 1 Current=0.600000
-Motor 1 Home=0
-Motor 1 BL Size=650
-Motor 1 BL Dir=1
-Motor 1 Max Step=69000
-Motor 1 Min Step=-200
-Motor 1 Mix WL=1064.000000
-Motor 1 Name="UV"
-Motor 1 Park=0
-Motor 1 Ramp=150.000000
-Motor 1 Slope=10.000000
-Motor 1 First=0.600000
-Motor 2 Equation=0
-Motor 2 Coeff=""
-Motor 2 Speed=150.000000
-Motor 2 Acceleration=10.000000
-Motor 2 Current=0.600000
-Motor 2 Home=0
-Motor 2 BL Size=650
-Motor 2 BL Dir=1
-Motor 2 Max Step=200000
-Motor 2 Min Step=-20000
-Motor 2 Mix WL=1064.000000
-Motor 2 Name="Beamguide"
-Motor 2 Park=0
-Motor 2 Ramp=150.000000
-Motor 2 Slope=10.000000
-Motor 2 First=0.600000
-Motor 3 Equation=0
-Motor 3 Coeff=""
-Motor 3 Speed=150.000000
-Motor 3 Acceleration=10.000000
-Motor 3 Current=0.600000
-Motor 3 Home=0
-Motor 3 BL Size=650
-Motor 3 BL Dir=1
-Motor 3 Max Step=69000
-Motor 3 Min Step=-200
-Motor 3 Mix WL=1064.000000
-Motor 3 Name="UV L2"
-Motor 3 Park=0
-Motor 3 Ramp=150.000000
-Motor 3 Slope=10.000000
-Motor 3 First=0.600000
-
-[Motor Config 2]
-Double BL=1
-Name="UV-1"
-Default Wavelength=230.000000
-Motor 0 Equation=4
-Motor 0 Coeff="-10034351.9962601084000000000|66823.5712450537248000000|-182.2028426992165750000|0.2617740803347156640|-0.0002092387122824080|0.0000000881876090298|-0.0000000000152863918|146.4419507104903460000"
-Motor 0 Speed=150.000000
-Motor 0 Acceleration=10.000000
-Motor 0 Current=0.600000
-Motor 0 Home=0
-Motor 0 BL Size=0
-Motor 0 BL Dir=1
-Motor 0 Max Step=50000
-Motor 0 Min Step=0
-Motor 0 Mix WL=1064.000000
-Motor 0 Name="OPO"
-Motor 0 Park=0
-Motor 0 Ramp=150.000000
-Motor 0 Slope=10.000000
-Motor 0 First=0.600000
-Motor 1 Equation=3
-Motor 1 Coeff=""
-Motor 1 Speed=150.000000
-Motor 1 Acceleration=10.000000
-Motor 1 Current=0.600000
-Motor 1 Home=0
-Motor 1 BL Size=650
-Motor 1 BL Dir=1
-Motor 1 Max Step=69000
-Motor 1 Min Step=-200
-Motor 1 Mix WL=1064.000000
-Motor 1 Name="UV"
-Motor 1 Park=0
-Motor 1 Ramp=150.000000
-Motor 1 Slope=10.000000
-Motor 1 First=0.600000
-Motor 2 Equation=0
-Motor 2 Coeff=""
-Motor 2 Speed=150.000000
-Motor 2 Acceleration=10.000000
-Motor 2 Current=0.600000
-Motor 2 Home=0
-Motor 2 BL Size=650
-Motor 2 BL Dir=1
-Motor 2 Max Step=200000
-Motor 2 Min Step=-20000
-Motor 2 Mix WL=1064.000000
-Motor 2 Name="Beamguide"
-Motor 2 Park=0
-Motor 2 Ramp=150.000000
-Motor 2 Slope=10.000000
-Motor 2 First=0.600000
-Motor 3 Equation=0
-Motor 3 Coeff=""
-Motor 3 Speed=150.000000
-Motor 3 Acceleration=10.000000
-Motor 3 Current=0.600000
-Motor 3 Home=0
-Motor 3 BL Size=650
-Motor 3 BL Dir=1
-Motor 3 Max Step=69000
-Motor 3 Min Step=-200
-Motor 3 Mix WL=1064.000000
-Motor 3 Name="UV L2"
-Motor 3 Park=0
-Motor 3 Ramp=150.000000
-Motor 3 Slope=10.000000
-Motor 3 First=0.600000
-
-[Motor Config 3]
-Double BL=1
-Name="UV-2"
-Default Wavelength=400.000000
-Motor 0 Equation=4
-Motor 0 Coeff="-10034351.9962601084000000000|66823.5712450537248000000|-182.2028426992165750000|0.2617740803347156640|-0.0002092387122824080|0.0000000881876090298|-0.0000000000152863918|146.4419507104903460000"
-Motor 0 Speed=150.000000
-Motor 0 Acceleration=10.000000
-Motor 0 Current=0.600000
-Motor 0 Home=0
-Motor 0 BL Size=0
-Motor 0 BL Dir=1
-Motor 0 Max Step=50000
-Motor 0 Min Step=0
-Motor 0 Mix WL=1064.000000
-Motor 0 Name="OPO"
-Motor 0 Park=0
-Motor 0 Ramp=150.000000
-Motor 0 Slope=10.000000
-Motor 0 First=0.600000
-Motor 1 Equation=3
-Motor 1 Coeff=""
-Motor 1 Speed=150.000000
-Motor 1 Acceleration=10.000000
-Motor 1 Current=0.600000
-Motor 1 Home=0
-Motor 1 BL Size=650
-Motor 1 BL Dir=1
-Motor 1 Max Step=69000
-Motor 1 Min Step=-200
-Motor 1 Mix WL=1064.000000
-Motor 1 Name="UV"
-Motor 1 Park=0
-Motor 1 Ramp=150.000000
-Motor 1 Slope=10.000000
-Motor 1 First=0.600000
-Motor 2 Equation=0
-Motor 2 Coeff=""
-Motor 2 Speed=150.000000
-Motor 2 Acceleration=10.000000
-Motor 2 Current=0.600000
-Motor 2 Home=0
-Motor 2 BL Size=650
-Motor 2 BL Dir=1
-Motor 2 Max Step=200000
-Motor 2 Min Step=-20000
-Motor 2 Mix WL=1064.000000
-Motor 2 Name="Beamguide"
-Motor 2 Park=0
-Motor 2 Ramp=150.000000
-Motor 2 Slope=10.000000
-Motor 2 First=0.600000
-Motor 3 Equation=0
-Motor 3 Coeff=""
-Motor 3 Speed=150.000000
-Motor 3 Acceleration=10.000000
-Motor 3 Current=0.600000
-Motor 3 Home=0
-Motor 3 BL Size=650
-Motor 3 BL Dir=1
-Motor 3 Max Step=69000
-Motor 3 Min Step=-200
-Motor 3 Mix WL=1064.000000
-Motor 3 Name="UV L2"
-Motor 3 Park=0
-Motor 3 Ramp=150.000000
-Motor 3 Slope=10.000000
-Motor 3 First=0.600000
-
-[Motor Config 4]
-Double BL=1
-Name="UV-3"
-Default Wavelength=365.000000
-Motor 0 Equation=5
-Motor 0 Coeff="-10034351.9962601084000000000|66823.5712450537248000000|-182.2028426992165750000|0.2617740803347156640|-0.0002092387122824080|0.0000000881876090298|-0.0000000000152863918|146.4419507104903460000"
-Motor 0 Speed=150.000000
-Motor 0 Acceleration=10.000000
-Motor 0 Current=0.600000
-Motor 0 Home=0
-Motor 0 BL Size=0
-Motor 0 BL Dir=1
-Motor 0 Max Step=50000
-Motor 0 Min Step=0
-Motor 0 Mix WL=1064.000000
-Motor 0 Name="OPO"
-Motor 0 Park=0
-Motor 0 Ramp=150.000000
-Motor 0 Slope=10.000000
-Motor 0 First=0.600000
-Motor 1 Equation=3
-Motor 1 Coeff=""
-Motor 1 Speed=150.000000
-Motor 1 Acceleration=10.000000
-Motor 1 Current=0.600000
-Motor 1 Home=0
-Motor 1 BL Size=650
-Motor 1 BL Dir=1
-Motor 1 Max Step=69000
-Motor 1 Min Step=-200
-Motor 1 Mix WL=1064.000000
-Motor 1 Name="UV"
-Motor 1 Park=0
-Motor 1 Ramp=150.000000
-Motor 1 Slope=10.000000
-Motor 1 First=0.600000
-Motor 2 Equation=0
-Motor 2 Coeff=""
-Motor 2 Speed=150.000000
-Motor 2 Acceleration=10.000000
-Motor 2 Current=0.600000
-Motor 2 Home=0
-Motor 2 BL Size=650
-Motor 2 BL Dir=1
-Motor 2 Max Step=200000
-Motor 2 Min Step=-20000
-Motor 2 Mix WL=1064.000000
-Motor 2 Name="Beamguide"
-Motor 2 Park=0
-Motor 2 Ramp=150.000000
-Motor 2 Slope=10.000000
-Motor 2 First=0.600000
-Motor 3 Equation=0
-Motor 3 Coeff=""
-Motor 3 Speed=150.000000
-Motor 3 Acceleration=10.000000
-Motor 3 Current=0.600000
-Motor 3 Home=0
-Motor 3 BL Size=650
-Motor 3 BL Dir=1
-Motor 3 Max Step=69000
-Motor 3 Min Step=-200
-Motor 3 Mix WL=1064.000000
-Motor 3 Name="UV L2"
-Motor 3 Park=0
-Motor 3 Ramp=150.000000
-Motor 3 Slope=10.000000
-Motor 3 First=0.600000
-
-[Motor Config 5]
-Double BL=1
-Name="UV-X"
-Default Wavelength=450.000000
-Motor 0 Equation=6
-Motor 0 Coeff="-10034351.9962601084000000000|66823.5712450537248000000|-182.2028426992165750000|0.2617740803347156640|-0.0002092387122824080|0.0000000881876090298|-0.0000000000152863918|146.4419507104903460000"
-Motor 0 Speed=150.000000
-Motor 0 Acceleration=10.000000
-Motor 0 Current=0.600000
-Motor 0 Home=0
-Motor 0 BL Size=0
-Motor 0 BL Dir=1
-Motor 0 Max Step=50000
-Motor 0 Min Step=0
-Motor 0 Mix WL=1064.000000
-Motor 0 Name="OPO"
-Motor 0 Park=0
-Motor 0 Ramp=150.000000
-Motor 0 Slope=10.000000
-Motor 0 First=0.600000
-Motor 1 Equation=3
-Motor 1 Coeff=""
-Motor 1 Speed=150.000000
-Motor 1 Acceleration=10.000000
-Motor 1 Current=0.600000
-Motor 1 Home=0
-Motor 1 BL Size=650
-Motor 1 BL Dir=1
-Motor 1 Max Step=69000
-Motor 1 Min Step=-200
-Motor 1 Mix WL=1064.000000
-Motor 1 Name="UV"
-Motor 1 Park=0
-Motor 1 Ramp=150.000000
-Motor 1 Slope=10.000000
-Motor 1 First=0.600000
-Motor 2 Equation=0
-Motor 2 Coeff=""
-Motor 2 Speed=150.000000
-Motor 2 Acceleration=10.000000
-Motor 2 Current=0.600000
-Motor 2 Home=0
-Motor 2 BL Size=650
-Motor 2 BL Dir=1
-Motor 2 Max Step=200000
-Motor 2 Min Step=-20000
-Motor 2 Mix WL=1064.000000
-Motor 2 Name="Beamguide"
-Motor 2 Park=0
-Motor 2 Ramp=150.000000
-Motor 2 Slope=10.000000
-Motor 2 First=0.600000
-Motor 3 Equation=0
-Motor 3 Coeff=""
-Motor 3 Speed=150.000000
-Motor 3 Acceleration=10.000000
-Motor 3 Current=0.600000
-Motor 3 Home=0
-Motor 3 BL Size=650
-Motor 3 BL Dir=1
-Motor 3 Max Step=69000
-Motor 3 Min Step=-200
-Motor 3 Mix WL=1064.000000
-Motor 3 Name="UV L2"
-Motor 3 Park=0
-Motor 3 Ramp=150.000000
-Motor 3 Slope=10.000000
-Motor 3 First=0.600000
-
-[Port Config]
-Port=7
-Baud=19200
-Data Bits=8
-Parity=0
-Stop BIts=10
-Flow=0
-
-[Laser Serial Port]
-Port=5
-Baud=115200
-Data Bits=8
-Parity=0
-Stop BIts=10
-Flow=0
-
-[SSC Serial Port]
-Port=0
-Baud=9600
-Data Bits=8
-Parity=0
-Stop BIts=10
-Flow=0
-
-[Laser Config]
-Laser Type=6
-Rep Rate=20
-MAX Power Param.=10.000000
-MIN Power Param.=100.000000
-Soft-Start=FALSE
-SS Initial %=10.000000
-SS Steps=10
-Check Safety Interlocks=FALSE
-Old Brilliant (no Q-switch control)=FALSE
-Load Configuration=0
-Use External Timing=FALSE
-
-[Spectrometer]
-Spectrometer=FALSE
-Integration Time=8
-Trigger Mode=3
-Model=0
-Closed-Loop Tuning=FALSE
-CL Resolution=0.500000
-
-[Module Config]
-Pump Wavelength=532.000000
-System Type=9
-Signal-lo=690.000000
-Signal-hi=950.000000
-Idler-lo=1200.000000
-Idler-hi=2400.000000
-UV-1=FALSE
-UV-1-lo=0.000000
-UV-1-hi=0.000000
-UV-2=FALSE
-UV-2-lo=0.000000
-UV-2-hi=0.000000
-UV-3=FALSE
-UV-3-lo=0.000000
-UV-3-hi=0.000000
-UV-M=FALSE
-UV-M-lo=0.000000
-UV-M-hi=0.000000
-UV-0=FALSE
-UV-0-lo=0.000000
-UV-0-hi=0.000000
-Beamguide=FALSE
-
-[Miscellaneous]
-OPO Recalibrate Max Step=1000
-UV Module Present=FALSE
-Beamguide Present=FALSE
-Period Decimal Notation=TRUE
-OPO Cal. Limit Lo=0
-OPO Cal. Limit Hi=0
-Laser Control Mode=0
-Show User's LSODMM=FALSE
-Hide System Configuration menu=TRUE
-Closed-loop Tuning=FALSE
-Digits of Precision=0
-Polarizer Present=FALSE
-Attenuator Present=FALSE
-LSODMM=FALSE
-Show "Shutter (axis#1)"=FALSE
-Shutter (axis#1).Label=""
-Disable Tuning=FALSE
-Suppress Polarizer Messages=FALSE
-
-[Automated Polarizer]
-Automated Polarizer=FALSE
-SIGNAL Position=293
-IDLER Position=438
-Stepper Current=0.600000
-
-[Motorized Harmonics]
-Motorized Harmonics=TRUE
-SHG Min=-200000
-SHG Max=200000
-SHG Last=0
-THG Min=-200000
-THG Max=200000
-THG Last=0
-Fine Step=10
-Medium Step=20
-Coarse Step=50
-Stepper Current=0.600000
-Speed=100
-BL Size=200
-Steps per Revolution=96000
-Auto Optimization=TRUE
-Feedback Device=2
-OPO Wavelength=760.000000
-OPO Threshold=0.000050
-Multi-Input Fiber=FALSE
-532 Input=FALSE
-532 Threshold=425.000000
-355 Input=FALSE
-355 Threshold=425.000000
-Energy=90.000000
-Averaging=5
-
-[DAQ Device]
-DAQ Installed=FALSE
-Model=1
-Device S/N=0
-
-[Motorized Attenuator]
-Motorized Attenuator=FALSE
-Current Position=100.000000
-Attenuator Coeff=""
-Stepper Current=0.600000
-
-[Motor Controller]
-Controller Type=1
-Auto Module Detection=FALSE
-Motor Addresses="-1|4"
-Wiring Scheme=1
-
-[KAE Parameters]
-Speed Mode=0
-Min Speed=10
-Run Current=20
-Hold Current=10
-Thermal Limit=0
-Output 1=FALSE
-Output 2=TRUE
-Output 3=TRUE
-Output 4=TRUE
-Output 5=FALSE
-Ignore Limits=FALSE
-Ignore E-Stop=TRUE
-Off on E-Stop=TRUE
-
-[Scan Parameters]
-Start WL=690.000000
-Period=50.000000
-End WL=950.000000
-Nr of shots/set=10
-Rep Rate=0
-Laser Energy=0.000000
-
-[Advanced Scan Parameters]
-Wavelengths=""
-No. Cycles=0
-
-[Burst Parameters]
-Wavelength=690
-Nr of shots=10
-Rep Rate=0
-Laser Energy=0.000000
-
-[Fast-Scan Parameters]
-Start WL=0
-Period=50
-End WL=0
-Laser Energy=0.000000
-
-[Shutter Parameters]
-SSC32 Installed=FALSE
-Shutter0_SSC32_Channel=0
-Shutter0_SIGNAL_Position=0
-Shutter0_IDLER_Position=0
-Shutter0_UV-1_Position=0
-Shutter0_UV-2_Position=0
-Shutter0_UV-3_Position=0
-Shutter0_UV-M_Position=0
-Shutter0_UV-0_Position=0
-Shutter1_SSC32_Channel=0
-Shutter1_SIGNAL_Position=0
-Shutter1_IDLER_Position=0
-Shutter1_UV-1_Position=0
-Shutter1_UV-2_Position=0
-Shutter1_UV-3_Position=0
-Shutter1_UV-M_Position=0
-Shutter1_UV-0_Position=0
-Shutter2_SSC32_Channel=0
-Shutter2_SIGNAL_Position=0
-Shutter2_IDLER_Position=0
-Shutter2_UV-1_Position=0
-Shutter2_UV-2_Position=0
-Shutter2_UV-3_Position=0
-Shutter2_UV-M_Position=0
-Shutter2_UV-0_Position=0
-Shutter3_SSC32_Channel=0
-Shutter3_SIGNAL_Position=0
-Shutter3_IDLER_Position=0
-Shutter3_UV-1_Position=0
-Shutter3_UV-2_Position=0
-Shutter3_UV-3_Position=0
-Shutter3_UV-M_Position=0
-Shutter3_UV-0_Position=0
-Shutter4_SSC32_Channel=0
-Shutter4_SIGNAL_Position=0
-Shutter4_IDLER_Position=0
-Shutter4_UV-1_Position=0
-Shutter4_UV-2_Position=0
-Shutter4_UV-3_Position=0
-Shutter4_UV-M_Position=0
-Shutter4_UV-0_Position=0
-
-[Demo Parameters]
-Motor Speed=80
-Start WL=0.000000
-End WL=0.000000
-
-[Energy Metering]
-Meter Installed=FALSE
-Device=0
-Use Range #=0
-Device S/N="786441"
-OPO S/N="781544"
-OPO Channel=-1
-532nm S/N=""
-532nm Scale Factor=0.000000
-532nm Channel=-1
-1064nm S/N=""
-1064nm Scale Factor=0.000000
-1064nm Channel=-1
-355nm S/N=""
-355nm Scale Factor=0.000000
-355nm Channel=-1
-Motor Config 0 Wavelengths="690.0|695.2|700.4|705.6|710.8|716.0|721.2|726.4|731.6|736.8|742.0|747.2|752.4|757.6|762.8|768.0|773.2|778.4|783.6|788.8|794.0|799.2|804.4|809.6|814.8|820.0|825.2|830.4|835.6|840.8|846.0|851.2|856.4|861.6|866.8|872.0|877.2|882.4|887.6|892.8|898.0|903.2|908.4|913.6|918.8|924.0|929.2|934.4|939.6|944.8"
-Motor Config 0 Amplitudes="0.000727|0.000726|0.000764|0.000795|0.000824|0.000817|0.000832|0.000893|0.000898|0.000881|0.000870|0.000834|0.000849|0.000793|0.000778|0.000753|0.000755|0.000812|0.000843|0.000818|0.000843|0.000824|0.000829|0.000837|0.000832|0.000796|0.000808|0.000796|0.000774|0.000778|0.000760|0.000741|0.000724|0.000725|0.000703|0.000703|0.000695|0.000697|0.000671|0.000702|0.000679|0.000671|0.000676|0.000647|0.000660|0.000674|0.000686|0.000664|0.000658|0.000643"
-Motor Config 0 Energies="0.042647|0.043251|0.045291|0.047462|0.048515|0.049305|0.049513|0.050434|0.049656|0.050895|0.048269|0.049129|0.050182|0.049334|0.046761|0.045675|0.045061|0.049129|0.050357|0.049206|0.050050|0.048745|0.048822|0.049041|0.048976|0.047813|0.047082|0.046980|0.046980|0.046442|0.045445|0.044063|0.043909|0.042451|0.041058|0.041760|0.042374|0.041683|0.040269|0.042374|0.041299|0.038996|0.041069|0.040736|0.039994|0.040839|0.040225|0.039994|0.038613|0.037692"
-Motor Config 1 Wavelengths=""
-Motor Config 1 Amplitudes=""
-Motor Config 1 Energies=""
-Motor Config 2 Wavelengths=""
-Motor Config 2 Amplitudes=""
-Motor Config 2 Energies=""
-Motor Config 3 Wavelengths=""
-Motor Config 3 Amplitudes=""
-Motor Config 3 Energies=""
-Motor Config 4 Wavelengths=""
-Motor Config 4 Amplitudes=""
-Motor Config 4 Energies=""
-Motor Config 5 Wavelengths=""
-Motor Config 5 Amplitudes=""
-Motor Config 5 Energies=""
-
-[Ophir Sensor Settings]
-Sensor1.Model Number="PE25-C"
-Sensor1.Sensor Type="Pyroelectric"
-Sensor1.Sensor S/N="781544"
-Sensor1.Mode=1
-Sensor1.Wavelength=750
-Sensor1.Range=4
-Sensor1.Diffuser=FALSE
-Sensor1.Pulsewidth=0
-Sensor1.Threshold=0
-Sensor1.Ext. Trigger=FALSE
-Sensor2.Model Number=""
-Sensor2.Sensor Type=""
-Sensor2.Sensor S/N=""
-Sensor2.Mode=0
-Sensor2.Wavelength=0
-Sensor2.Range=0
-Sensor2.Diffuser=FALSE
-Sensor2.Pulsewidth=0
-Sensor2.Threshold=0
-Sensor2.Ext. Trigger=FALSE
-Sensor3.Model Number=""
-Sensor3.Sensor Type=""
-Sensor3.Sensor S/N=""
-Sensor3.Mode=0
-Sensor3.Wavelength=0
-Sensor3.Range=0
-Sensor3.Diffuser=FALSE
-Sensor3.Pulsewidth=0
-Sensor3.Threshold=0
-Sensor3.Ext. Trigger=FALSE
-Sensor4.Model Number=""
-Sensor4.Sensor Type=""
-Sensor4.Sensor S/N=""
-Sensor4.Mode=0
-Sensor4.Wavelength=0
-Sensor4.Range=0
-Sensor4.Diffuser=FALSE
-Sensor4.Pulsewidth=0
-Sensor4.Threshold=0
-Sensor4.Ext. Trigger=FALSE
-
-[UV Look-up Table]
-UV-1 Use Lookup Table=FALSE
-UV-1 Wavelengths=""
-UV-1 Steps=""
-UV-2 Use Lookup Table=FALSE
-UV-2 Wavelengths=""
-UV-2 Steps=""
-UV-3 Use Lookup Table=FALSE
-UV-3 Wavelengths=""
-UV-3 Steps=""
-UV-M Use Lookup Table=FALSE
-UV-M Wavelengths=""
-UV-M Steps=""
-UV-0 Use Lookup Table=FALSE
-UV-0 Wavelengths=""
-UV-0 Steps=""
-
-[Fast Tuning]
-Fast Tuning=TRUE
-Kp=0.000000
-Ki=0.000000
-Kd=0.000000
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/test.dmc b/Modules/PhotoacousticsHardware/Resources/test.dmc
deleted file mode 100644
index af11477497..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/test.dmc
+++ /dev/null
@@ -1,46 +0,0 @@
-#FASTTUNE
-rtf=-1
-II1
-'AMP SETTINGS
-AU 0
-BR 1
-'AG 0
-TM 1000
-TL 3
-TK 9.998
-'
-'GENERAL SETTINGS
-ER 10000
-OE 1
-'MT -1
-'CE 0
-CN-1
-'PID PARAMETERS
-KD 17.5
-KP 15
-KI 0
-'
-SHX
-WT 1000
-SP 1500000
-AC 120000000
-DC 120000000
-count=0;idx=0;DM pos[2]
-pos[0]=27200
-pos[1]=30900
-points=pos[-1]
-#MOVE;
-II 1
-WT 10
-JP #MOVE;
-EN
-'SUBROUTINE
-'**************************************
-#ININT
-rtf=count+10000000;
-idx = count % points
-'PA pos[idx];BG;AM;
-'BG;AM;
-count = count + 1
-WT 1
-RI 1;
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/Resources/tuneOPOto700.dmc b/Modules/PhotoacousticsHardware/Resources/tuneOPOto700.dmc
deleted file mode 100644
index ac97c28bc2..0000000000
--- a/Modules/PhotoacousticsHardware/Resources/tuneOPOto700.dmc
+++ /dev/null
@@ -1,13 +0,0 @@
-#AUTO
-#MAIN
-rt=0
-'
-SP 150000
-AC 12000000
-DC 12000000
-pos=36459
-PA pos;BG;AM;
-BG;AM;
-WT 100
-rt=1
-EN
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/files.cmake b/Modules/PhotoacousticsHardware/files.cmake
deleted file mode 100644
index d6d5d51880..0000000000
--- a/Modules/PhotoacousticsHardware/files.cmake
+++ /dev/null
@@ -1,23 +0,0 @@
-set(CPP_FILES
- mitkQuantelLaser.cpp
- mitkGalilMotor.cpp
- mitkOphirPyro.cpp
-)
-
-set(RESOURCE_FILES
- homeOPO.dmc
-
- GHOME.dmc
- STUNE.dmc
- FTUNE.dmc
-
- configSlowTuneOPO.dmc
- executeSlowTuneOPO.dmc
-
- configFastTuneOPO.dmc
- executeFastTuneOPO.dmc
-
- test.dmc
- tuneOPOto700.dmc
- OpotekPhocusMobile.xml
-)
\ No newline at end of file
diff --git a/Modules/PhotoacousticsHardware/mitkGalilMotor.cpp b/Modules/PhotoacousticsHardware/mitkGalilMotor.cpp
deleted file mode 100644
index 74cbef697b..0000000000
--- a/Modules/PhotoacousticsHardware/mitkGalilMotor.cpp
+++ /dev/null
@@ -1,277 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkGalilMotor.h"
-
-#include <chrono>
-#include <thread>
-
-#include <math.h>
-
-#include "gclib.h"
-#include "gclib_errors.h"
-
-#include "gclibo.h"
-
-mitk::GalilMotor::GalilMotor() :
-m_ComPort(0),
-m_BaudRate(0),
-m_ErrorMessage("undefined"),
-m_CurrentWavelength(0),
-m_HomePosition(32561)
-{
-}
-
-mitk::GalilMotor::~GalilMotor()
-{
- this->CloseConnection();
- MITK_INFO << "[GalilMotor Debug] destroyed that motor";
-}
-
-void mitk::GalilMotor::LoadResorceFile(std::string filename, std::string* lines)
-{
- us::ModuleResource resorceFile = us::GetModuleContext()->GetModule()->GetResource(filename);
- std::string line;
- if (resorceFile.IsValid() && resorceFile.IsFile())
- {
- us::ModuleResourceStream stream(resorceFile);
- while (std::getline(stream, line))
- {
- *lines = *lines + line + "\n";
- }
- }
- else
- {
- MITK_ERROR << "Resource file was not valid";
- }
-}
-
-bool mitk::GalilMotor::OpenConnection(std::string configuration)
-{
- m_GalilSystem = 0;
- m_ReturnCode = G_NO_ERROR;
- LoadResorceFile(configuration + ".xml", &m_XmlOpoConfiguration);
- TiXmlDocument xmlDoc;
-
- if (xmlDoc.Parse(m_XmlOpoConfiguration.c_str(), 0, TIXML_ENCODING_UTF8))
- {
- TiXmlElement* root = xmlDoc.FirstChildElement("Motor");
- if (root)
- {
- TiXmlElement* elementNode = root->FirstChildElement("Coefficients");
- TiXmlElement* element = elementNode->FirstChildElement("lambda0");
- m_WavelengthToStepCalibration[0] = std::stod(element->GetText());
- element = elementNode->FirstChildElement("lambda1");
- m_WavelengthToStepCalibration[1] = std::stod(element->GetText());
- element = elementNode->FirstChildElement("lambda2");
- m_WavelengthToStepCalibration[2] = std::stod(element->GetText());
- element = elementNode->FirstChildElement("lambda3");
- m_WavelengthToStepCalibration[3] = std::stod(element->GetText());
- element = elementNode->FirstChildElement("lambda4");
- m_WavelengthToStepCalibration[4] = std::stod(element->GetText());
- element = elementNode->FirstChildElement("lambda5");
- m_WavelengthToStepCalibration[5] = std::stod(element->GetText());
- element = elementNode->FirstChildElement("lambda6");
- m_WavelengthToStepCalibration[6] = std::stod(element->GetText());
- element = elementNode->FirstChildElement("home");
- m_HomePosition = std::stod(element->GetText());
- elementNode = root->FirstChildElement("Signal");
- element = elementNode->FirstChildElement("Signal-low");
- m_MinWavelength = std::stod(element->GetText());
- element = elementNode->FirstChildElement("Signal-default");
- m_CurrentWavelength = std::stod(element->GetText());
- element = elementNode->FirstChildElement("Signal-high");
- m_MaxWavelength = std::stod(element->GetText());
- elementNode = root->FirstChildElement("Seriell");
- element = elementNode->FirstChildElement("PortNumber");
- m_ComPort = std::stoi(element->GetText());
- element = elementNode->FirstChildElement("Baud");
- m_BaudRate = std::stoi(element->GetText());
- }
- }
- else
- {
- MITK_ERROR << "[GalilMotor Debug] Could not load configuration xml ";
- }
- std::string openCommand("COM" + std::to_string(m_ComPort) + " --baud " + std::to_string(m_BaudRate) + " --subscribe ALL --direct");
- MITK_INFO << "[Galil Debug] before GOpen(" << openCommand << ") = " << m_ReturnCode << "; m_GalilSystem = " << m_GalilSystem;
- m_ReturnCode = GOpen(openCommand.c_str(), &m_GalilSystem);
- MITK_INFO << "[Galil Debug] after GOpen = " << m_ReturnCode << "; m_GalilSystem = " << m_GalilSystem;
- this->Home();
- return true;
-}
-
-bool mitk::GalilMotor::CloseConnection()
-{
- if (m_GalilSystem)
- {
- this->Home();
- m_ReturnCode = GClose(m_GalilSystem);
- m_GalilSystem = 0;
- return true;
- }
- else
- return false;
-}
-
-int mitk::GalilMotor::GetPositionFromWavelength(double wavelength)
-{
- double posDouble = 0;
- posDouble = m_WavelengthToStepCalibration[0] - m_HomePosition;
- posDouble += (m_WavelengthToStepCalibration[1] * wavelength);
- posDouble += (m_WavelengthToStepCalibration[2] * std::pow(wavelength, 2));
- posDouble += (m_WavelengthToStepCalibration[3] * std::pow(wavelength, 3));
- posDouble += (m_WavelengthToStepCalibration[4] * std::pow(wavelength, 4));
- posDouble += (m_WavelengthToStepCalibration[5] * std::pow(wavelength, 5));
- posDouble += (m_WavelengthToStepCalibration[6] * std::pow(wavelength, 6));
- int pos = posDouble;
- return pos;
-}
-
-bool mitk::GalilMotor::TuneToWavelength(double wavelength, bool isRecalibrating)
-{
- std::string positionCommand;
- if (!isRecalibrating)
- {
- positionCommand = "pos=" + std::to_string(this->GetPositionFromWavelength(wavelength));
- }
- else
- {
- int posAbs = wavelength - m_HomePosition;
- positionCommand = "pos=" + std::to_string(posAbs);
- }
-
- m_ReturnCode = GCmd(m_GalilSystem, "AB"); // Abort any running programs
- MITK_INFO << "[Galil Debug] after AB: " << m_ReturnCode << "";
- m_ReturnCode = GCmd(m_GalilSystem, "BV"); // Burn all variables
- MITK_INFO << "[Galil Debug] after BV: " << m_ReturnCode << "";
- m_ReturnCode = GProgramDownload(m_GalilSystem, "", 0); // Erase the program on the system
- MITK_INFO << "[Galil Debug] after empty GProgramDownload: " << m_ReturnCode << "";
-
- m_ReturnCode = GCmd(m_GalilSystem, positionCommand.c_str());
- MITK_INFO << "[Galil Debug] after sending tune position(" << positionCommand << "): " << m_ReturnCode << "";
-
- std::string galilProgramSTUNE;
- this->LoadResorceFile("STUNE.dmc", &galilProgramSTUNE);
- m_ReturnCode = GProgramDownload(m_GalilSystem, galilProgramSTUNE.c_str(), 0);
- MITK_INFO << "[Galil Debug] after STUNE progam: " << m_ReturnCode << galilProgramSTUNE;
-
- GSleep(10);
- m_ReturnCode = GCmd(m_GalilSystem, "XQ#STUNE");
- MITK_INFO << "[Galil Debug] after sending XQ#STUNE = " << m_ReturnCode;
- GSleep(10000);
- int success, pos = -1;
- m_ReturnCode = GCmdI(m_GalilSystem, "suc=?", &success);
- MITK_INFO << "[Galil Debug] after asking suc=? = " << m_ReturnCode << "; successfulTune = " << success;
- m_ReturnCode = GCmdI(m_GalilSystem, "pos=?", &pos);
- MITK_INFO << "[Galil Debug] after asking pos=? = " << m_ReturnCode << "; pos = " << pos;
- if (success == 1)
- {
- m_CurrentWavelength = wavelength;
- return true;
- }
- else
- return false;
-}
-
-bool mitk::GalilMotor::FastTuneWavelengths(std::vector<double> wavelengthList)
-{
- m_ReturnCode = GCmd(m_GalilSystem, "AB"); // Abort any running programs
- GSleep(1000);
- MITK_INFO << "[Galil Debug] after AB: " << m_ReturnCode << "";
- m_ReturnCode = GCmd(m_GalilSystem, "BV"); // Burn all variables
- GSleep(2000);
- MITK_INFO << "[Galil Debug] after BV: " << m_ReturnCode << "";
-
- m_ReturnCode = GProgramDownload(m_GalilSystem, "", 0); // Erase the program on the system
- MITK_INFO << "[Galil Debug] after empty GProgramDownload: " << m_ReturnCode << "";
- GSleep(1000);
- std::string positionsCommand("#AUTO\n#PARA\nDA pos[0]\npoints = "+std::to_string(wavelengthList.size())+"\nDM pos[" + std::to_string(wavelengthList.size()) + "];\n");
-
- for (int wavelengthIterator = 0; wavelengthIterator < wavelengthList.size(); wavelengthIterator++)
- {
- positionsCommand += "pos[" + std::to_string(wavelengthIterator) + "]=" + std::to_string(this->GetPositionFromWavelength(wavelengthList[wavelengthIterator])) + "\n";
- }
- positionsCommand += "EN\n";
-
- m_ReturnCode = GProgramDownload(m_GalilSystem, positionsCommand.c_str(), 0);
- MITK_INFO << "[Galil Debug] after sending positions command(" << positionsCommand << "): " << m_ReturnCode << "";
- GSleep(1000);
- m_ReturnCode = GCmd(m_GalilSystem, "XQ"); // FTUNE
- MITK_INFO << "[Galil Debug] after asking XQ#PARA = " << m_ReturnCode;
- m_ReturnCode = GProgramDownload(m_GalilSystem, "", 0); // Erase the program on the system
- MITK_INFO << "[Galil Debug] after empty GProgramDownload: " << m_ReturnCode << "";
- GSleep(1000);
- std::string galilProgramFTUNE;
- this->LoadResorceFile("FTUNE.dmc", &galilProgramFTUNE);
- m_ReturnCode = GProgramDownload(m_GalilSystem, galilProgramFTUNE.c_str(), 0);
- MITK_INFO << "[Galil Debug] after FTUNE progam upload: " << m_ReturnCode << "";
-
- GSleep(1000);
- m_ReturnCode = GCmd(m_GalilSystem, "XQ"); // FTUNE
- MITK_INFO << "[Galil Debug] after asking XQ#FTUNE = " << m_ReturnCode;
- GSleep(10000);
- int count = -1;
- m_ReturnCode = GCmdI(m_GalilSystem, "count=?", &count);
- MITK_INFO << "[Galil Debug] cycles = " << count;
- m_ReturnCode = GCmdI(m_GalilSystem, "pos=?", &count);
- MITK_INFO << "[Galil Debug] pos = " << count;
- m_ReturnCode = GCmdI(m_GalilSystem, "points=?", &count);
- MITK_INFO << "[Galil Debug] points = " << count;
-
- if (count > 0)
- return true;
- else
- return false;
-}
-
-bool mitk::GalilMotor::Home()
-{
- m_ReturnCode = GCmd(m_GalilSystem, "AB"); // Abort any running programs
- MITK_INFO << "[Galil Debug] after AB: " << m_ReturnCode << "";
- GSleep(1000);
- m_ReturnCode = GCmd(m_GalilSystem, "BV"); // Burn all variables
- MITK_INFO << "[Galil Debug] after BV: " << m_ReturnCode << "";
- GSleep(1000);
- m_ReturnCode = GProgramDownload(m_GalilSystem, "", 0); // Erase the program on the system
- MITK_INFO << "[Galil Debug] after empty GProgramDownload: " << m_ReturnCode << "";
-
- std::string galilProgram;
- this->LoadResorceFile("GHOME.dmc", &galilProgram);
-
- m_ReturnCode = GProgramDownload(m_GalilSystem, galilProgram.c_str(), 0);
- MITK_INFO << "[Galil Debug] after home GProgramDownloadFile = " << m_ReturnCode << "; m_GalilSystem = " << m_GalilSystem;
-
- m_ReturnCode = GCmd(m_GalilSystem, "XQ"); // HOME
- GSleep(15000);
- int val = -2;
- m_ReturnCode = GCmdI(m_GalilSystem, "suc=?", &val);
-
- MITK_INFO << "[Galil Debug] after home execution = " << m_ReturnCode << "; m_GalilSystem = " << m_GalilSystem << " homed = " << val;
-
- return true;
-}
-
-double mitk::GalilMotor::GetMinWavelength()
-{
- return m_MinWavelength;
-}
-
-double mitk::GalilMotor::GetMaxWavelength()
-{
- return m_MaxWavelength;
-}
-
-double mitk::GalilMotor::GetCurrentWavelength()
-{
- return m_CurrentWavelength;
-}
diff --git a/Modules/PhotoacousticsHardware/mitkGalilMotor.h b/Modules/PhotoacousticsHardware/mitkGalilMotor.h
deleted file mode 100644
index 966dfe707d..0000000000
--- a/Modules/PhotoacousticsHardware/mitkGalilMotor.h
+++ /dev/null
@@ -1,76 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef MITKGalilAPI_H_HEADER_INCLUDED
-#define MITKGalilAPI_H_HEADER_INCLUDED
-
-#include "itkObject.h"
-#include "mitkCommon.h"
-
-#include "vector"
-#include "MitkPhotoacousticsHardwareExports.h"
-
-#include "gclib.h"
-#include "gclibo.h"
-
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usGetModuleContext.h>
-#include <usModuleContext.h>
-#include <usModuleResourceStream.h>
-
-#include <tinyxml.h>
-
-namespace mitk {
-
- class MITKPHOTOACOUSTICSHARDWARE_EXPORT GalilMotor : public itk::Object
- {
- public:
- mitkClassMacroItkParent(mitk::GalilMotor, itk::Object);
- itkFactorylessNewMacro(Self);
-
- virtual bool OpenConnection(std::string configuration);
- virtual bool CloseConnection();
-
- double GetMinWavelength();
- double GetMaxWavelength();
- double GetCurrentWavelength();
-
- bool TuneToWavelength(double wavelength, bool isRecalibrating);
-
- bool FastTuneWavelengths(std::vector<double> wavelengthList);
-
- protected:
- virtual bool Home();
- void LoadResorceFile(std::string filename, std::string* lines);
- int GetPositionFromWavelength(double wavelength);
- GalilMotor();
- virtual ~GalilMotor();
-
- int m_ComPort;
- int m_BaudRate;
- std::string m_ErrorMessage;
- GCon m_GalilSystem;
- GReturn m_ReturnCode;
-
- std::string m_XmlOpoConfiguration;
- double m_MinWavelength;
- double m_MaxWavelength;
- double m_CurrentWavelength;
- double m_WavelengthToStepCalibration[7];
- double m_HomePosition;
-
- };
-} // namespace mitk
-
-#endif /* MITKGalilAPI_H_HEADER_INCLUDED */
diff --git a/Modules/PhotoacousticsHardware/mitkOphirPyro.cpp b/Modules/PhotoacousticsHardware/mitkOphirPyro.cpp
deleted file mode 100644
index 54081c8922..0000000000
--- a/Modules/PhotoacousticsHardware/mitkOphirPyro.cpp
+++ /dev/null
@@ -1,333 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkOphirPyro.h"
-
-#include <chrono>
-#include <ctime>
-#include <thread>
-#include <exception>
-
-mitk::OphirPyro::OphirPyro() :
-m_CurrentWavelength(0),
-m_DeviceHandle(0),
-m_Connected(false),
-m_Streaming(false),
-m_SerialNumber(nullptr),
-m_GetDataThread(),
-m_ImagePyroDelay(0),
-m_EnergyMultiplicator(60000)
-{
- m_PulseEnergy.clear();
- m_PulseTime.clear();
- m_PulseStatus.clear();
- m_TimeStamps.clear();
-}
-
-mitk::OphirPyro::~OphirPyro()
-{
- if (m_Connected)
- {
- this->CloseConnection();
- if (m_GetDataThread.joinable())
- {
- m_GetDataThread.join();
- MITK_INFO << "[OphirPyro Debug] joined data thread";
- }
- }
- MITK_INFO << "[OphirPyro Debug] destroying that Pyro";
- /* cleanup thread */
-}
-
-bool mitk::OphirPyro::StartDataAcquisition()
-{
- if (ophirAPI.StartStream(m_DeviceHandle))
- {
- m_Streaming = true;
- m_GetDataThread = std::thread(&mitk::OphirPyro::GetDataFromSensorThread, this);
- }
- return m_Streaming;
-}
-
-// this is just a little function to set the filenames below right
-inline void replaceAll(std::string& str, const std::string& from, const std::string& to) {
- if (from.empty())
- return;
- size_t start_pos = 0;
- while ((start_pos = str.find(from, start_pos)) != std::string::npos) {
- str.replace(start_pos, from.length(), to);
- start_pos += to.length(); // In case 'to' contains 'from', like replacing 'x' with 'yx'
- }
-}
-
-void mitk::OphirPyro::SaveCsvData()
-{
- // get the time and date, put them into a nice string and create a folder for the images
- time_t time = std::time(nullptr);
- time_t* timeptr = &time;
- std::string currentDate = std::ctime(timeptr);
- replaceAll(currentDate, ":", "-");
- currentDate.pop_back();
-
- std::string pathTS = "c:\\ImageData\\" + currentDate + " pyro-ts" + ".csv";
-
- std::ofstream timestampFile;
- timestampFile.open(pathTS);
-
- timestampFile << ",timestamp,PulseEnergy,PulseTime";
-
- int currentSize = m_TimeStamps.size();
-
- for (int index = 0; index < currentSize; ++index)
- {
- timestampFile << "\n" << index << "," << m_TimeStamps.at(index) << ","<< m_PulseEnergySaved.at(index) << "," << (long)m_PulseTimeSaved.at(index);
- }
- timestampFile.close();
-}
-
-void mitk::OphirPyro::SaveData()
-{
- SaveCsvData();
-}
-
-bool mitk::OphirPyro::StopDataAcquisition()
-{
- if (ophirAPI.StopStream(m_DeviceHandle))
- m_Streaming = false;
-
- SaveCsvData();
- MITK_INFO << "[OphirPyro Debug] m_Streaming = "<< m_Streaming;
- std::this_thread::sleep_for(std::chrono::milliseconds(50));
- if (m_GetDataThread.joinable())
- {
- m_GetDataThread.join();
- }
- return !m_Streaming;
-}
-
-unsigned int mitk::OphirPyro::GetDataFromSensor()
-{
- if (m_Streaming)
- {
- std::vector<double> newEnergy;
- std::vector<double> newTimestamp;
- std::vector<int> newStatus;
- unsigned int noPackages = 0;
- try
- {
- noPackages = ophirAPI.GetData(m_DeviceHandle, &newEnergy, &newTimestamp, &newStatus);
- if (noPackages > 0)
- {
- m_PulseEnergy.insert(m_PulseEnergy.end(), newEnergy.begin(), newEnergy.end());
- for (unsigned int i=0; i<noPackages; i++)
- m_TimeStamps.push_back(std::chrono::high_resolution_clock::now().time_since_epoch().count());
-
- m_PulseTime.insert(m_PulseTime.end(), newTimestamp.begin(), newTimestamp.end());
- m_PulseStatus.insert(m_PulseStatus.end(), newStatus.begin(), newStatus.end());
-
- m_PulseEnergySaved.insert(m_PulseEnergySaved.end(), newEnergy.begin(), newEnergy.end());
- m_PulseTimeSaved.insert(m_PulseTimeSaved.end(), newTimestamp.begin(), newTimestamp.end());
- m_PulseStatusSaved.insert(m_PulseStatusSaved.end(), newStatus.begin(), newStatus.end());
- }
- }
- catch (std::exception& ex)
- {
- MITK_INFO << "this is weird: " << ex.what();
- }
- return noPackages;
- }
- return 0;
-}
-
-void mitk::OphirPyro::GetDataFromSensorThread()
-{
- while(m_Connected && m_Streaming)
- {
- this->GetDataFromSensor();
- std::this_thread::sleep_for(std::chrono::milliseconds(50));
- }
- return;
-}
-
-double mitk::OphirPyro::LookupCurrentPulseEnergy()
-{
- if (m_Connected && !m_PulseEnergy.empty())
- {
- MITK_INFO << m_PulseEnergy.size();
- return m_PulseEnergy.back();
- }
- return 0;
-}
-
-double mitk::OphirPyro::GetClosestEnergyInmJ(long long ImageTimeStamp, double interval)
-{
- if (m_PulseTime.size() == 0)
- return 0;
-
- long long searchTime = (ImageTimeStamp/1000000) - m_ImagePyroDelay; // conversion from ns to ms
-
- //MITK_INFO << "searchTime = " << searchTime;
- int foundIndex = -1;
- long long shortestDifference = 250*interval;
-
- // search the list for a fitting energy value time
- for (int index = 0; index < m_PulseTime.size();++index)
- {
- long long newDifference = abs(((int)m_PulseTime[index]) - searchTime);
- //MITK_INFO << "newDifference[" << index << "] = " << newDifference;
- if (newDifference < shortestDifference)
- {
- shortestDifference = newDifference;
- foundIndex = index;
- //MITK_INFO << "foundIndex = " << foundIndex;
- }
- }
-
- if (abs(shortestDifference) < interval)
- {
- // delete all elements before the one found
- m_PulseEnergy.erase(m_PulseEnergy.begin(), m_PulseEnergy.begin() + foundIndex);
- m_PulseTime.erase(m_PulseTime.begin(), m_PulseTime.begin() + foundIndex);
- m_PulseStatus.erase(m_PulseStatus.begin(), m_PulseStatus.begin() + foundIndex);
-
- // multipy with m_EnergyMultiplicator, because the Pyro gives just a fraction of the actual Laser Energy
- return (GetNextPulseEnergy()*m_EnergyMultiplicator);
- }
-
- //MITK_INFO << "No matching energy value for image found in interval of " << interval << "ms. sd: " << shortestDifference;
- return -1;
-}
-
-double mitk::OphirPyro::GetNextEnergyInmJ(long long ImageTimeStamp, double interval)
-{
- if (m_Connected && !(m_PulseTime.size() > 0))
- return 0;
-
- long long searchTime = (ImageTimeStamp / 1000000) - m_ImagePyroDelay; // conversion from ns to ms
-
- if (abs(searchTime - m_PulseTime.front()) < interval)
- {
- return (GetNextPulseEnergy()*m_EnergyMultiplicator); // multipy with m_EnergyMultiplicator, because the Pyro gives just a fraction of the actual Laser Energy
- }
-
- MITK_INFO << "Image aquisition and energy measurement ran out of sync";
- return -1;
-}
-
-void mitk::OphirPyro::SetSyncDelay(long long FirstImageTimeStamp)
-{
- while (!m_PulseTime.size())
- {
- std::this_thread::sleep_for(std::chrono::milliseconds(1));
- }
- m_ImagePyroDelay = (FirstImageTimeStamp / 1000000) - m_PulseTime.at(0);
-
- MITK_INFO << "m_ImagePyroDelay = " << m_ImagePyroDelay;
- return;
-}
-
-bool mitk::OphirPyro::IsSyncDelaySet()
-{
- return (m_ImagePyroDelay != 0);
-}
-
-double mitk::OphirPyro::GetNextPulseEnergy()
-{
- if (m_Connected && m_PulseEnergy.size()>=1)
- {
- double out = m_PulseEnergy.front();
- m_PulseEnergy.erase(m_PulseEnergy.begin());
- m_PulseTime.erase(m_PulseTime.begin());
- m_PulseStatus.erase(m_PulseStatus.begin());
- return out;
- }
- return 0;
-}
-
-double mitk::OphirPyro::LookupCurrentPulseEnergy(double* timestamp, int* status)
-{
- if (m_Connected)
- {
- *timestamp = m_PulseTime.back();
- *status = m_PulseStatus.back();
- return m_PulseEnergy.back();
- }
- return 0;
-}
-
-double mitk::OphirPyro::GetNextPulseEnergy(double* timestamp, int* status)
-{
- if (m_Connected)
- {
- double out = m_PulseEnergy.front();
- *timestamp = m_PulseTime.front();
- *status = m_PulseStatus.front();
- m_PulseEnergy.erase(m_PulseEnergy.begin());
- m_PulseTime.erase(m_PulseTime.begin());
- m_PulseStatus.erase(m_PulseStatus.begin());
- return out;
- }
- return 0;
-}
-
-bool mitk::OphirPyro::OpenConnection()
-{
- if (!m_Connected)
- {
- char* m_SerialNumber;
- try {
- MITK_INFO << "Scanning for Ophir connection";
- m_SerialNumber = ophirAPI.ScanUSB();
- }
- catch (...)
- {
- MITK_INFO << "Scanning failed, trying again in 2 seconds...";
- std::this_thread::sleep_for(std::chrono::seconds(2));
- MITK_INFO << "Scanning for Ophir connection";
- m_SerialNumber = ophirAPI.ScanUSB();
- }
-
- if (m_SerialNumber != 0)
- {
- try {
- MITK_INFO << "Opening Ophir connection";
- m_DeviceHandle = ophirAPI.OpenDevice(m_SerialNumber);
- }
- catch (...)
- {
- MITK_INFO << "Ophir connection failed, trying again in 2 seconds...";
- std::this_thread::sleep_for(std::chrono::seconds(2));
- MITK_INFO << "Opening Ophir connection";
- m_DeviceHandle = ophirAPI.OpenDevice(m_SerialNumber);
- }
-
- if (m_DeviceHandle != 0)
- {
- m_Connected = true;
- return true;
- }
- }
- }
- return false;
-}
-
-bool mitk::OphirPyro::CloseConnection()
-{
- if (m_Connected)
- {
- bool closed = ophirAPI.CloseDevice(m_DeviceHandle);
- if (closed) m_DeviceHandle = 0;
- m_Connected = !closed;
- return closed;
- }
- return false;
-}
diff --git a/Modules/PhotoacousticsHardware/mitkOphirPyro.h b/Modules/PhotoacousticsHardware/mitkOphirPyro.h
deleted file mode 100644
index b6f09654a7..0000000000
--- a/Modules/PhotoacousticsHardware/mitkOphirPyro.h
+++ /dev/null
@@ -1,90 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef MITKOPHIRPYRO_H_HEADER_INCLUDED
-#define MITKOPHIRPYRO_H_HEADER_INCLUDED
-
-#include "itkObject.h"
-#include "mitkCommon.h"
-
-#include "vector"
-#include "MitkPhotoacousticsHardwareExports.h"
-
-#include "OphirPyroWrapper.h"
-
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usGetModuleContext.h>
-#include <usModuleContext.h>
-#include <usModuleResourceStream.h>
-#include <iostream>
-#include <fstream>
-#include <chrono>
-#include <thread>
-
-namespace mitk {
-
- class MITKPHOTOACOUSTICSHARDWARE_EXPORT OphirPyro : public itk::Object
- {
- public:
- mitkClassMacroItkParent(mitk::OphirPyro, itk::Object);
- itkFactorylessNewMacro(Self);
-
- virtual bool OpenConnection();
- virtual bool CloseConnection();
- virtual bool StartDataAcquisition();
- virtual bool StopDataAcquisition();
- unsigned int GetDataFromSensor();
- void GetDataFromSensorThread();
- void SaveData();
-
- virtual double LookupCurrentPulseEnergy();
- virtual double GetNextPulseEnergy();
- virtual double LookupCurrentPulseEnergy(double* timestamp, int* status);
- virtual double GetNextPulseEnergy(double* timestamp, int* status);
-
- virtual double GetClosestEnergyInmJ(long long ImageTimeStamp, double interval=20);
- virtual double GetNextEnergyInmJ(long long ImageTimeStamp, double interval = 20);
- virtual void SetSyncDelay(long long FirstImageTimeStamp);
- virtual bool IsSyncDelaySet();
-
-
- protected:
- OphirPyro();
- virtual ~OphirPyro();
- void SaveCsvData();
- OphirPyroWrapper ophirAPI;
- char* m_SerialNumber;
- int m_DeviceHandle;
- bool m_Connected;
- bool m_Streaming;
- std::vector<double> m_PulseEnergy;
- std::vector<double> m_PulseTime;
- std::vector<int> m_PulseStatus;
- std::vector<long long> m_TimeStamps;
-
- std::vector<double> m_PulseEnergySaved;
- std::vector<double> m_PulseTimeSaved;
- std::vector<int> m_PulseStatusSaved;
- std::vector<long long> m_TimeStampsSaved;
-
- double m_CurrentWavelength;
- double m_CurrentEnergyRange;
- long long m_ImagePyroDelay;
- float m_EnergyMultiplicator;
-
- std::thread m_GetDataThread;
- };
-} // namespace mitk
-
-#endif /* MITKOPHIRPYRO_H_HEADER_INCLUDED */
diff --git a/Modules/PhotoacousticsHardware/mitkQuantelLaser.cpp b/Modules/PhotoacousticsHardware/mitkQuantelLaser.cpp
deleted file mode 100644
index c742b8b072..0000000000
--- a/Modules/PhotoacousticsHardware/mitkQuantelLaser.cpp
+++ /dev/null
@@ -1,405 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkQuantelLaser.h"
-
-#include <chrono>
-#include <thread>
-#include <mutex>
-
-#include <tinyxml.h>
-
-#include <usModuleContext.h>
-#include <usGetModuleContext.h>
-
-const unsigned char CR = 0xD; // == '\r' - carriage return
-const unsigned char LF = 0xA; // == '\n' - line feed
-
-mitk::QuantelLaser::QuantelLaser() :
- m_State(mitk::QuantelLaser::UNCONNECTED),
- m_FlashlampRunning(false),
- m_ShutterOpen(false),
- m_LaserEmission(false),
- m_DeviceName(),
- m_PortNumber(mitk::SerialCommunication::COM6),
- m_BaudRate(mitk::SerialCommunication::BaudRate115200),
- m_DataBits(mitk::SerialCommunication::DataBits8),
- m_Parity(mitk::SerialCommunication::None),
- m_StopBits(mitk::SerialCommunication::StopBits1),
- m_HardwareHandshake(mitk::SerialCommunication::HardwareHandshakeOff),
- m_SerialCommunication(nullptr),
- m_StayAliveMessageThread(),
- m_SerialCommunicationMutex()
-{
-}
-
-mitk::QuantelLaser::~QuantelLaser()
-{
- /* stop tracking and disconnect from tracking device */
- if ((GetState() == STATE3) || (GetState() == STATE4) || (GetState() == STATE5) || (GetState() == STATE6))
- {
- this->StopQswitching();
- this->StopFlashing();
- }
- if (GetState() == STATE2)
- {
- this->CloseConnection();
- }
- /* cleanup stay alive thread */
- if (m_StayAliveMessageThread.joinable())
- m_StayAliveMessageThread.join();
-
- /* free serial communication interface */
- if (m_SerialCommunication.IsNotNull())
- {
- m_SerialCommunication->ClearReceiveBuffer();
- m_SerialCommunication->ClearSendBuffer();
- m_SerialCommunication->CloseConnection();
- m_SerialCommunication = nullptr;
- }
-}
-
-std::string mitk::QuantelLaser::SendAndReceiveLine(const std::string* input, std::string* answer)
-{
- MITK_INFO << "[Quantel Laser Debug] sending: " << input->c_str();
- if (input == nullptr)
- return "SERIALSENDERROR";
-
- std::string message;
-
- message = *input + '\n';
-
- // Clear send buffer
- m_SerialCommunication->ClearSendBuffer();
- m_SerialCommunication->Send(message);
- std::this_thread::sleep_for(std::chrono::milliseconds(50));
- std::string m;
- do
- {
- long returnvalue = m_SerialCommunication->Receive(m, 1);
- if ((returnvalue == 0) || (m.size() != 1))
- return "SERIALRECEIVEERROR";
- *answer += m;
- } while (m.at(0) != LF);
- m_SerialCommunication->ClearReceiveBuffer();
- std::this_thread::sleep_for(std::chrono::milliseconds(100));
- m_SerialCommunication->ClearReceiveBuffer();
- MITK_INFO << "[Quantel Laser Debug] received: " << answer->c_str();
- return "OK";
-}
-
-void mitk::QuantelLaser::LoadResorceFile(std::string filename, std::string* lines)
-{
- us::ModuleResource resorceFile = us::GetModuleContext()->GetModule()->GetResource(filename);
- std::string line;
- if (resorceFile.IsValid() && resorceFile.IsFile())
- {
- us::ModuleResourceStream stream(resorceFile);
- while (std::getline(stream, line))
- {
- *lines = *lines + line + "\n";
- }
- }
- else
- {
- MITK_ERROR << "[Quantel Laser Debug] Resource file was not valid";
- }
-}
-
-bool mitk::QuantelLaser::OpenConnection(std::string configurationFile)
-{
- LoadResorceFile(configurationFile + ".xml", &m_XmlPumpLaserConfiguration);
- TiXmlDocument xmlDoc;
-
- if (xmlDoc.Parse(m_XmlPumpLaserConfiguration.c_str(), 0, TIXML_ENCODING_UTF8))
- {
- TiXmlElement* root = xmlDoc.FirstChildElement("PumpLaser");
- if (root)
- {
- TiXmlElement* elementNode = root->FirstChildElement("Seriell");
- TiXmlElement* element = elementNode->FirstChildElement("PortNumber");
- m_PortNumber = mitk::SerialCommunication::PortNumber(std::stoi(element->GetText()));
- element = elementNode->FirstChildElement("Baud");
- m_BaudRate = mitk::SerialCommunication::BaudRate(std::stoi(element->GetText()));
-
- MITK_INFO << m_PortNumber << m_BaudRate;
- }
- }
- else
- {
- MITK_ERROR << "[Quantel Laser Debug] Could not load configuration xml ";
- return false;
- }
-
- m_SerialCommunication = mitk::SerialCommunication::New();
-
- if (m_DeviceName.empty())
- m_SerialCommunication->SetPortNumber(m_PortNumber);
- else
- m_SerialCommunication->SetDeviceName(m_DeviceName);
-
- m_SerialCommunication->SetBaudRate(m_BaudRate);
- m_SerialCommunication->SetDataBits(m_DataBits);
- m_SerialCommunication->SetParity(m_Parity);
- m_SerialCommunication->SetStopBits(m_StopBits);
- m_SerialCommunication->SetSendTimeout(1000);
- m_SerialCommunication->SetReceiveTimeout(1000);
- if (m_SerialCommunication->OpenConnection() == 0) // 0 == ERROR_VALUE
- {
- m_SerialCommunication->CloseConnection();
- m_SerialCommunication = nullptr;
- MITK_ERROR << "[Quantel Laser Debug] " << "Can not open serial port";
- return false;
- }
-
- if (this->GetState() != UNCONNECTED)
- {
- std::string *command = new std::string;
- std::string answer("");
- command->assign("STOP");
- this->SendAndReceiveLine(command, &answer);
- return true;
- }
- else
- return false;
-}
-
-bool mitk::QuantelLaser::CloseConnection()
-{
- if (this->GetState() != UNCONNECTED)
- {
- this->StopQswitching();
- this->StopFlashing();
-
- // close the serial connection
- m_SerialCommunication->CloseConnection();
- m_SerialCommunication = nullptr;
- this->GetState();
- }
- return true;
-}
-
-mitk::QuantelLaser::LaserState mitk::QuantelLaser::GetState()
-{
- if (m_SerialCommunication == nullptr)
- {
- m_State = UNCONNECTED;
- return m_State;
- }
-
- if (!m_SerialCommunication->IsConnected())
- {
- m_State = UNCONNECTED;
- return m_State;
- }
-
- std::string *command = new std::string;
- std::string answer("");
- command->assign("STATE");
- this->SendAndReceiveLine(command, &answer);
- MITK_INFO << "[Quantel Laser Debug] get state:" << answer;
- if (answer == "STATE = 0\n")
- m_State = STATE0;
- else if(answer == "STATE = 1\n")
- {
- m_State = STATE1;
- m_FlashlampRunning = false;
- m_ShutterOpen = false;
- m_LaserEmission = false;
- }
- else if(answer == "STATE = 2\n") // laser ready for RUN
- {
- m_State = STATE2;
- m_FlashlampRunning = false;
- m_ShutterOpen = false;
- m_LaserEmission = false;
- }
- else if(answer == "STATE = 3\n")
- {
- m_State = STATE3;
- m_FlashlampRunning = true;
- m_ShutterOpen = false;
- m_LaserEmission = false;
- }
- else if(answer == "STATE = 4\n")
- {
- m_State = STATE4;
- m_FlashlampRunning = true;
- m_ShutterOpen = false;
- m_LaserEmission = false;
- }
- else if (answer == "STATE = 5\n")
- {
- m_State = STATE5;
- m_FlashlampRunning = true;
- m_ShutterOpen = true;
- m_LaserEmission = false;
- }
- else if (answer == "STATE = 6\n")
- {
- m_State = STATE6;
- m_FlashlampRunning = true;
- m_ShutterOpen = true;
- m_LaserEmission = true;
- }
- else if (answer == "STATE = 7\n")
- {
- m_State = STATE7;
- m_FlashlampRunning = true;
- m_ShutterOpen = true;
- m_LaserEmission = true;
- }
- else
- {
- m_State = UNCONNECTED;
- m_FlashlampRunning = false;
- m_ShutterOpen = false;
- m_LaserEmission = false;
- }
-
- return m_State;
-}
-
-
-void mitk::QuantelLaser::StayAlive()
-{
- do{
- std::this_thread::sleep_for(std::chrono::seconds(2));
- std::string *command = new std::string;
- std::string answer("");
- command->assign("STATE");
- this->SendAndReceiveLine(command, &answer);
- } while (m_KeepAlive);
-}
-
-bool mitk::QuantelLaser::StartFlashing()
-{
- this->GetState();
- if (!m_FlashlampRunning)
- {
- if (m_LaserEmission)
- this->StopQswitching();
-
- std::string *command = new std::string;
- std::string answer("");
- command->assign("RUN");
- this->SendAndReceiveLine(command, &answer);
- MITK_INFO << answer;
- if (answer.at(0) == 'O' && answer.at(1) == 'K')
- {
- m_FlashlampRunning = true;
- m_ShutterOpen = false;
- m_KeepAlive = true;
- //m_StayAliveMessageThread = std::thread(&mitk::QuantelLaser::StayAlive, this);
- }
- else
- {
- MITK_ERROR << "[Quantel Laser Debug] " << "Cannot start flashlamps." << " Laser is telling me: " << answer;
- return false;
- }
- }
- else
- MITK_INFO << "[Quantel Laser Debug] " << "Flashlamps are already running";
-
- return true;
-}
-
-bool mitk::QuantelLaser::StopFlashing()
-{
- this->GetState();
- if (m_FlashlampRunning)
- {
- if (m_LaserEmission)
- this->StopQswitching();
-
- std::string *command = new std::string;
- std::string answer("");
- command->assign("STOP");
- this->SendAndReceiveLine(command, &answer);
- MITK_INFO << answer;
- if (answer.at(0) == 'O' && answer.at(1) == 'K')
- {
- m_FlashlampRunning = false;
- m_ShutterOpen = false;
- m_KeepAlive = false;
- }
- else
- {
- MITK_ERROR << "[Quantel Laser Debug] " << "Cannot Stop flashlamps." << " Laser is telling me: " << answer;
- return false;
- }
-
- }
- else
- MITK_INFO << "[Quantel Laser Debug] " << "Flashlamps are not running";
-
- return true;
-}
-
-bool mitk::QuantelLaser::StartQswitching()
-{
- this->GetState();
- if (!m_LaserEmission)
- {
- std::string *command = new std::string;
- std::string answer("");
- command->assign("QSW 1");
- this->SendAndReceiveLine(command, &answer);
- MITK_INFO << answer;
- if (answer.at(0) == 'O' && answer.at(1) == 'K')
- {
- m_FlashlampRunning = true;
- m_ShutterOpen = true;
- return true;
- }
- else
- {
- MITK_ERROR << "[Quantel Laser Debug] " << "Cannot start Qswitch." << " Laser is telling me: " << answer;
- return false;
- }
- }
- else
- {
- MITK_INFO << "[Quantel Laser Debug] " << "Laser is already emitting";
- return true;
- }
-}
-
-bool mitk::QuantelLaser::StopQswitching()
-{
- this->GetState();
- if (m_FlashlampRunning && m_LaserEmission)
- {
- std::string *command = new std::string;
- std::string answer("");
- command->assign("QSW 0");
- this->SendAndReceiveLine(command, &answer);
- MITK_INFO << answer;
- if (answer.at(0) == 'O' && answer.at(1) == 'K')
- {
- m_LaserEmission = false;
- }
- else
- MITK_ERROR << "[Quantel Laser Debug] " << "Cannot stop Q-switch.";
-
- }
- return true;
-}
-
-bool mitk::QuantelLaser::IsEmitting()
-{
- return m_LaserEmission;
-}
-bool mitk::QuantelLaser::IsFlashing()
-{
- return m_FlashlampRunning;
-}
diff --git a/Modules/PhotoacousticsHardware/mitkQuantelLaser.h b/Modules/PhotoacousticsHardware/mitkQuantelLaser.h
deleted file mode 100644
index 761fcb66ee..0000000000
--- a/Modules/PhotoacousticsHardware/mitkQuantelLaser.h
+++ /dev/null
@@ -1,105 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef MITKQUANTELLASER_H_HEADER_INCLUDED
-#define MITKQUANTELLASER_H_HEADER_INCLUDED
-
-#include "itkObject.h"
-#include "mitkCommon.h"
-
-#include <chrono>
-#include <thread>
-#include <mutex>
-
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usGetModuleContext.h>
-#include <usModuleContext.h>
-#include <usModuleResourceStream.h>
-
-#include "mitkSerialCommunication.h"
-#include "MitkPhotoacousticsHardwareExports.h"
-
-namespace mitk {
-
- class MITKPHOTOACOUSTICSHARDWARE_EXPORT QuantelLaser : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(QuantelLaser, itk::LightObject);
- itkFactorylessNewMacro(Self);
-
- enum LaserState { UNCONNECTED, STATE0, STATE1, STATE2, STATE3, STATE4, STATE5, STATE6, STATE7 }; ///< Type for STATE variable. The LaserDevice is always in one of these states
- /**
- * \brief Opens a connection to the device
- *
- * This may only be called if there is currently no connection to the device.
- * If OpenConnection() is successful, the object will change from UNCONNECTED state to a STATE state
- */
- virtual bool OpenConnection(std::string configurationFile);
-
- /**
- * \brief Closes the connection to the device
- *
- * This may only be called if there is currently a connection to the device. (e.g. object is in a STATE state)
- */
- virtual bool CloseConnection(); ///< Closes the connection with the device
-
- virtual std::string SendAndReceiveLine(const std::string* input, std::string* answer);
-
- virtual void StayAlive();
- virtual bool StartFlashing();
- virtual bool StopFlashing();
-
- virtual bool StartQswitching();
- virtual bool StopQswitching();
- virtual bool IsEmitting();
- virtual bool IsFlashing();
-
- virtual LaserState GetState();
-
- typedef mitk::SerialCommunication::PortNumber PortNumber; ///< Port number of the serial connection
- typedef mitk::SerialCommunication::BaudRate BaudRate; ///< Baud rate of the serial connection
- typedef mitk::SerialCommunication::DataBits DataBits; ///< Number of data bits used in the serial connection
- typedef mitk::SerialCommunication::Parity Parity; ///< Parity mode used in the serial connection
- typedef mitk::SerialCommunication::StopBits StopBits; ///< Number of stop bits used in the serial connection
- typedef mitk::SerialCommunication::HardwareHandshake HardwareHandshake; ///< Hardware handshake mode of the serial connection
-
- private:
- LaserState m_State; ///< current Laser state
- protected:
-
- QuantelLaser();
- virtual ~QuantelLaser();
-
- bool m_KeepAlive = false;
- bool m_FlashlampRunning = false;
- bool m_ShutterOpen = false;
- bool m_LaserEmission = false;
- void LoadResorceFile(std::string filename, std::string* lines);
-
- std::string m_DeviceName;///< Device Name
- PortNumber m_PortNumber; ///< COM Port Number
- BaudRate m_BaudRate; ///< COM Port Baud Rate
- DataBits m_DataBits; ///< Number of Data Bits per token
- Parity m_Parity; ///< Parity mode for communication
- StopBits m_StopBits; ///< number of stop bits per token
- HardwareHandshake m_HardwareHandshake; ///< use hardware handshake for serial port connection
-
- std::string m_XmlPumpLaserConfiguration;
- mitk::SerialCommunication::Pointer m_SerialCommunication; ///< serial communication interface
- std::thread m_StayAliveMessageThread;
- std::mutex m_SerialCommunicationMutex; ///< mutex for coordinated access of serial communication interface
- };
-} // namespace mitk
-
-#endif /* MITKQUANTELLASER_H_HEADER_INCLUDED */
diff --git a/Modules/PhotoacousticsLib/CMakeLists.txt b/Modules/PhotoacousticsLib/CMakeLists.txt
deleted file mode 100644
index 83269bc48d..0000000000
--- a/Modules/PhotoacousticsLib/CMakeLists.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-MITK_CREATE_MODULE(
- INCLUDE_DIRS PUBLIC include
- INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
- DEPENDS PUBLIC MitkAlgorithmsExt tinyxml
- PACKAGE_DEPENDS
- tinyxml Vigra
- PUBLIC ITK
-)
-
-add_subdirectory(MitkMCxyz)
-
-add_subdirectory(MitkTissueBatchGenerator)
-add_subdirectory(MitkPAPhantomGenerator)
-add_subdirectory(MitkSpectralUnmixing)
-
-add_subdirectory(test)
diff --git a/Modules/PhotoacousticsLib/MitkMCxyz/CMakeLists.txt b/Modules/PhotoacousticsLib/MitkMCxyz/CMakeLists.txt
deleted file mode 100644
index 8e528dc475..0000000000
--- a/Modules/PhotoacousticsLib/MitkMCxyz/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-OPTION(BUILD_PhotoacousticSimulationMCxyz "Build MiniApp for Photoacoustic Simulation Module (mcxyz)" OFF)
-
-IF(BUILD_PhotoacousticSimulationMCxyz)
- PROJECT( MitkMCxyz )
- mitk_create_executable(MCxyz
- DEPENDS MitkCommandLine MitkCore MitkPhotoacousticsLib
- PACKAGE_DEPENDS
- CPP_FILES MitkMCxyz.cpp)
-
- install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
- ENDIF()
diff --git a/Modules/PhotoacousticsLib/MitkMCxyz/MitkMCxyz.cpp b/Modules/PhotoacousticsLib/MitkMCxyz/MitkMCxyz.cpp
deleted file mode 100644
index 103c01275e..0000000000
--- a/Modules/PhotoacousticsLib/MitkMCxyz/MitkMCxyz.cpp
+++ /dev/null
@@ -1,1470 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-// Please retain the following copyright notice
-/******************************************************************
- * based on mcxyz.c Oct2014
- *
- * mcxyz.c, in ANSI Standard C programing language
- *
- * created 2010, 2012 by
- * Steven L. JACQUES
- * Ting LI
- * Oregon Health & Science University
- *
- *******************************************************************/
-
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
-#include <sstream>
-#include <stdlib.h>
-#include <time.h>
-#include <thread>
-#include <chrono>
-
-#include <vector>
-#include <iostream>
-
-#include "mitkCommandLineParser.h"
-#include "mitkIOUtil.h"
-#include "mitkImageCast.h"
-#include <mitkImage.h>
-#include <mitkImageReadAccessor.h>
-#include <mitkCoreServices.h>
-#include <mitkPropertyPersistence.h>
-#include <mitkPropertyPersistenceInfo.h>
-
-#include <mitkPAProbe.h>
-#include <mitkPALightSource.h>
-#include <mitkPAMonteCarloThreadHandler.h>
-
-#ifdef _WIN32
-#include <direct.h>
-#else
-#include <sys/types.h>
-#include <sys/stat.h>
-#endif
-
-#define ls 1.0E-7 /* Moving photon a little bit off the voxel face */
-#define PI 3.1415926
-#define ALIVE 1 /* if photon not yet terminated */
-#define DEAD 0 /* if photon is to be terminated */
-#define THRESHOLD 0.01 /* used in roulette */
-#define CHANCE 0.1 /* used in roulette */
-#define SQR(x) (x*x)
-#define SIGN(x) ((x)>=0 ? 1:-1)
-#define ONE_MINUS_COSZERO 1.0E-12 /* If 1-cos(theta) <= ONE_MINUS_COSZERO, fabs(theta) <= 1e-6 rad. */
- /* If 1+cos(theta) <= ONE_MINUS_COSZERO, fabs(PI-theta) <= 1e-6 rad. */
-
- /* Struct for storing x,y and z coordinates */
-struct Location
-{
- int x, y, z;
- double absorb;
-};
-
-struct Location initLocation(int x, int y, int z, double absorb)
-{
- struct Location loc;
- loc.x = x;
- loc.y = y;
- loc.z = z;
- loc.absorb = absorb;
- return loc;
-}
-
-class DetectorVoxel
-{
-public:
- Location location;
- std::vector<Location>* recordedPhotonRoute = new std::vector<Location>();
- double* fluenceContribution;
- double m_PhotonNormalizationValue;
- long m_NumberPhotonsCurrent;
-
- DetectorVoxel(Location location, long totalNumberOfVoxels, double photonNormalizationValue)
- {
- this->location = location;
- this->fluenceContribution = (double *)malloc(totalNumberOfVoxels * sizeof(double));
- for (int j = 0; j < totalNumberOfVoxels; j++) fluenceContribution[j] = 0; // ensure fluenceContribution[] starts empty.
- m_NumberPhotonsCurrent = 0;
- m_PhotonNormalizationValue = photonNormalizationValue;
- }
-};
-
-bool verbose(false);
-
-class InputValues
-{
-private:
- std::string inputFilename;
- int tissueIterator;
- long long ix, iy, iz;
-public:
- int mcflag, launchflag, boundaryflag;
- double xfocus, yfocus, zfocus;
- double ux0, uy0, uz0;
- double radius;
- double waist;
- double xs, ys, zs; /* launch position */
- int Nx, Ny, Nz, numberOfTissueTypes; /* # of bins */
-
- char* tissueType;
- double* muaVector;
- double* musVector;
- double* gVector;
- double* normalizationVector;
-
- double xSpacing, ySpacing, zSpacing;
- double simulationTimeFromFile;
- long long Nphotons;
- long totalNumberOfVoxels;
- double* totalFluence;
- std::string myname;
- DetectorVoxel* detectorVoxel;
- mitk::Image::Pointer m_inputImage;
- mitk::Image::Pointer m_normalizationImage;
-
- InputValues()
- {
- tissueType = nullptr;
- muaVector = nullptr;
- musVector = nullptr;
- gVector = nullptr;
- detectorVoxel = nullptr;
- normalizationVector = nullptr;
-
- mcflag = 0;
- launchflag = 0;
- boundaryflag = 0;
- }
-
- double GetNormalizationValue(int x, int y, int z)
- {
- if (normalizationVector)
- return normalizationVector[z*Ny*Nx + x*Ny + y];
- else
- return 1;
- }
-
- void LoadValues(std::string localInputFilename, float yOffset, std::string normalizationFilename, bool simulatePVFC)
- {
- inputFilename = localInputFilename;
- try
- {
- if (verbose) std::cout << "Loading input image..." << std::endl;
- m_inputImage = mitk::IOUtil::Load<mitk::Image>(inputFilename);
- if (verbose) std::cout << "Loading input image... [Done]" << std::endl;
- }
- catch (...)
- {
- if (verbose) std::cout << "No .nrrd file found ... switching to legacy mode." << std::endl;
- }
-
- try
- {
- if (simulatePVFC && !normalizationFilename.empty())
- m_normalizationImage = mitk::IOUtil::Load<mitk::Image>(normalizationFilename);
- }
- catch (...)
- {
- if (verbose) std::cout << "No normalization .nrrd file found ... will not normalize PVFC" << std::endl;
- }
-
- if (m_normalizationImage.IsNotNull())
- {
- mitk::ImageReadAccessor readAccess3(m_normalizationImage, m_normalizationImage->GetVolumeData(0));
- normalizationVector = (double *)readAccess3.GetData();
- }
-
- if (m_inputImage.IsNotNull()) // load stuff from nrrd file
- {
- simulationTimeFromFile = 0;
-
- Nx = m_inputImage->GetDimensions()[1];
- Ny = m_inputImage->GetDimensions()[0];
- Nz = m_inputImage->GetDimensions()[2];
-
- xSpacing = m_inputImage->GetGeometry(0)->GetSpacing()[0];
- ySpacing = m_inputImage->GetGeometry(0)->GetSpacing()[1];
- zSpacing = m_inputImage->GetGeometry(0)->GetSpacing()[2];
-
- mcflag = std::stoi(m_inputImage->GetProperty("mcflag")->GetValueAsString().c_str()); // mcflag, 0 = uniform, 1 = Gaussian, 2 = iso-pt, 4 = monospectral fraunhofer setup
- launchflag = std::stoi(m_inputImage->GetProperty("launchflag")->GetValueAsString().c_str());// 0 = let mcxyz calculate trajectory, 1 = manually set launch vector
- boundaryflag = std::stoi(m_inputImage->GetProperty("boundaryflag")->GetValueAsString().c_str());// 0 = no boundaries, 1 = escape at boundaries, 2 = escape at surface only
-
- xs = std::stod(m_inputImage->GetProperty("launchPointX")->GetValueAsString().c_str());
- ys = std::stod(m_inputImage->GetProperty("launchPointY")->GetValueAsString().c_str()) + yOffset;
- zs = std::stod(m_inputImage->GetProperty("launchPointZ")->GetValueAsString().c_str());
-
- xfocus = std::stod(m_inputImage->GetProperty("focusPointX")->GetValueAsString().c_str());
- yfocus = std::stod(m_inputImage->GetProperty("focusPointY")->GetValueAsString().c_str());
- zfocus = std::stod(m_inputImage->GetProperty("focusPointZ")->GetValueAsString().c_str());
-
- ux0 = std::stod(m_inputImage->GetProperty("trajectoryVectorX")->GetValueAsString().c_str());
- uy0 = std::stod(m_inputImage->GetProperty("trajectoryVectorY")->GetValueAsString().c_str());
- uz0 = std::stod(m_inputImage->GetProperty("trajectoryVectorZ")->GetValueAsString().c_str());
-
- radius = std::stod(m_inputImage->GetProperty("radius")->GetValueAsString().c_str());
- waist = std::stod(m_inputImage->GetProperty("waist")->GetValueAsString().c_str());
-
- totalNumberOfVoxels = Nx*Ny*Nz;
- if (verbose) std::cout << totalNumberOfVoxels << " = sizeof totalNumberOfVoxels" << std::endl;
-
- muaVector = (double *)malloc(totalNumberOfVoxels * sizeof(double)); /* tissue structure */
- musVector = (double *)malloc(totalNumberOfVoxels * sizeof(double)); /* tissue structure */
- gVector = (double *)malloc(totalNumberOfVoxels * sizeof(double)); /* tissue structure */
-
- mitk::ImageReadAccessor readAccess0(m_inputImage, m_inputImage->GetVolumeData(0));
- muaVector = (double *)readAccess0.GetData();
- mitk::ImageReadAccessor readAccess1(m_inputImage, m_inputImage->GetVolumeData(1));
- musVector = (double *)readAccess1.GetData();
- mitk::ImageReadAccessor readAccess2(m_inputImage, m_inputImage->GetVolumeData(2));
- gVector = (double *)readAccess2.GetData();
- }
- else
- {
- mitkThrow() << "No longer support loading of binary tissue files.";
- }
- }
-};
-
-class ReturnValues
-{
-private:
- long i1 = 0, i2 = 31; // used Random Generator
- long ma[56]; // used Random Generator /* ma[0] is not used. */
- long mj, mk;
- short i, ii;
-public:
- long long Nphotons;
- double* totalFluence;
- std::string myname;
- DetectorVoxel* detectorVoxel;
-
- ReturnValues()
- {
- detectorVoxel = nullptr;
- Nphotons = 0;
- totalFluence = nullptr;
- }
-
- /* SUBROUTINES */
-
- /**************************************************************************
- * RandomGen
- * A random number generator that generates uniformly
- * distributed random numbers between 0 and 1 inclusive.
- * The algorithm is based on:
- * W.H. Press, S.A. Teukolsky, W.T. Vetterling, and B.P.
- * Flannery, "Numerical Recipes in C," Cambridge University
- * Press, 2nd edition, (1992).
- * and
- * D.E. Knuth, "Seminumerical Algorithms," 2nd edition, vol. 2
- * of "The Art of Computer Programming", Addison-Wesley, (1981).
- *
- * When Type is 0, sets Seed as the seed. Make sure 0<Seed<32000.
- * When Type is 1, returns a random number.
- * When Type is 2, gets the status of the generator.
- * When Type is 3, restores the status of the generator.
- *
- * The status of the generator is represented by Status[0..56].
- *
- * Make sure you initialize the seed before you get random
- * numbers.
- ****/
-#define MBIG 1000000000
-#define MSEED 161803398
-#define MZ 0
-#define FAC 1.0E-9
-
- double RandomGen(char Type, long Seed, long *Status) {
- if (Type == 0) { /* set seed. */
- if (verbose) std::cout << "Initialized random generator " << this << " with seed: " << Seed << std::endl;
- mj = MSEED - (Seed < 0 ? -Seed : Seed);
- mj %= MBIG;
- ma[55] = mj;
- mk = 1;
- for (i = 1; i <= 54; i++) {
- ii = (21 * i) % 55;
- ma[ii] = mk;
- mk = mj - mk;
- if (mk < MZ)
- mk += MBIG;
- mj = ma[ii];
- }
- for (ii = 1; ii <= 4; ii++)
- for (i = 1; i <= 55; i++) {
- ma[i] -= ma[1 + (i + 30) % 55];
- if (ma[i] < MZ)
- ma[i] += MBIG;
- }
- i1 = 0;
- i2 = 31;
- }
- else if (Type == 1) { /* get a number. */
- if (++i1 == 56)
- i1 = 1;
- if (++i2 == 56)
- i2 = 1;
- mj = ma[i1] - ma[i2];
- if (mj < MZ)
- mj += MBIG;
- ma[i1] = mj;
- return (mj * FAC);
- }
- else if (Type == 2) { /* get status. */
- for (i = 0; i < 55; i++)
- Status[i] = ma[i + 1];
- Status[55] = i1;
- Status[56] = i2;
- }
- else if (Type == 3) { /* restore status. */
- for (i = 0; i < 55; i++)
- ma[i + 1] = Status[i];
- i1 = Status[55];
- i2 = Status[56];
- }
- else
- puts("Wrong parameter to RandomGen().");
- return (0);
- }
-#undef MBIG
-#undef MSEED
-#undef MZ
-#undef FAC
-
- /***********************************************************
- * Determine if the two position are located in the same voxel
- * Returns 1 if same voxel, 0 if not same voxel.
- ****/
- bool SameVoxel(double x1, double y1, double z1, double x2, double y2, double z2, double dx, double dy, double dz)
- {
- double xmin = min2((floor)(x1 / dx), (floor)(x2 / dx))*dx;
- double ymin = min2((floor)(y1 / dy), (floor)(y2 / dy))*dy;
- double zmin = min2((floor)(z1 / dz), (floor)(z2 / dz))*dz;
- double xmax = xmin + dx;
- double ymax = ymin + dy;
- double zmax = zmin + dz;
- bool sv = 0;
-
- sv = (x1 <= xmax && x2 <= xmax && y1 <= ymax && y2 <= ymax && z1 < zmax && z2 <= zmax);
- return (sv);
- }
-
- /***********************************************************
- * max2
- ****/
- double max2(double a, double b) {
- double m;
- if (a > b)
- m = a;
- else
- m = b;
- return m;
- }
-
- /***********************************************************
- * min2
- ****/
- double min2(double a, double b) {
- double m;
- if (a >= b)
- m = b;
- else
- m = a;
- return m;
- }
- /***********************************************************
- * min3
- ****/
- double min3(double a, double b, double c) {
- double m;
- if (a <= min2(b, c))
- m = a;
- else if (b <= min2(a, c))
- m = b;
- else
- m = c;
- return m;
- }
-
- /********************
- * my version of FindVoxelFace for no scattering.
- * s = ls + FindVoxelFace2(x,y,z, tempx, tempy, tempz, dx, dy, dz, ux, uy, uz);
- ****/
- double FindVoxelFace2(double x1, double y1, double z1, double /*x2*/, double /*y2*/, double /*z2*/, double dx, double dy, double dz, double ux, double uy, double uz)
- {
- int ix1 = floor(x1 / dx);
- int iy1 = floor(y1 / dy);
- int iz1 = floor(z1 / dz);
-
- int ix2, iy2, iz2;
- if (ux >= 0)
- ix2 = ix1 + 1;
- else
- ix2 = ix1;
-
- if (uy >= 0)
- iy2 = iy1 + 1;
- else
- iy2 = iy1;
-
- if (uz >= 0)
- iz2 = iz1 + 1;
- else
- iz2 = iz1;
-
- double xs = fabs((ix2*dx - x1) / ux);
- double ys = fabs((iy2*dy - y1) / uy);
- double zs = fabs((iz2*dz - z1) / uz);
-
- double s = min3(xs, ys, zs);
-
- return s;
- }
-
- /***********************************************************
- * FRESNEL REFLECTANCE
- * Computes reflectance as photon passes from medium 1 to
- * medium 2 with refractive indices n1,n2. Incident
- * angle a1 is specified by cosine value ca1 = cos(a1).
- * Program returns value of transmitted angle a1 as
- * value in *ca2_Ptr = cos(a2).
- ****/
- double RFresnel(double n1, /* incident refractive index.*/
- double n2, /* transmit refractive index.*/
- double ca1, /* cosine of the incident */
- /* angle a1, 0<a1<90 degrees. */
- double *ca2_Ptr) /* pointer to the cosine */
-/* of the transmission */
-/* angle a2, a2>0. */
- {
- double r;
-
- if (n1 == n2) { /** matched boundary. **/
- *ca2_Ptr = ca1;
- r = 0.0;
- }
- else if (ca1 > (1.0 - 1.0e-12)) { /** normal incidence. **/
- *ca2_Ptr = ca1;
- r = (n2 - n1) / (n2 + n1);
- r *= r;
- }
- else if (ca1 < 1.0e-6) { /** very slanted. **/
- *ca2_Ptr = 0.0;
- r = 1.0;
- }
- else { /** general. **/
- double sa1, sa2; /* sine of incident and transmission angles. */
- double ca2; /* cosine of transmission angle. */
- sa1 = sqrt(1 - ca1*ca1);
- sa2 = n1*sa1 / n2;
- if (sa2 >= 1.0) {
- /* double check for total internal reflection. */
- *ca2_Ptr = 0.0;
- r = 1.0;
- }
- else {
- double cap, cam; /* cosines of sum ap or diff am of the two */
- /* angles: ap = a1 + a2, am = a1 - a2. */
- double sap, sam; /* sines. */
- *ca2_Ptr = ca2 = sqrt(1 - sa2*sa2);
- cap = ca1*ca2 - sa1*sa2; /* c+ = cc - ss. */
- cam = ca1*ca2 + sa1*sa2; /* c- = cc + ss. */
- sap = sa1*ca2 + ca1*sa2; /* s+ = sc + cs. */
- sam = sa1*ca2 - ca1*sa2; /* s- = sc - cs. */
- r = 0.5*sam*sam*(cam*cam + cap*cap) / (sap*sap*cam*cam);
- /* rearranged for speed. */
- }
- }
- return(r);
- } /******** END SUBROUTINE **********/
-
- /***********************************************************
- * the boundary is the face of some voxel
- * find the the photon's hitting position on the nearest face of the voxel and update the step size.
- ****/
- double FindVoxelFace(double x1, double y1, double z1, double x2, double y2, double z2, double dx, double dy, double dz, double ux, double uy, double uz)
- {
- double x_1 = x1 / dx;
- double y_1 = y1 / dy;
- double z_1 = z1 / dz;
- double x_2 = x2 / dx;
- double y_2 = y2 / dy;
- double z_2 = z2 / dz;
- double fx_1 = floor(x_1);
- double fy_1 = floor(y_1);
- double fz_1 = floor(z_1);
- double fx_2 = floor(x_2);
- double fy_2 = floor(y_2);
- double fz_2 = floor(z_2);
- double x = 0, y = 0, z = 0, x0 = 0, y0 = 0, z0 = 0, s = 0;
-
- if ((fx_1 != fx_2) && (fy_1 != fy_2) && (fz_1 != fz_2)) { //#10
- fx_2 = fx_1 + SIGN(fx_2 - fx_1);//added
- fy_2 = fy_1 + SIGN(fy_2 - fy_1);//added
- fz_2 = fz_1 + SIGN(fz_2 - fz_1);//added
-
- x = (max2(fx_1, fx_2) - x_1) / ux;
- y = (max2(fy_1, fy_2) - y_1) / uy;
- z = (max2(fz_1, fz_2) - z_1) / uz;
- if (x == min3(x, y, z)) {
- x0 = max2(fx_1, fx_2);
- y0 = (x0 - x_1) / ux*uy + y_1;
- z0 = (x0 - x_1) / ux*uz + z_1;
- }
- else if (y == min3(x, y, z)) {
- y0 = max2(fy_1, fy_2);
- x0 = (y0 - y_1) / uy*ux + x_1;
- z0 = (y0 - y_1) / uy*uz + z_1;
- }
- else {
- z0 = max2(fz_1, fz_2);
- y0 = (z0 - z_1) / uz*uy + y_1;
- x0 = (z0 - z_1) / uz*ux + x_1;
- }
- }
- else if ((fx_1 != fx_2) && (fy_1 != fy_2)) { //#2
- fx_2 = fx_1 + SIGN(fx_2 - fx_1);//added
- fy_2 = fy_1 + SIGN(fy_2 - fy_1);//added
- x = (max2(fx_1, fx_2) - x_1) / ux;
- y = (max2(fy_1, fy_2) - y_1) / uy;
- if (x == min2(x, y)) {
- x0 = max2(fx_1, fx_2);
- y0 = (x0 - x_1) / ux*uy + y_1;
- z0 = (x0 - x_1) / ux*uz + z_1;
- }
- else {
- y0 = max2(fy_1, fy_2);
- x0 = (y0 - y_1) / uy*ux + x_1;
- z0 = (y0 - y_1) / uy*uz + z_1;
- }
- }
- else if ((fy_1 != fy_2) && (fz_1 != fz_2)) { //#3
- fy_2 = fy_1 + SIGN(fy_2 - fy_1);//added
- fz_2 = fz_1 + SIGN(fz_2 - fz_1);//added
- y = (max2(fy_1, fy_2) - y_1) / uy;
- z = (max2(fz_1, fz_2) - z_1) / uz;
- if (y == min2(y, z)) {
- y0 = max2(fy_1, fy_2);
- x0 = (y0 - y_1) / uy*ux + x_1;
- z0 = (y0 - y_1) / uy*uz + z_1;
- }
- else {
- z0 = max2(fz_1, fz_2);
- x0 = (z0 - z_1) / uz*ux + x_1;
- y0 = (z0 - z_1) / uz*uy + y_1;
- }
- }
- else if ((fx_1 != fx_2) && (fz_1 != fz_2)) { //#4
- fx_2 = fx_1 + SIGN(fx_2 - fx_1);//added
- fz_2 = fz_1 + SIGN(fz_2 - fz_1);//added
- x = (max2(fx_1, fx_2) - x_1) / ux;
- z = (max2(fz_1, fz_2) - z_1) / uz;
- if (x == min2(x, z)) {
- x0 = max2(fx_1, fx_2);
- y0 = (x0 - x_1) / ux*uy + y_1;
- z0 = (x0 - x_1) / ux*uz + z_1;
- }
- else {
- z0 = max2(fz_1, fz_2);
- x0 = (z0 - z_1) / uz*ux + x_1;
- y0 = (z0 - z_1) / uz*uy + y_1;
- }
- }
- else if (fx_1 != fx_2) { //#5
- fx_2 = fx_1 + SIGN(fx_2 - fx_1);//added
- x0 = max2(fx_1, fx_2);
- y0 = (x0 - x_1) / ux*uy + y_1;
- z0 = (x0 - x_1) / ux*uz + z_1;
- }
- else if (fy_1 != fy_2) { //#6
- fy_2 = fy_1 + SIGN(fy_2 - fy_1);//added
- y0 = max2(fy_1, fy_2);
- x0 = (y0 - y_1) / uy*ux + x_1;
- z0 = (y0 - y_1) / uy*uz + z_1;
- }
- else { //#7
- z0 = max2(fz_1, fz_2);
- fz_2 = fz_1 + SIGN(fz_2 - fz_1);//added
- x0 = (z0 - z_1) / uz*ux + x_1;
- y0 = (z0 - z_1) / uz*uy + y_1;
- }
- //s = ( (x0-fx_1)*dx + (y0-fy_1)*dy + (z0-fz_1)*dz )/3;
- //s = sqrt( SQR((x0-x_1)*dx) + SQR((y0-y_1)*dy) + SQR((z0-z_1)*dz) );
- //s = sqrt(SQR(x0-x_1)*SQR(dx) + SQR(y0-y_1)*SQR(dy) + SQR(z0-z_1)*SQR(dz));
- s = sqrt(SQR((x0 - x_1)*dx) + SQR((y0 - y_1)*dy) + SQR((z0 - z_1)*dz));
- return (s);
- }
-};
-
-/* DECLARE FUNCTIONS */
-
-void runMonteCarlo(InputValues* inputValues, ReturnValues* returnValue, int thread, mitk::pa::MonteCarloThreadHandler::Pointer threadHandler);
-
-int detector_x = -1;
-int detector_z = -1;
-bool interpretAsTime = true;
-bool simulatePVFC = false;
-int requestedNumberOfPhotons = 100000;
-float requestedSimulationTime = 0; // in minutes
-int concurentThreadsSupported = -1;
-float yOffset = 0; // in mm
-bool saveLegacy = false;
-std::string normalizationFilename;
-std::string inputFilename;
-std::string outputFilename;
-
-mitk::pa::Probe::Pointer m_PhotoacousticProbe;
-
-int main(int argc, char * argv[]) {
- mitkCommandLineParser parser;
- // set general information
- parser.setCategory("MITK-Photoacoustics");
- parser.setTitle("Mitk MCxyz");
- parser.setDescription("Runs Monte Carlo simulations on inputed tissues.");
- parser.setContributor("CAI, DKFZ based on code by Jacques and Li");
-
- // how should arguments be prefixed
- parser.setArgumentPrefix("--", "-");
- // add each argument, unless specified otherwise each argument is optional
- // see mitkCommandLineParser::addArgument for more information
- parser.beginGroup("Required I/O parameters");
- parser.addArgument(
- "input", "i", mitkCommandLineParser::File,
- "Input tissue file", "input tissue file (*.nrrd)",
- us::Any(), false, false, false, mitkCommandLineParser::Input);
- parser.addArgument(
- "output", "o", mitkCommandLineParser::File,
- "Output fluence file", "where to save the simulated fluence (*.nrrd)",
- us::Any(), false, false, false, mitkCommandLineParser::Output);
- parser.endGroup();
- parser.beginGroup("Optional parameters");
- parser.addArgument(
- "verbose", "v", mitkCommandLineParser::Bool,
- "Verbose Output", "Whether to produce verbose, or rather debug output");
- parser.addArgument(
- "detector-x", "dx", mitkCommandLineParser::Int,
- "Detector voxel x position", "Determines the x position of the detector voxel (default: -1 = dont use detector voxel)", -1);
- parser.addArgument(
- "detector-z", "dz", mitkCommandLineParser::Int,
- "Detector voxel z position", "Determines the z position of the detector voxel (default: -1 = dont use detector voxel)", -1);
- parser.addArgument(
- "number-of-photons", "n", mitkCommandLineParser::Int,
- "Number of photons", "Specifies the number of photons (default: 100000). Simulation stops after that number. Use -t --timer to define a timer instead");
- parser.addArgument(
- "timer", "t", mitkCommandLineParser::Float,
- "Simulation time in min", "Specifies the amount of time for simutation (default: 0). Simulation stops after that number of minutes. -n --number-of-photons is the override and default behavior and defines the maximum number of photons instead. If no simulation time or number of photons is specified the file time is taken.");
- parser.addArgument(
- "y-offset", "yo", mitkCommandLineParser::Float,
- "Probe Y-Offset in mm", "Specifies an offset of the photoacoustic probe in the y direction depending on the initial probe position (default: 0) in mm.");
- parser.addArgument(
- "jobs", "j", mitkCommandLineParser::Int,
- "Number of jobs", "Specifies the number of jobs for simutation (default: -1 which starts as many jobs as supported).");
- parser.addArgument(
- "probe-xml", "p", mitkCommandLineParser::File,
- "Xml definition of the probe", "Specifies the absolute path of the location of the xml definition file of the probe design.", us::Any(), true, false, false, mitkCommandLineParser::Input);
- parser.addArgument("normalization-file", "nf", mitkCommandLineParser::File,
- "Input normalization file", "The input normalization file is used for normalization of the number of photons in the PVFC calculations.", us::Any(), true, false, false, mitkCommandLineParser::Input);
- parser.endGroup();
-
- // parse arguments, this method returns a mapping of long argument names and their values
- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
- if (parsedArgs.size() == 0)
- return EXIT_FAILURE;
- // parse, cast and set required arguments
- inputFilename = us::any_cast<std::string>(parsedArgs["input"]);
- // strip ending
- inputFilename = inputFilename.substr(0, inputFilename.find("_H.mci"));
- inputFilename = inputFilename.substr(0, inputFilename.find("_T.bin"));
-
- outputFilename = us::any_cast<std::string>(parsedArgs["output"]);
- // add .nrrd if not there
- std::string suffix = ".nrrd";
- if (outputFilename.compare(outputFilename.size() - suffix.size(), suffix.size(), suffix) != 0)
- outputFilename = outputFilename + suffix;
-
- // default values for optional arguments
- // parse, cast and set optional arguments if given
- if (parsedArgs.count("verbose"))
- {
- verbose = us::any_cast<bool>(parsedArgs["verbose"]);
- }
- if (parsedArgs.count("detector-x"))
- {
- detector_x = us::any_cast<int>(parsedArgs["detector-x"]);
- }
- if (parsedArgs.count("detector-z"))
- {
- detector_z = us::any_cast<int>(parsedArgs["detector-z"]);
- }
- if (parsedArgs.count("timer"))
- {
- requestedSimulationTime = us::any_cast<float>(parsedArgs["timer"]);
- if (requestedSimulationTime > 0) interpretAsTime = true;
- }
- if (parsedArgs.count("y-offset"))
- {
- yOffset = us::any_cast<float>(parsedArgs["y-offset"]);
- }
- if (parsedArgs.count("number-of-photons"))
- {
- requestedNumberOfPhotons = us::any_cast<int>(parsedArgs["number-of-photons"]);
- if (requestedNumberOfPhotons > 0) interpretAsTime = false;
- }
- if (parsedArgs.count("jobs"))
- {
- concurentThreadsSupported = us::any_cast<int>(parsedArgs["jobs"]);
- }
- if (parsedArgs.count("probe-xml"))
- {
- std::string inputXmlProbeDesign = us::any_cast<std::string>(parsedArgs["probe-xml"]);
- m_PhotoacousticProbe = mitk::pa::Probe::New(inputXmlProbeDesign, verbose);
- if (!m_PhotoacousticProbe->IsValid())
- {
- std::cerr << "Xml File was not valid. Simulation failed." << std::endl;
- return EXIT_FAILURE;
- }
- }
- if (parsedArgs.count("normalization-file"))
- {
- normalizationFilename = us::any_cast<std::string>(parsedArgs["normalization-file"]);
- }
-
- if (concurentThreadsSupported == 0 || concurentThreadsSupported == -1)
- {
- concurentThreadsSupported = std::thread::hardware_concurrency();
- if (concurentThreadsSupported == 0)
- {
- std::cout << "Could not determine number of available threads. Launching only one." << std::endl;
- concurentThreadsSupported = 1;
- }
- }
-
- if (detector_x != -1 && detector_z != -1)
- {
- if (verbose)
- std::cout << "Performing PVFC calculation for x=" << detector_x << " and z=" << detector_z << std::endl;
- simulatePVFC = true;
- }
- else
- {
- if (verbose)
- std::cout << "Will not perform PVFC calculation due to x=" << detector_x << " and/or z=" << detector_z << std::endl;
- }
-
- InputValues allInput = InputValues();
- allInput.LoadValues(inputFilename, yOffset, normalizationFilename, simulatePVFC);
-
- std::vector<ReturnValues> allValues(concurentThreadsSupported);
- auto* threads = new std::thread[concurentThreadsSupported];
-
- for (long i = 0; i < concurentThreadsSupported; i++)
- {
- auto* tmp = new ReturnValues();
- allValues.push_back(*tmp);
- }
-
- if (verbose) std::cout << "Initializing MonteCarloThreadHandler" << std::endl;
-
- long timeMetric;
- if (interpretAsTime)
- {
- if (requestedSimulationTime < mitk::eps)
- requestedSimulationTime = allInput.simulationTimeFromFile;
-
- timeMetric = requestedSimulationTime * 60 * 1000;
- }
- else
- {
- timeMetric = requestedNumberOfPhotons;
- }
-
- mitk::pa::MonteCarloThreadHandler::Pointer threadHandler = mitk::pa::MonteCarloThreadHandler::New(timeMetric, interpretAsTime);
-
- if (simulatePVFC)
- threadHandler->SetPackageSize(1000);
-
- if (verbose) std::cout << "\nStarting simulation ...\n" << std::endl;
-
- auto simulationStartTime = std::chrono::system_clock::now();
-
- for (int i = 0; i < concurentThreadsSupported; i++)
- {
- threads[i] = std::thread(runMonteCarlo, &allInput, &allValues[i], (i + 1), threadHandler);
- }
-
- for (int i = 0; i < concurentThreadsSupported; i++)
- {
- threads[i].join();
- }
-
- auto simulationFinishTime = std::chrono::system_clock::now();
- auto simulationTimeElapsed = simulationFinishTime - simulationStartTime;
-
- if (verbose) std::cout << "\n\nFinished simulation\n\n" << std::endl;
- std::cout << "total time for simulation: "
- << (int)std::chrono::duration_cast<std::chrono::seconds>(simulationTimeElapsed).count() << "sec " << std::endl;
-
- /**** SAVE
- Convert data to relative fluence rate [cm^-2] and save.
- *****/
-
- if (!simulatePVFC)
- {
- if (verbose) std::cout << "Allocating memory for normal simulation result ... ";
- auto* finalTotalFluence = (double *)malloc(allInput.totalNumberOfVoxels * sizeof(double));
- if (verbose) std::cout << "[OK]" << std::endl;
- if (verbose) std::cout << "Cleaning memory for normal simulation result ...";
- for (int i = 0; i < allInput.totalNumberOfVoxels; i++) {
- finalTotalFluence[i] = 0;
- }
- if (verbose) std::cout << "[OK]" << std::endl;
-
- if (verbose) std::cout << "Calculating resulting fluence ... ";
- double tdx = 0, tdy = 0, tdz = 0;
- long long tNphotons = 0;
- for (int t = 0; t < concurentThreadsSupported; t++)
- {
- tdx = allInput.xSpacing;
- tdy = allInput.ySpacing;
- tdz = allInput.zSpacing;
- tNphotons += allValues[t].Nphotons;
- for (int voxelNumber = 0; voxelNumber < allInput.totalNumberOfVoxels; voxelNumber++) {
- finalTotalFluence[voxelNumber] += allValues[t].totalFluence[voxelNumber];
- }
- }
- if (verbose) std::cout << "[OK]" << std::endl;
- std::cout << "total number of photons simulated: "
- << tNphotons << std::endl;
-
- // Normalize deposition (A) to yield fluence rate (F).
- double temp = tdx*tdy*tdz*tNphotons;
- for (int i = 0; i < allInput.totalNumberOfVoxels; i++) {
- finalTotalFluence[i] /= temp*allInput.muaVector[i];
- }
-
- if (verbose) std::cout << "Saving normal simulated fluence result to " << outputFilename << " ... ";
-
- mitk::Image::Pointer resultImage = mitk::Image::New();
- mitk::PixelType TPixel = mitk::MakeScalarPixelType<double>();
- auto* dimensionsOfImage = new unsigned int[3];
-
- // Copy dimensions
- dimensionsOfImage[0] = allInput.Ny;
- dimensionsOfImage[1] = allInput.Nx;
- dimensionsOfImage[2] = allInput.Nz;
-
- resultImage->Initialize(TPixel, 3, dimensionsOfImage);
-
- mitk::Vector3D spacing;
- spacing[0] = allInput.ySpacing;
- spacing[1] = allInput.xSpacing;
- spacing[2] = allInput.zSpacing;
- resultImage->SetSpacing(spacing);
- resultImage->SetImportVolume(finalTotalFluence, 0, 0, mitk::Image::CopyMemory);
-
- resultImage->GetPropertyList()->SetFloatProperty("y-offset", yOffset);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("y-offset"));
-
- mitk::IOUtil::Save(resultImage, outputFilename);
-
- if (verbose) std::cout << "[OK]" << std::endl;
-
- if (verbose)
- {
- std::cout << "x spacing = " << tdx << std::endl;
- std::cout << "y spacing = " << tdy << std::endl;
- std::cout << "z spacing = " << tdz << std::endl;
- std::cout << "total number of voxels = " << allInput.totalNumberOfVoxels << std::endl;
- std::cout << "number of photons = " << (int)tNphotons << std::endl;
- }
- }
- else // if simulate PVFC
- {
- if (verbose) std::cout << "Allocating memory for PVFC simulation result ... ";
- double* detectorFluence = ((double*)malloc(allInput.totalNumberOfVoxels * sizeof(double)));
- if (verbose) std::cout << "[OK]" << std::endl;
- if (verbose) std::cout << "Cleaning memory for PVFC simulation result ...";
- for (int i = 0; i < allInput.totalNumberOfVoxels; i++) {
- detectorFluence[i] = 0;
- }
- if (verbose) std::cout << "[OK]" << std::endl;
-
- if (verbose) std::cout << "Calculating resulting PVFC fluence ... ";
- double tdx = 0, tdy = 0, tdz = 0;
- long long tNphotons = 0;
- long pvfcPhotons = 0;
- for (int t = 0; t < concurentThreadsSupported; t++)
- {
- tdx = allInput.xSpacing;
- tdy = allInput.ySpacing;
- tdz = allInput.zSpacing;
- tNphotons += allValues[t].Nphotons;
- pvfcPhotons += allValues[t].detectorVoxel->m_NumberPhotonsCurrent;
- for (int voxelNumber = 0; voxelNumber < allInput.totalNumberOfVoxels; voxelNumber++) {
- detectorFluence[voxelNumber] +=
- allValues[t].detectorVoxel->fluenceContribution[voxelNumber];
- }
- }
- if (verbose) std::cout << "[OK]" << std::endl;
- std::cout << "total number of photons simulated: "
- << tNphotons << std::endl;
-
- // Normalize deposition (A) to yield fluence rate (F).
- double temp = tdx*tdy*tdz*tNphotons;
- for (int i = 0; i < allInput.totalNumberOfVoxels; i++) {
- detectorFluence[i] /= temp*allInput.muaVector[i];
- }
-
- if (verbose) std::cout << "Saving PVFC ...";
-
- std::stringstream detectorname("");
- double detectorX = allValues[0].detectorVoxel->location.x;
- double detectorY = allValues[0].detectorVoxel->location.y;
- double detectorZ = allValues[0].detectorVoxel->location.z;
- detectorname << detectorX << "," << detectorY << ","
- << detectorZ << "FluenceContribution.nrrd";
- // Save the binary file
- std::string outputFileBase = outputFilename.substr(0, outputFilename.find(".nrrd"));
- outputFilename = outputFileBase + "_p" + detectorname.str().c_str();
-
- mitk::Image::Pointer pvfcImage = mitk::Image::New();
- auto* dimensionsOfPvfcImage = new unsigned int[3];
-
- // Copy dimensions
- dimensionsOfPvfcImage[0] = allInput.Ny;
- dimensionsOfPvfcImage[1] = allInput.Nx;
- dimensionsOfPvfcImage[2] = allInput.Nz;
-
- pvfcImage->Initialize(mitk::MakeScalarPixelType<double>(), 3, dimensionsOfPvfcImage);
-
- mitk::Vector3D pvfcSpacing;
- pvfcSpacing[0] = allInput.ySpacing;
- pvfcSpacing[1] = allInput.xSpacing;
- pvfcSpacing[2] = allInput.zSpacing;
- pvfcImage->SetSpacing(pvfcSpacing);
- pvfcImage->SetImportVolume(detectorFluence, 0, 0, mitk::Image::CopyMemory);
-
- pvfcImage->GetPropertyList()->SetFloatProperty("detector-x", detectorX);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("detector-x"));
- pvfcImage->GetPropertyList()->SetFloatProperty("detector-y", detectorY);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("detector-y"));
- pvfcImage->GetPropertyList()->SetFloatProperty("detector-z", detectorZ);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("detector-z"));
- pvfcImage->GetPropertyList()->SetFloatProperty("normalization-factor", allValues[0].detectorVoxel->m_PhotonNormalizationValue);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("normalization-factor"));
- pvfcImage->GetPropertyList()->SetFloatProperty("simulated-photons", pvfcPhotons);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("simulated-photons"));
-
- mitk::IOUtil::Save(pvfcImage, outputFilename);
-
- if (verbose) std::cout << "[OK]" << std::endl;
-
- if (verbose)
- {
- std::cout << "x spacing = " << tdx << std::endl;
- std::cout << "y spacing = " << tdy << std::endl;
- std::cout << "z spacing = " << tdz << std::endl;
- std::cout << "total number of voxels = " << allInput.totalNumberOfVoxels << std::endl;
- std::cout << "number of photons = " << (int)tNphotons << std::endl;
- }
- }
-
- exit(EXIT_SUCCESS);
-} /* end of main */
-
-/* CORE FUNCTION */
-void runMonteCarlo(InputValues* inputValues, ReturnValues* returnValue, int thread, mitk::pa::MonteCarloThreadHandler::Pointer threadHandler)
-{
- if (verbose) std::cout << "Thread " << thread << ": Locking Mutex ..." << std::endl;
- if (verbose) std::cout << "[OK]" << std::endl;
- if (verbose) std::cout << "Initializing ... ";
-
- /* Propagation parameters */
- double x, y, z; /* photon position */
- double ux, uy, uz; /* photon trajectory as cosines */
- double uxx, uyy, uzz; /* temporary values used during SPIN */
- double s; /* step sizes. s = -log(RND)/mus [cm] */
- double sleft; /* dimensionless */
- double costheta; /* cos(theta) */
- double sintheta; /* sin(theta) */
- double cospsi; /* cos(psi) */
- double sinpsi; /* sin(psi) */
- double psi; /* azimuthal angle */
- long photonIterator = 0; /* current photon */
- double W; /* photon weight */
- double absorb; /* weighted deposited in a step due to absorption */
- short photon_status; /* flag = ALIVE=1 or DEAD=0 */
- bool sv; /* Are they in the same voxel? */
-
- /* dummy variables */
- double rnd; /* assigned random value 0-1 */
- double r, phi; /* dummy values */
- long i, j; /* dummy indices */
- double tempx, tempy, tempz; /* temporary variables, used during photon step. */
- int ix, iy, iz; /* Added. Used to track photons */
- double temp; /* dummy variable */
- int bflag; /* boundary flag: 0 = photon inside volume. 1 = outside volume */
- int CNT = 0;
-
- returnValue->totalFluence = (double *)malloc(inputValues->totalNumberOfVoxels * sizeof(double)); /* relative fluence rate [W/cm^2/W.delivered] */
-
- if (detector_x != -1 && detector_z != -1)
- {
- if (detector_x<0 || detector_x>inputValues->Nx)
- {
- std::cout << "Requested detector x position not valid. Needs to be >= 0 and <= " << inputValues->Nx << std::endl;
- exit(EXIT_FAILURE);
- }
- if (detector_z<1 || detector_z>inputValues->Nz)
- {
- std::cout << "Requested detector z position not valid. Needs to be > 0 and <= " << inputValues->Nz << std::endl;
- exit(EXIT_FAILURE);
- }
-
- double photonNormalizationValue = 1 / inputValues->GetNormalizationValue(detector_x, inputValues->Ny / 2, detector_z);
- returnValue->detectorVoxel = new DetectorVoxel(initLocation(detector_x, inputValues->Ny / 2, detector_z, 0), inputValues->totalNumberOfVoxels, photonNormalizationValue);
- }
-
- /**** ======================== MAJOR CYCLE ============================ *****/
-
- auto duration = std::chrono::system_clock::now().time_since_epoch();
- returnValue->RandomGen(0, (std::chrono::duration_cast<std::chrono::milliseconds>(duration).count() + thread) % 32000, nullptr); /* initiate with seed = 1, or any long integer. */
- for (j = 0; j < inputValues->totalNumberOfVoxels; j++) returnValue->totalFluence[j] = 0; // ensure F[] starts empty.
-
- /**** RUN Launch N photons, initializing each one before progation. *****/
-
- long photonsToSimulate = 0;
-
- do {
- photonsToSimulate = threadHandler->GetNextWorkPackage();
- if (returnValue->detectorVoxel != nullptr)
- {
- photonsToSimulate = photonsToSimulate * returnValue->detectorVoxel->m_PhotonNormalizationValue;
- }
-
- if (verbose)
- MITK_INFO << "Photons to simulate: " << photonsToSimulate;
-
- photonIterator = 0L;
-
- do {
- /**** LAUNCH Initialize photon position and trajectory. *****/
-
- photonIterator += 1; /* increment photon count */
- W = 1.0; /* set photon weight to one */
- photon_status = ALIVE; /* Launch an ALIVE photon */
- CNT = 0;
-
- /**** SET SOURCE* Launch collimated beam at x,y center.****/
- /****************************/
- /* Initial position. */
-
- if (m_PhotoacousticProbe.IsNotNull())
- {
- double rnd1 = -1;
- double rnd2 = -1;
- double rnd3 = -1;
- double rnd4 = -1;
- double rnd5 = -1;
- double rnd6 = -1;
- double rnd7 = -1;
- double rnd8 = -1;
-
- while ((rnd1 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- while ((rnd2 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- while ((rnd3 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- while ((rnd4 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- while ((rnd5 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- while ((rnd6 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- while ((rnd7 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- while ((rnd8 = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
-
- mitk::pa::LightSource::PhotonInformation info = m_PhotoacousticProbe->GetNextPhoton(rnd1, rnd2, rnd3, rnd4, rnd5, rnd6, rnd7, rnd8);
- x = info.xPosition;
- y = yOffset + info.yPosition;
- z = info.zPosition;
- ux = info.xAngle;
- uy = info.yAngle;
- uz = info.zAngle;
- if (verbose)
- std::cout << "Created photon at position (" << x << "|" << y << "|" << z << ") with angles (" << ux << "|" << uy << "|" << uz << ")." << std::endl;
- }
- else
- {
- /* trajectory */
- if (inputValues->launchflag == 1) // manually set launch
- {
- x = inputValues->xs;
- y = inputValues->ys;
- z = inputValues->zs;
- ux = inputValues->ux0;
- uy = inputValues->uy0;
- uz = inputValues->uz0;
- }
- else // use mcflag
- {
- if (inputValues->mcflag == 0) // uniform beam
- {
- // set launch point and width of beam
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0); // avoids rnd = 0
- r = inputValues->radius*sqrt(rnd); // radius of beam at launch point
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0); // avoids rnd = 0
- phi = rnd*2.0*PI;
- x = inputValues->xs + r*cos(phi);
- y = inputValues->ys + r*sin(phi);
- z = inputValues->zs;
- // set trajectory toward focus
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0); // avoids rnd = 0
- r = inputValues->waist*sqrt(rnd); // radius of beam at focus
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0); // avoids rnd = 0
- phi = rnd*2.0*PI;
-
- // !!!!!!!!!!!!!!!!!!!!!!! setting input values will braek
-
- inputValues->xfocus = r*cos(phi);
- inputValues->yfocus = r*sin(phi);
- temp = sqrt((x - inputValues->xfocus)*(x - inputValues->xfocus)
- + (y - inputValues->yfocus)*(y - inputValues->yfocus) + inputValues->zfocus*inputValues->zfocus);
- ux = -(x - inputValues->xfocus) / temp;
- uy = -(y - inputValues->yfocus) / temp;
- uz = sqrt(1 - ux*ux + uy*uy);
- }
- else if (inputValues->mcflag == 5) // Multispectral DKFZ prototype
- {
- // set launch point and width of beam
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
-
- //offset in x direction in cm (random)
- x = (rnd*2.5) - 1.25;
-
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- double b = ((rnd)-0.5);
- y = (b > 0 ? yOffset + 1.5 : yOffset - 1.5);
- z = 0.1;
- ux = 0;
-
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
-
- //Angle of beam in y direction
- uy = sin((rnd*0.42) - 0.21 + (b < 0 ? 1.0 : -1.0) * 0.436);
-
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
-
- // angle of beam in x direction
- ux = sin((rnd*0.42) - 0.21);
- uz = sqrt(1 - ux*ux - uy*uy);
- }
- else if (inputValues->mcflag == 4) // Monospectral prototype DKFZ
- {
- // set launch point and width of beam
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
-
- //offset in x direction in cm (random)
- x = (rnd*2.5) - 1.25;
-
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- double b = ((rnd)-0.5);
- y = (b > 0 ? yOffset + 0.83 : yOffset - 0.83);
- z = 0.1;
- ux = 0;
-
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
-
- //Angle of beam in y direction
- uy = sin((rnd*0.42) - 0.21 + (b < 0 ? 1.0 : -1.0) * 0.375);
-
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
-
- // angle of beam in x direction
- ux = sin((rnd*0.42) - 0.21);
- uz = sqrt(1 - ux*ux - uy*uy);
- }
- else { // isotropic pt source
- costheta = 1.0 - 2.0 * returnValue->RandomGen(1, 0, nullptr);
- sintheta = sqrt(1.0 - costheta*costheta);
- psi = 2.0 * PI * returnValue->RandomGen(1, 0, nullptr);
- cospsi = cos(psi);
- if (psi < PI)
- sinpsi = sqrt(1.0 - cospsi*cospsi);
- else
- sinpsi = -sqrt(1.0 - cospsi*cospsi);
- x = inputValues->xs;
- y = inputValues->ys;
- z = inputValues->zs;
- ux = sintheta*cospsi;
- uy = sintheta*sinpsi;
- uz = costheta;
- }
- } // end use mcflag
- }
- /****************************/
-
- /* Get tissue voxel properties of launchpoint.
- * If photon beyond outer edge of defined voxels,
- * the tissue equals properties of outermost voxels.
- * Therefore, set outermost voxels to infinite background value.
- */
- ix = (int)(inputValues->Nx / 2 + x / inputValues->xSpacing);
- iy = (int)(inputValues->Ny / 2 + y / inputValues->ySpacing);
- iz = (int)(z / inputValues->zSpacing);
- if (ix >= inputValues->Nx) ix = inputValues->Nx - 1;
- if (iy >= inputValues->Ny) iy = inputValues->Ny - 1;
- if (iz >= inputValues->Nz) iz = inputValues->Nz - 1;
- if (ix < 0) ix = 0;
- if (iy < 0) iy = 0;
- if (iz < 0) iz = 0;
- /* Get the tissue type of located voxel */
- i = (long)(iz*inputValues->Ny*inputValues->Nx + ix*inputValues->Ny + iy);
-
- bflag = 1; // initialize as 1 = inside volume, but later check as photon propagates.
-
- if (returnValue->detectorVoxel != nullptr)
- returnValue->detectorVoxel->recordedPhotonRoute->clear();
-
- /* HOP_DROP_SPIN_CHECK
- Propagate one photon until it dies as determined by ROULETTE.
- *******/
- do {
- /**** HOP
- Take step to new position
- s = dimensionless stepsize
- x, uy, uz are cosines of current photon trajectory
- *****/
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0); /* yields 0 < rnd <= 1 */
- sleft = -log(rnd); /* dimensionless step */
- CNT += 1;
-
- do { // while sleft>0
- s = sleft / inputValues->musVector[i]; /* Step size [cm].*/
- tempx = x + s*ux; /* Update positions. [cm] */
- tempy = y + s*uy;
- tempz = z + s*uz;
-
- sv = returnValue->SameVoxel(x, y, z, tempx, tempy, tempz, inputValues->xSpacing, inputValues->ySpacing, inputValues->zSpacing);
- if (sv) /* photon in same voxel */
- {
- x = tempx; /* Update positions. */
- y = tempy;
- z = tempz;
-
- /**** DROP
- Drop photon weight (W) into local bin.
- *****/
-
- absorb = W*(1 - exp(-inputValues->muaVector[i] * s)); /* photon weight absorbed at this step */
- W -= absorb; /* decrement WEIGHT by amount absorbed */
- // If photon within volume of heterogeneity, deposit energy in F[].
- // Normalize F[] later, when save output.
- if (bflag)
- {
- i = (long)(iz*inputValues->Ny*inputValues->Nx + ix*inputValues->Ny + iy);
- returnValue->totalFluence[i] += absorb;
- // only save data if blag==1, i.e., photon inside simulation cube
-
- //For each detectorvoxel
- if (returnValue->detectorVoxel != nullptr)
- {
- //Add photon position to the recorded photon route
- returnValue->detectorVoxel->recordedPhotonRoute->push_back(initLocation(ix, iy, iz, absorb));
-
- //If the photon is currently at the detector position
- if ((returnValue->detectorVoxel->location.x == ix)
- && ((returnValue->detectorVoxel->location.y == iy)
- || (returnValue->detectorVoxel->location.y - 1 == iy))
- && (returnValue->detectorVoxel->location.z == iz))
- {
- //For each voxel in the recorded photon route
- for (unsigned int routeIndex = 0; routeIndex < returnValue->detectorVoxel->recordedPhotonRoute->size(); routeIndex++)
- {
- //increment the fluence contribution at that particular position
- i = (long)(returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).z*inputValues->Ny*inputValues->Nx
- + returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).x*inputValues->Ny
- + returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).y);
- returnValue->detectorVoxel->fluenceContribution[i] += returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).absorb;
- }
-
- //Clear the recorded photon route
- returnValue->detectorVoxel->m_NumberPhotonsCurrent++;
- returnValue->detectorVoxel->recordedPhotonRoute->clear();
- }
- }
- }
-
- /* Update sleft */
- sleft = 0; /* dimensionless step remaining */
- }
- else /* photon has crossed voxel boundary */
- {
- /* step to voxel face + "littlest step" so just inside new voxel. */
- s = ls + returnValue->FindVoxelFace2(x, y, z, tempx, tempy, tempz, inputValues->xSpacing, inputValues->ySpacing, inputValues->zSpacing, ux, uy, uz);
-
- /**** DROP
- Drop photon weight (W) into local bin.
- *****/
- absorb = W*(1 - exp(-inputValues->muaVector[i] * s)); /* photon weight absorbed at this step */
- W -= absorb; /* decrement WEIGHT by amount absorbed */
- // If photon within volume of heterogeneity, deposit energy in F[].
- // Normalize F[] later, when save output.
- if (bflag)
- {
- // only save data if bflag==1, i.e., photon inside simulation cube
-
- //For each detectorvoxel
- if (returnValue->detectorVoxel != nullptr)
- {
- //Add photon position to the recorded photon route
- returnValue->detectorVoxel->recordedPhotonRoute->push_back(initLocation(ix, iy, iz, absorb));
-
- //If the photon is currently at the detector position
- if ((returnValue->detectorVoxel->location.x == ix)
- && ((returnValue->detectorVoxel->location.y == iy)
- || (returnValue->detectorVoxel->location.y - 1 == iy))
- && (returnValue->detectorVoxel->location.z == iz))
- {
- //For each voxel in the recorded photon route
- for (unsigned int routeIndex = 0; routeIndex < returnValue->detectorVoxel->recordedPhotonRoute->size(); routeIndex++)
- {
- //increment the fluence contribution at that particular position
- i = (long)(returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).z*inputValues->Ny*inputValues->Nx
- + returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).x*inputValues->Ny
- + returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).y);
- returnValue->detectorVoxel->fluenceContribution[i] += returnValue->detectorVoxel->recordedPhotonRoute->at(routeIndex).absorb;
- }
-
- //Clear the recorded photon route
- returnValue->detectorVoxel->m_NumberPhotonsCurrent++;
- returnValue->detectorVoxel->recordedPhotonRoute->clear();
- }
- }
-
- i = (long)(iz*inputValues->Ny*inputValues->Nx + ix*inputValues->Ny + iy);
- returnValue->totalFluence[i] += absorb;
- }
-
- /* Update sleft */
- sleft -= s*inputValues->musVector[i]; /* dimensionless step remaining */
- if (sleft <= ls) sleft = 0;
-
- /* Update positions. */
- x += s*ux;
- y += s*uy;
- z += s*uz;
-
- // pointers to voxel containing optical properties
- ix = (int)(inputValues->Nx / 2 + x / inputValues->xSpacing);
- iy = (int)(inputValues->Ny / 2 + y / inputValues->ySpacing);
- iz = (int)(z / inputValues->zSpacing);
-
- bflag = 1; // Boundary flag. Initialize as 1 = inside volume, then check.
- if (inputValues->boundaryflag == 0) { // Infinite medium.
- // Check if photon has wandered outside volume.
- // If so, set tissue type to boundary value, but let photon wander.
- // Set blag to zero, so DROP does not deposit energy.
- if (iz >= inputValues->Nz) { iz = inputValues->Nz - 1; bflag = 0; }
- if (ix >= inputValues->Nx) { ix = inputValues->Nx - 1; bflag = 0; }
- if (iy >= inputValues->Ny) { iy = inputValues->Ny - 1; bflag = 0; }
- if (iz < 0) { iz = 0; bflag = 0; }
- if (ix < 0) { ix = 0; bflag = 0; }
- if (iy < 0) { iy = 0; bflag = 0; }
- }
- else if (inputValues->boundaryflag == 1) { // Escape at boundaries
- if (iz >= inputValues->Nz) { iz = inputValues->Nz - 1; photon_status = DEAD; sleft = 0; }
- if (ix >= inputValues->Nx) { ix = inputValues->Nx - 1; photon_status = DEAD; sleft = 0; }
- if (iy >= inputValues->Ny) { iy = inputValues->Ny - 1; photon_status = DEAD; sleft = 0; }
- if (iz < 0) { iz = 0; photon_status = DEAD; sleft = 0; }
- if (ix < 0) { ix = 0; photon_status = DEAD; sleft = 0; }
- if (iy < 0) { iy = 0; photon_status = DEAD; sleft = 0; }
- }
- else if (inputValues->boundaryflag == 2) { // Escape at top surface, no x,y bottom z boundaries
- if (iz >= inputValues->Nz) { iz = inputValues->Nz - 1; bflag = 0; }
- if (ix >= inputValues->Nx) { ix = inputValues->Nx - 1; bflag = 0; }
- if (iy >= inputValues->Ny) { iy = inputValues->Ny - 1; bflag = 0; }
- if (iz < 0) { iz = 0; photon_status = DEAD; sleft = 0; }
- if (ix < 0) { ix = 0; bflag = 0; }
- if (iy < 0) { iy = 0; bflag = 0; }
- }
-
- // update pointer to tissue type
- i = (long)(iz*inputValues->Ny*inputValues->Nx + ix*inputValues->Ny + iy);
- } //(sv) /* same voxel */
- } while (sleft > 0); //do...while
-
- /**** SPIN
- Scatter photon into new trajectory defined by theta and psi.
- Theta is specified by cos(theta), which is determined
- based on the Henyey-Greenstein scattering function.
- Convert theta and psi into cosines ux, uy, uz.
- *****/
- /* Sample for costheta */
- while ((rnd = returnValue->RandomGen(1, 0, nullptr)) <= 0.0);
- if (inputValues->gVector[i] == 0.0)
- {
- costheta = 2.0 * rnd - 1.0;
- }
- else
- {
- double temp = (1.0 - inputValues->gVector[i] * inputValues->gVector[i])
- / (1.0 - inputValues->gVector[i] + 2 * inputValues->gVector[i] * rnd);
- costheta = (1.0 + inputValues->gVector[i] * inputValues->gVector[i] - temp*temp) / (2.0*inputValues->gVector[i]);
- }
- sintheta = sqrt(1.0 - costheta*costheta); /* sqrt() is faster than sin(). */
-
- /* Sample psi. */
- psi = 2.0*PI*returnValue->RandomGen(1, 0, nullptr);
- cospsi = cos(psi);
- if (psi < PI)
- sinpsi = sqrt(1.0 - cospsi*cospsi); /* sqrt() is faster than sin(). */
- else
- sinpsi = -sqrt(1.0 - cospsi*cospsi);
-
- /* New trajectory. */
- if (1 - fabs(uz) <= ONE_MINUS_COSZERO) { /* close to perpendicular. */
- uxx = sintheta * cospsi;
- uyy = sintheta * sinpsi;
- uzz = costheta * SIGN(uz); /* SIGN() is faster than division. */
- }
- else { /* usually use this option */
- temp = sqrt(1.0 - uz * uz);
- uxx = sintheta * (ux * uz * cospsi - uy * sinpsi) / temp + ux * costheta;
- uyy = sintheta * (uy * uz * cospsi + ux * sinpsi) / temp + uy * costheta;
- uzz = -sintheta * cospsi * temp + uz * costheta;
- }
-
- /* Update trajectory */
- ux = uxx;
- uy = uyy;
- uz = uzz;
-
- /**** CHECK ROULETTE
- If photon weight below THRESHOLD, then terminate photon using Roulette technique.
- Photon has CHANCE probability of having its weight increased by factor of 1/CHANCE,
- and 1-CHANCE probability of terminating.
- *****/
- if (W < THRESHOLD) {
- if (returnValue->RandomGen(1, 0, nullptr) <= CHANCE)
- W /= CHANCE;
- else photon_status = DEAD;
- }
- } while (photon_status == ALIVE); /* end STEP_CHECK_HOP_SPIN */
- /* if ALIVE, continue propagating */
- /* If photon DEAD, then launch new photon. */
- } while (photonIterator < photonsToSimulate); /* end RUN */
-
- returnValue->Nphotons += photonsToSimulate;
- } while (photonsToSimulate > 0);
-
- if (verbose) std::cout << "------------------------------------------------------" << std::endl;
- if (verbose) std::cout << "Thread " << thread << " is finished." << std::endl;
-}
diff --git a/Modules/PhotoacousticsLib/MitkMCxyz/files.cmake b/Modules/PhotoacousticsLib/MitkMCxyz/files.cmake
deleted file mode 100644
index 284bae1500..0000000000
--- a/Modules/PhotoacousticsLib/MitkMCxyz/files.cmake
+++ /dev/null
@@ -1,3 +0,0 @@
-set(CPP_FILES
- MitkMCxyz.cpp
-)
diff --git a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/CMakeLists.txt b/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/CMakeLists.txt
deleted file mode 100644
index 8ebf2fa24d..0000000000
--- a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-OPTION(BUILD_PhotoacousticPhantomGenerator "Build MiniApp for generating a PA phantom in silico" OFF)
-
-IF(BUILD_PhotoacousticPhantomGenerator)
- PROJECT( MitkPAPhantomGenerator )
- mitk_create_executable(PAPhantomGenerator
- DEPENDS MitkCommandLine MitkCore MitkPhotoacousticsLib
- PACKAGE_DEPENDS
- CPP_FILES PAPhantomGenerator.cpp)
-
- install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
- ENDIF()
diff --git a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/PAPhantomGenerator.cpp b/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/PAPhantomGenerator.cpp
deleted file mode 100644
index 1f81720dbb..0000000000
--- a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/PAPhantomGenerator.cpp
+++ /dev/null
@@ -1,225 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkCommon.h>
-#include <chrono>
-#include <mitkPATissueGeneratorParameters.h>
-#include <mitkPATissueGenerator.h>
-#include <mitkPAPhantomTissueGenerator.h>
-#include <mitkIOUtil.h>
-#include <mitkCommandLineParser.h>
-#include <mitkUIDGenerator.h>
-#include <mitkException.h>
-
-#include <itksys/SystemTools.hxx>
-
-using namespace mitk::pa;
-
-TissueGeneratorParameters::Pointer CreatePhantom_04_04_18_Parameters()
-{
- auto returnParameters = TissueGeneratorParameters::New();
- returnParameters->SetAirThicknessInMillimeters(12);
- returnParameters->SetMinBackgroundAbsorption(0.1);
- returnParameters->SetMaxBackgroundAbsorption(0.1);
- returnParameters->SetBackgroundAnisotropy(0.9);
- returnParameters->SetBackgroundScattering(15);
- returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewDirectionVectorInStraightLine);
- returnParameters->SetDoPartialVolume(true);
- returnParameters->SetMinNumberOfVessels(1);
- returnParameters->SetMaxNumberOfVessels(8);
- returnParameters->SetMinVesselAbsorption(1);
- returnParameters->SetMaxVesselAbsorption(10);
- returnParameters->SetMinVesselAnisotropy(0.9);
- returnParameters->SetMaxVesselAnisotropy(0.9);
- returnParameters->SetMinVesselBending(0.1);
- returnParameters->SetMaxVesselBending(0.3);
- returnParameters->SetMinVesselRadiusInMillimeters(0.25);
- returnParameters->SetMaxVesselRadiusInMillimeters(4);
- returnParameters->SetMinVesselScattering(15);
- returnParameters->SetMaxVesselScattering(15);
- returnParameters->SetMinVesselZOrigin(1.6);
- returnParameters->SetMaxVesselZOrigin(4);
- returnParameters->SetVesselBifurcationFrequency(5000);
- returnParameters->SetRandomizePhysicalProperties(false);
- returnParameters->SetSkinThicknessInMillimeters(0);
- returnParameters->SetUseRngSeed(false);
- returnParameters->SetVoxelSpacingInCentimeters(0.03);
- returnParameters->SetXDim(140);
- returnParameters->SetYDim(100);
- returnParameters->SetZDim(180);
- //returnParameters->SetVoxelSpacingInCentimeters(0.015);
- //returnParameters->SetXDim(280);
- //returnParameters->SetYDim(200);
- //returnParameters->SetZDim(360);
- returnParameters->SetForceVesselsMoveAlongYDirection(true);
- //returnParameters->SetVoxelSpacingInCentimeters(0.0075);
- //returnParameters->SetXDim(560);
- //returnParameters->SetYDim(400);
- //returnParameters->SetZDim(720);
- return returnParameters;
-}
-
-struct InputParameters
-{
- std::string saveFolderPath;
- std::string identifyer;
- std::string exePath;
- std::string probePath;
- bool empty;
- bool verbose;
-};
-
-InputParameters parseInput(int argc, char* argv[])
-{
- MITK_INFO << "Parsing arguments...";
- mitkCommandLineParser parser;
-
- parser.setCategory("MITK-Photoacoustics");
- parser.setTitle("Mitk Tissue Batch Generator");
- parser.setDescription("Creates in silico tissue in batch processing and automatically calculates fluence values for the central slice of the volume.");
- parser.setContributor("Computer Assisted Medical Interventions, DKFZ");
-
- parser.setArgumentPrefix("--", "-");
-
- parser.beginGroup("Required parameters");
- parser.addArgument(
- "savePath", "s", mitkCommandLineParser::Directory,
- "Input save folder (directory)", "input save folder",
- us::Any(), false, false, false, mitkCommandLineParser::Input);
- parser.addArgument(
- "mitkMcxyz", "m", mitkCommandLineParser::File,
- "MitkMcxyz binary (file)", "path to the MitkMcxyz binary",
- us::Any(), false, false, false, mitkCommandLineParser::Output);
- parser.endGroup();
-
- parser.beginGroup("Optional parameters");
- parser.addArgument(
- "probe", "p", mitkCommandLineParser::File,
- "xml probe file (file)", "file to the definition of the used probe (*.xml)",
- us::Any(), true, false, false, mitkCommandLineParser::Output);
- parser.addArgument(
- "verbose", "v", mitkCommandLineParser::Bool,
- "Verbose Output", "Whether to produce verbose, or rather debug output");
- parser.addArgument(
- "identifyer", "i", mitkCommandLineParser::String,
- "Generator identifyer (string)", "A unique identifyer for the calculation instance");
- parser.addArgument(
- "empty-volume", "e", mitkCommandLineParser::Bool,
- "omit vessel structures (boolean flag)", "Whether to create an empty volume with no structures inside.");
- parser.endGroup();
-
- InputParameters input;
-
- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
- if (parsedArgs.size() == 0)
- exit(-1);
-
- if (parsedArgs.count("empty-volume"))
- {
- input.empty = us::any_cast<bool>(parsedArgs["empty-volume"]);
- }
- else
- {
- input.empty = false;
- }
-
- if (parsedArgs.count("verbose"))
- {
- input.verbose = us::any_cast<bool>(parsedArgs["verbose"]);
- }
- else
- {
- input.verbose = false;
- }
-
- if (parsedArgs.count("savePath"))
- {
- input.saveFolderPath = us::any_cast<std::string>(parsedArgs["savePath"]);
- }
-
- if (parsedArgs.count("mitkMcxyz"))
- {
- input.exePath = us::any_cast<std::string>(parsedArgs["mitkMcxyz"]);
- }
-
- if (parsedArgs.count("probe"))
- {
- input.probePath = us::any_cast<std::string>(parsedArgs["probe"]);
- }
-
- if (parsedArgs.count("identifyer"))
- {
- input.identifyer = us::any_cast<std::string>(parsedArgs["identifyer"]);
- }
- else
- {
- input.identifyer = mitk::UIDGenerator().GetUID();
- }
- MITK_INFO << "Parsing arguments...[Done]";
- return input;
-}
-
-int main(int argc, char * argv[])
-{
- auto input = parseInput(argc, argv);
- auto parameters = CreatePhantom_04_04_18_Parameters();
- if (input.empty)
- {
- parameters->SetMaxNumberOfVessels(0);
- parameters->SetMinNumberOfVessels(0);
- }
- MITK_INFO(input.verbose) << "Generating tissue..";
- auto resultTissue = InSilicoTissueGenerator::GenerateInSilicoData(parameters);
- MITK_INFO(input.verbose) << "Generating tissue..[Done]";
-
- auto inputfolder = std::string(input.saveFolderPath + "input/");
- auto outputfolder = std::string(input.saveFolderPath + "output/");
- if (!itksys::SystemTools::FileIsDirectory(inputfolder))
- {
- itksys::SystemTools::MakeDirectory(inputfolder);
- }
- if (!itksys::SystemTools::FileIsDirectory(outputfolder))
- {
- itksys::SystemTools::MakeDirectory(outputfolder);
- }
-
- std::string savePath = input.saveFolderPath + "input/Phantom_" + input.identifyer +
- ".nrrd";
- mitk::IOUtil::Save(resultTissue->ConvertToMitkImage(), savePath);
- std::string outputPath = input.saveFolderPath + "output/Phantom_" + input.identifyer +
- "/";
-
- resultTissue = nullptr;
-
- if (!itksys::SystemTools::FileIsDirectory(outputPath))
- {
- itksys::SystemTools::MakeDirectory(outputPath);
- }
-
- outputPath = outputPath + "Fluence_Phantom_" + input.identifyer;
-
- MITK_INFO(input.verbose) << "Simulating fluence..";
-
- int result = -4;
-
- std::string cmdString = std::string(input.exePath + " -i " + savePath + " -o " +
- (outputPath + ".nrrd") +
- " -yo " + "0" + " -p " + input.probePath +
- " -n 10000000");
-
- MITK_INFO << "Executing: " << cmdString;
-
- result = std::system(cmdString.c_str());
-
- MITK_INFO << result;
- MITK_INFO(input.verbose) << "Simulating fluence..[Done]";
-}
diff --git a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/files.cmake b/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/files.cmake
deleted file mode 100644
index 07f708562d..0000000000
--- a/Modules/PhotoacousticsLib/MitkPAPhantomGenerator/files.cmake
+++ /dev/null
@@ -1,3 +0,0 @@
-set(CPP_FILES
- PAPhantomGenerator.cpp
-)
diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/CMakeLists.txt b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/CMakeLists.txt
deleted file mode 100644
index f2faf72a92..0000000000
--- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-OPTION(BUILD_PhotoacousticSpectralUnmixing "Build MiniApp for batch generating of photoacoustic spectral unmixing" OFF)
-
-IF(BUILD_PhotoacousticSpectralUnmixing)
- PROJECT( MitkSpectralUnmxing )
- mitk_create_executable(SpectralUnmxingApp
- DEPENDS MitkCommandLine MitkCore MitkPhotoacousticsLib
- PACKAGE_DEPENDS
- CPP_FILES SpectralUnmixingApp.cpp)
-
- install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
- ENDIF()
diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/ReadMe.txt b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/ReadMe.txt
deleted file mode 100644
index 5c2e7e3d2b..0000000000
--- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/ReadMe.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-/**
- \spectral unmixing mini App (SUMA)
-
- \brief The SUMA is designed to enable batch processing for spectral unmixing. To use the SUMA one has to build the MitkSpectralUnmixingApp located in the PAlib. Afterwards a .bat script is available int the suberbuild/MITK-build/bin. This script takes 4 required and one optional parameter:
-
-Required parameters
- -i, --inputFilename, input filename // "E:/mydata/awesome_exp/first_image.nrrd" image has to be an integer multiple of the number of wavelengths
- -o, --outputFileStruct, input save name // "E:/mydata/awesome_exp_unmixed/first_image_ctr" will be saved as "_HbO2_SU_.nrrd", "_Hb_SU_.nrrd" and "_sO2_.nrrd"; it is recommended to add an counter (ctr) to the savenames otherwise they will be overwritten.
- -l, --inputWavelengths, input wavelengths // (int) 299 < wavelength < 1001 with format: int blank int blank int blank ...
- -a, --inputAlg, input algorithm // insert alg: "QR", "NNLS", "WLS", "SVD", "LU"
- -w, --inputWeights, input weights (optional) // int weights in % format and order corresponding to the wavelength: int blank int blank ...
-
-To costumize the SUMA for batch processing of a whole directory, you can either write a script which calls the SUMA for every image again oR insert a loop arround the actual unmixing in the code entering your file structure (see comments inside the code).
-
-For further questions please contact Niklas Holzwarth (n.holzwarth@dkfz-heidelberg.de or niklas.holzwarth@gmail.com)
\ No newline at end of file
diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp
deleted file mode 100644
index 89b3e472ad..0000000000
--- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingApp.cpp
+++ /dev/null
@@ -1,311 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <chrono>
-#include <mitkCommon.h>
-#include "mitkPALinearSpectralUnmixingFilter.h"
-#include "mitkPASpectralUnmixingFilterBase.h"
-#include "mitkPASpectralUnmixingFilterVigra.h"
-#include "mitkPASpectralUnmixingSO2.h"
-#include <mitkCommandLineParser.h>
-#include <mitkException.h>
-#include <mitkIOUtil.h>
-#include <mitkUIDGenerator.h>
-#include <itksys/SystemTools.hxx>
-#include "mitkPreferenceListReaderOptionsFunctor.h"
-
-
-/* \brief The spectral unmixing mini app (SUMA) is designed to enable batch processing
- for spectral unmixing. For detailed documentation look into the header files of the
- included spectral unmixing filters.*/
-
-struct InputParameters
-{
- std::string inputFilename;
- std::string outputFileStruct; // "E:/mydata/awesome_exp_unmixed/a" will be saved as "a_HbO2_SU_.nrrd", "a_Hb_SU_.nrrd" and "a_sO2_.nrrd";
- std::string inputAlg;
- std::string outputFileNumber;
- mitkCommandLineParser::StringContainerType inputWavelengths;
- mitkCommandLineParser::StringContainerType inputWeights;
-};
-
-InputParameters parseInput(int argc, char *argv[])
-{
- //MITK_INFO << "Parsing arguments...";
- mitkCommandLineParser parser;
-
- parser.setCategory("MITK-Photoacoustics");
- parser.setTitle("Mitk Spectral Unmixing App");
- parser.setDescription("Batch processing for spectral unmixing.");
- parser.setContributor("Computer Assisted Medical Interventions, DKFZ");
-
- parser.setArgumentPrefix("--", "-");
-
- parser.beginGroup("Required parameters");
- parser.addArgument("inputFilename",
- "i",
- mitkCommandLineParser::Directory,
- "Input Filename (NAME.nrrd)",
- "input filename",
- us::Any(),
- false);
- parser.addArgument("outputFileStruct",
- "o",
- mitkCommandLineParser::Directory,
- "Output save name (name without ending!)",
- "Output save name",
- us::Any(),
- false);
- parser.addArgument("outputFileNumber",
- "n",
- mitkCommandLineParser::String,
- "Output file number",
- "Output save number",
- us::Any(),
- false);
- parser.addArgument("inputWavelengths",
- "l",
- mitkCommandLineParser::StringList,
- "Input wavelengths (123 124 125 ... int blank int blank)",
- "input wavelengths",
- us::Any(),
- false);
- parser.addArgument("inputAlg",
- "a",
- mitkCommandLineParser::String,
- "Input algorithm (string)",
- "input algorithm",
- us::Any(),
- false);
- parser.addArgument("inputWeights",
- "w",
- mitkCommandLineParser::StringList,
- "Input weights (123 124 125 ... int in % blank int in % blank)",
- "input weights",
- us::Any(),
- true);
- parser.endGroup();
-
- InputParameters input;
-
- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
- if (argc == 0)
- exit(-1);
-
- //for (int i = 0; i < argc; ++i)
- //{
- // MITK_INFO << argv[i];
- //}
-
-
- if (parsedArgs.count("inputFilename"))
- {
-
- input.inputFilename = us::any_cast<std::string>(parsedArgs["inputFilename"]);
- }
- else
- {
- MITK_ERROR << "Error: No input file";
- mitkThrow() << "Error: No input file";
- }
-
- if (parsedArgs.count("outputFileStruct"))
- {
- input.outputFileStruct = us::any_cast<std::string>(parsedArgs["outputFileStruct"]);
- }
- else
- {
- MITK_ERROR << "Error: No output";
- mitkThrow() << "Error: No output";
- }
-
- if (parsedArgs.count("outputFileNumber"))
- {
- input.outputFileNumber = us::any_cast<std::string>(parsedArgs["outputFileNumber"]);
- }
- else
- {
- MITK_ERROR << "Error: No output number";
- mitkThrow() << "Error: No output number";
- }
-
- if (parsedArgs.count("inputWavelengths"))
- {
- input.inputWavelengths = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["inputWavelengths"]);
- }
- else
- {
- MITK_ERROR << "Error: No wavelengths";
- mitkThrow() << "Error: No wavelengths";
- }
- if (parsedArgs.count("inputAlg"))
- {
- input.inputAlg = us::any_cast<std::string>(parsedArgs["inputAlg"]);
- }
- else
- {
- MITK_ERROR << "Error: No algorithm";
- mitkThrow() << "Error: No algorithm";
- }
-
- if (parsedArgs.count("inputWeights"))
- {
- input.inputWeights = us::any_cast<mitkCommandLineParser::StringContainerType>(parsedArgs["inputWeights"]);
- }
-
- //MITK_INFO << "Parsing arguments...[Done]";
- return input;
-}
-
-// Class takes string and sets algorithm for spectral unmixing in the corresponding filter class
-mitk::pa::SpectralUnmixingFilterBase::Pointer GetFilterInstance(std::string algorithm, std::vector<int> weights = std::vector<int>())
-{
- mitk::pa::SpectralUnmixingFilterBase::Pointer spectralUnmixingFilter;
-
- if (algorithm == "QR")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
- }
-
- else if (algorithm == "SVD")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD);
- }
-
- else if (algorithm == "LU")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU);
- }
-
- else if (algorithm == "NNLS")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS);
- }
-
- else if (algorithm == "WLS")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED);
-
- std::vector<int> weightVec = weights;
-
- for (unsigned int i = 0; i < weightVec.size(); ++i)
- {
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra *>(spectralUnmixingFilter.GetPointer())
- ->AddWeight(weightVec[i]);
- }
- }
- return spectralUnmixingFilter;
-}
-
-int main(int argc, char *argv[])
-{
- auto input = parseInput(argc, argv);
-
- std::string algo = input.inputAlg;
- std::string outputDir = input.outputFileStruct;
- std::string outputNumber = input.outputFileNumber;
-
- auto inputWls = input.inputWavelengths;
-
- std::vector<int> wavelengths;
- for (unsigned int s = 0; s < inputWls.size(); ++s)
- {
- int wl = std::stoi(inputWls[s]);
- wavelengths.push_back(wl);
- //MITK_INFO << "Wavelength: " << wl << "\n";
- }
-
- mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter;
-
- if (algo == "WLS")
- {
- auto inputW = input.inputWeights;
-
- std::vector<int> Weights;
- for (unsigned int s = 0; s < inputW.size(); ++s)
- {
- int w = std::stoi(inputW[s]);
- Weights.push_back(w);
- //MITK_INFO << "Weights: " << w << "\n";
- }
-
- m_SpectralUnmixingFilter = GetFilterInstance(algo, Weights);
- }
- else
- {
- m_SpectralUnmixingFilter = GetFilterInstance(algo);
- }
-
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- for (unsigned int wIdx = 0; wIdx < wavelengths.size(); ++wIdx)
- {
- m_SpectralUnmixingFilter->AddWavelength(wavelengths[wIdx]);
- //MITK_INFO << wavelengths[wIdx];
- }
-
- //to add a batch processing: loop for a dir start here; don't forget to set a counter to the three output savenames!!!
- std::string inputImage = input.inputFilename;
- auto m_inputImage = mitk::IOUtil::Load<mitk::Image>(inputImage);
-
- m_SpectralUnmixingFilter->SetInput(m_inputImage);
-
- m_SpectralUnmixingFilter->Update();
-
- auto output1 = m_SpectralUnmixingFilter->GetOutput(0);
- auto output2 = m_SpectralUnmixingFilter->GetOutput(1);
- output1->SetSpacing(m_inputImage->GetGeometry()->GetSpacing());
- output2->SetSpacing(m_inputImage->GetGeometry()->GetSpacing());
-
- std::string unmixingOutputHbO2 = outputDir + "HbO2." + outputNumber + ".nrrd";
- std::string unmixingOutputHb = outputDir + "Hb." + outputNumber + ".nrrd";
- //mitk::IOUtil::Save(output1, unmixingOutputHbO2);
- //mitk::IOUtil::Save(output2, unmixingOutputHb);
-
- auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New();
- m_sO2->Verbose(false);
-
- m_sO2->SetInput(0, output1);
- m_sO2->SetInput(1, output2);
-
- m_sO2->Update();
-
- mitk::Image::Pointer sO2 = m_sO2->GetOutput(0);
- mitk::Image::Pointer tHb = m_sO2->GetOutput(1);
- sO2->SetSpacing(m_inputImage->GetGeometry()->GetSpacing());
- tHb->SetSpacing(m_inputImage->GetGeometry()->GetSpacing());
-
- std::string outputSo2 = outputDir + "sO2." + outputNumber + ".nrrd";
- mitk::IOUtil::Save(sO2, outputSo2);
-
- std::string outputTHb = outputDir + "tHb." + outputNumber + ".nrrd";
- mitk::IOUtil::Save(tHb, outputTHb);
-
- m_sO2 = nullptr;
- m_SpectralUnmixingFilter = nullptr;
- //to add a batch processing: loop for a dir end here
- MITK_INFO << "Spectral Unmixing DONE";
-}
diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingAppTimeEval.cpp b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingAppTimeEval.cpp
deleted file mode 100644
index 1c484128ba..0000000000
--- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/SpectralUnmixingAppTimeEval.cpp
+++ /dev/null
@@ -1,325 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-//#include <boost>
-#include <chrono>
-#include <mitkCommon.h>
-
-#include "mitkPALinearSpectralUnmixingFilter.h"
-#include "mitkPASpectralUnmixingFilterBase.h"
-#include "mitkPASpectralUnmixingFilterVigra.h"
-#include "mitkPASpectralUnmixingSO2.h"
-
-#include <mitkCommandLineParser.h>
-#include <mitkException.h>
-#include <mitkIOUtil.h>
-#include <mitkUIDGenerator.h>
-
-#include <itksys/SystemTools.hxx>
-
-
-#include "mitkPreferenceListReaderOptionsFunctor.h"
-
-
-struct InputParameters
-{
- std::string inputPath;
- std::string outputPath;
- int numberOfInputs;
-};
-
-InputParameters parseInput(int argc, char *argv[])
-{
- MITK_INFO << "Parsing arguments...";
- mitkCommandLineParser parser;
-
- parser.setCategory("MITK-Photoacoustics");
- parser.setTitle("Mitk Spectral Unmixing App");
- parser.setDescription("Batch processing for spectral unmixing.");
- parser.setContributor("Computer Assisted Medical Interventions, DKFZ");
-
- parser.setArgumentPrefix("--", "-");
-
- parser.beginGroup("Required parameters");
- parser.addArgument("inputPath",
- "i",
- mitkCommandLineParser::Directory,
- "Input folder (directory)",
- "input folder",
- us::Any(),
- false, false, false, mitkCommandLineParser::Input);
- parser.addArgument("outputPath",
- "o",
- mitkCommandLineParser::Directory,
- "Input save folder (directory)",
- "input save folder",
- us::Any(),
- false, false, false, mitkCommandLineParser::Output);
- parser.addArgument("numberOfInputs",
- "n",
- mitkCommandLineParser::Int,
- "Number of Input files",
- "number of inputs",
- us::Any(),
- false);
- parser.endGroup();
-
-
- InputParameters input;
-
-
- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
- if (argc == 0)
- exit(-1);
-
- for (int i = 0; i < argc; ++i)
- {
- MITK_INFO << argv[i];
- }
-
- if (parsedArgs.count("inputPath"))
- {
- input.inputPath = us::any_cast<std::string>(parsedArgs["inputPath"]);
- }
- else
- {
- MITK_ERROR << "Error: No inputPath";
- mitkThrow() << "Error: No inputPath";
- }
-
- if (parsedArgs.count("outputPath"))
- {
- input.outputPath = us::any_cast<std::string>(parsedArgs["outputPath"]);
- }
- else
- {
- MITK_ERROR << "Error: No outputPath";
- mitkThrow() << "Error: No outputPath";
- }
- if (parsedArgs.count("numberOfInputs"))
- {
- input.numberOfInputs = us::any_cast<int>(parsedArgs["numberOfInputs"]);
- }
- else
- {
- MITK_ERROR << "Error: No number of Inputs";
- mitkThrow() << "Error: No number of Inputs";
- }
- MITK_INFO << "Parsing arguments...[Done]";
- return input;
-}
-
-
-mitk::pa::SpectralUnmixingFilterBase::Pointer GetFilterInstance(std::string algorithm)
-{
- mitk::pa::SpectralUnmixingFilterBase::Pointer spectralUnmixingFilter;
-
- if (algorithm == "QR")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
- }
-
- else if (algorithm == "SVD")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD);
- }
-
- else if (algorithm == "LU")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU);
- }
-
- else if (algorithm == "NNLS")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS);
- }
-
- else if (algorithm == "WLS")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra *>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED);
-
- /*std::vector<int> weigthVec = {39, 45, 47};
-
- for (int i = 0; i < 3; ++i)
- {
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra *>(spectralUnmixingFilter.GetPointer())
- ->AddWeight(weigthVec[i]);
- }*/
- }
- return spectralUnmixingFilter;
-}
-
-void add_weight(int weights, mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter)
-{
- std::vector<int> weigthVec = { 30, 32, 33, 35, 37, 38, 40, 41, 43, 44, 45, 46, 47, 47,
- 47, 47, 47, 46, 46, 45, 44, 44, 43, 42, 42, 41 };
-
- for (int i = 0; i < weights; ++i)
- {
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra *>(m_SpectralUnmixingFilter.GetPointer())
- ->AddWeight(weigthVec[i]);
- }
-}
-
-
-
-int main(int argc, char *argv[])
-{
- auto input = parseInput(argc, argv);
-
- std::string inputDir = input.inputPath;
- std::string outputDir = input.outputPath;
- unsigned int N = input.numberOfInputs;
-
-/*
- //maybee try with "itk system tools"
-
- //auto test = itksys::SystemTools::GetFilenameName(argv[0]).c_str();
-
- //MITK_INFO << "test: " << test;
-
-
- / +++ temporary solution BEGIN +++
- std::vector<std::string> files;
- std::string file;
- for (int i = 1; i < 34; ++i)
- {
-
- if (i < 10)
- {
- file = "E:/NHDATA/sdmas_beamformed/merged/static-oxy_sdmas_00" + std::to_string(i) + "_merged.nrrd";
- }
- else
- {
- file = "E:/NHDATA/sdmas_beamformed/merged/static-oxy_sdmas_0" + std::to_string(i) + "_merged.nrrd";
- }
- files.push_back(file);
- }
- / +++ temporary solution END +++
-
- std::vector<std::string> files;
- std::string file;
- for (int i = 0; i < 7; ++i)
- {
- file = "E:/NHCAMI/cami-experimental/PAI/spectralUnmixing/inSilico/paImages/selection/noiselevel1_rep1000_wavelength_selction_data_" +
- std::to_string(i) + ".nrrd";
- files.push_back(file);
- }
- std::vector<std::string> files;
- std::string file;
- file = "E:/NHCAMI/cami-experimental/PAI/spectralUnmixing/inSilico/paImages/selection/noiselevel1_rep1000_wavelength_selction_data.nrrd";
- files.push_back(file);*/
-
- std::vector<std::string> algorithms = { "QR", "LU", "SVD", "NNLS", "WLS" };
- int repetition = 6000;
-
- for (unsigned alg = 0; alg < 5; ++alg)
- {
- ofstream myerrorfile;
- myerrorfile.open("E:/NHDATA/time/time_evaluation_" + std::to_string(repetition)+"_" + algorithms[alg] + "_new02.txt");
-
- int ctr = 0;
- for(int i = 2; i < 27; ++i)
- {
- myerrorfile << std::to_string(i) + "\t";
- std::string file;
- if (i < 10)
- file = "E:/NHDATA/time/input/time_0" + std::to_string(i) + ".nrrd";
- else
- file = "E:/NHDATA/time/input/time_" + std::to_string(i) + ".nrrd";
-
- auto m_inputImage = mitk::IOUtil::Load<mitk::Image>(file);
-
- MITK_INFO << "File: " << i;
-
- for (int j = 0; j < repetition; ++j)
- {
- std::chrono::steady_clock::time_point _start;
- _start = std::chrono::steady_clock::now();
-
- mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter = GetFilterInstance(algorithms[alg]);
- m_SpectralUnmixingFilter->SetInput(m_inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- for (int wl = 0; wl < i; ++wl)
- {
- m_SpectralUnmixingFilter->AddWavelength(700 + wl * 10);
- }
-
- if (alg == 4)
- {
- add_weight(i, m_SpectralUnmixingFilter);
- }
-
-
- m_SpectralUnmixingFilter->Update();
-
- auto output1 = m_SpectralUnmixingFilter->GetOutput(0);
- auto output2 = m_SpectralUnmixingFilter->GetOutput(1);
-
- m_SpectralUnmixingFilter = nullptr;
-
- std::chrono::steady_clock::time_point _end(std::chrono::steady_clock::now());
- myerrorfile << std::chrono::duration_cast<std::chrono::duration<double>>(_end - _start).count() << "\t";
-
- /*std::string unmixingOutputHbO2 = "E:/NHDATA/time/output/time_" + std::to_string(i) + ".nrrd";
- std::string unmixingOutputHb = "E:/NHDATA/time/output/time_" + std::to_string(i) + ".nrrd";
- mitk::IOUtil::Save(output1, unmixingOutputHbO2);
- mitk::IOUtil::Save(output2, unmixingOutputHb);
-
- //auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New();
- //m_sO2->Verbose(false);
- //auto output1 = m_SpectralUnmixingFilter->GetOutput(0);
- //auto output2 = m_SpectralUnmixingFilter->GetOutput(1);
-
-
- //std::string unmixingOutputHbO2 ="E:/NHDATA/time/input/time_" + std::to_string(i) + ".nrrd";
- //std::string unmixingOutputHb = outputDir + "/SUOutput/" + "Hb_" + algorithms[alg] + "_" + str_ctr + ".nrrd";
- //mitk::IOUtil::Save(output1, unmixingOutputHbO2);
- //mitk::IOUtil::Save(output2, unmixingOutputHb);
-
- //m_sO2->SetInput(0, output1);
- //m_sO2->SetInput(1, output2);
-
- //m_sO2->Update();
-
- //mitk::Image::Pointer sO2 = m_sO2->GetOutput(0);
- //sO2->SetSpacing(output1->GetGeometry()->GetSpacing());
-
- //std::string outputSo2 = outputDir + "/So2/" + algorithms[alg] + "/So2_" + algorithms[alg] + "_" + str_ctr + ".nrrd";
- //std::string outputSo2 = outputDir + "/" + algorithms[alg] + "_sel_" + str_ctr + ".nrrd";
- //std::string outputSo2 = outputDir + "/" + algorithms[alg] + "_sel.nrrd";
- //mitk::IOUtil::Save(sO2, outputSo2);
-
- //std::string outputSo2 = "E:/NHDATA/time/output/time_" + std::to_string(i) + algorithms[alg] + ".nrrd";
- //mitk::IOUtil::Save(sO2, outputSo2);*/
- }
- myerrorfile << "\n";
- }
- myerrorfile.close();
- }
- MITK_INFO << "Spectral Unmixing DONE";
-}
diff --git a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/files.cmake b/Modules/PhotoacousticsLib/MitkSpectralUnmixing/files.cmake
deleted file mode 100644
index a0a3a5cdb3..0000000000
--- a/Modules/PhotoacousticsLib/MitkSpectralUnmixing/files.cmake
+++ /dev/null
@@ -1,3 +0,0 @@
-set(CPP_FILES
- SpectralUnmixingApp.cpp
-)
diff --git a/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/CMakeLists.txt b/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/CMakeLists.txt
deleted file mode 100644
index 7158831299..0000000000
--- a/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-OPTION(BUILD_PhotoacousticTissueBatchGenerator "Build MiniApp for batch generating of photoacoustic tissue" OFF)
-
-IF(BUILD_PhotoacousticTissueBatchGenerator)
- PROJECT( MitkTissueBatchGenerator )
- mitk_create_executable(TissueBatchGenerator
- DEPENDS MitkCommandLine MitkCore MitkPhotoacousticsLib
- PACKAGE_DEPENDS
- CPP_FILES TissueBatchGenerator.cpp)
-
- install(TARGETS ${EXECUTABLE_TARGET} RUNTIME DESTINATION bin)
- ENDIF()
diff --git a/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/TissueBatchGenerator.cpp b/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/TissueBatchGenerator.cpp
deleted file mode 100644
index 7f2237754d..0000000000
--- a/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/TissueBatchGenerator.cpp
+++ /dev/null
@@ -1,389 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkCommon.h>
-#include <chrono>
-#include <mitkPATissueGeneratorParameters.h>
-#include <mitkPATissueGenerator.h>
-#include <mitkIOUtil.h>
-#include <mitkCommandLineParser.h>
-#include <mitkUIDGenerator.h>
-#include <mitkException.h>
-
-#include <itksys/SystemTools.hxx>
-
-using namespace mitk::pa;
-
-TissueGeneratorParameters::Pointer CreateMultiHB_13_02_18_Parameters()
-{
- auto returnParameters = TissueGeneratorParameters::New();
- returnParameters->SetAirThicknessInMillimeters(1.8);
- returnParameters->SetMinBackgroundAbsorption(0.001);
- returnParameters->SetMaxBackgroundAbsorption(0.2);
- returnParameters->SetBackgroundAnisotropy(0.9);
- returnParameters->SetBackgroundScattering(15);
- returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
- returnParameters->SetDoPartialVolume(true);
- returnParameters->SetMinNumberOfVessels(1);
- returnParameters->SetMaxNumberOfVessels(7);
- returnParameters->SetMinVesselAbsorption(1);
- returnParameters->SetMaxVesselAbsorption(12);
- returnParameters->SetMinVesselAnisotropy(0.9);
- returnParameters->SetMaxVesselAnisotropy(0.9);
- returnParameters->SetMinVesselBending(0);
- returnParameters->SetMaxVesselBending(0.2);
- returnParameters->SetMinVesselRadiusInMillimeters(0.5);
- returnParameters->SetMaxVesselRadiusInMillimeters(6);
- returnParameters->SetMinVesselScattering(15);
- returnParameters->SetMaxVesselScattering(15);
- returnParameters->SetMinVesselZOrigin(1);
- returnParameters->SetMaxVesselZOrigin(3);
- returnParameters->SetVesselBifurcationFrequency(5000);
- returnParameters->SetRandomizePhysicalProperties(false);
- returnParameters->SetSkinThicknessInMillimeters(0);
- returnParameters->SetUseRngSeed(false);
- returnParameters->SetVoxelSpacingInCentimeters(0.06);
- returnParameters->SetXDim(70);
- returnParameters->SetYDim(100);
- returnParameters->SetZDim(100);
- returnParameters->SetMCflag(4);
- return returnParameters;
-}
-
-TissueGeneratorParameters::Pointer CreateBaselineHB_13_02_18_Parameters()
-{
- auto returnParameters = TissueGeneratorParameters::New();
- returnParameters->SetAirThicknessInMillimeters(1.8);
- returnParameters->SetMinBackgroundAbsorption(0.001);
- returnParameters->SetMaxBackgroundAbsorption(0.2);
- returnParameters->SetBackgroundAnisotropy(0.9);
- returnParameters->SetBackgroundScattering(15);
- returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
- returnParameters->SetDoPartialVolume(true);
- returnParameters->SetMinNumberOfVessels(1);
- returnParameters->SetMaxNumberOfVessels(1);
- returnParameters->SetMinVesselAbsorption(4.73);
- returnParameters->SetMaxVesselAbsorption(4.73);
- returnParameters->SetMinVesselAnisotropy(0.9);
- returnParameters->SetMaxVesselAnisotropy(0.9);
- returnParameters->SetMinVesselBending(0);
- returnParameters->SetMaxVesselBending(0.2);
- returnParameters->SetMinVesselRadiusInMillimeters(3);
- returnParameters->SetMaxVesselRadiusInMillimeters(3);
- returnParameters->SetMinVesselScattering(15);
- returnParameters->SetMaxVesselScattering(15);
- returnParameters->SetMinVesselZOrigin(1);
- returnParameters->SetMaxVesselZOrigin(3);
- returnParameters->SetVesselBifurcationFrequency(5000);
- returnParameters->SetRandomizePhysicalProperties(false);
- returnParameters->SetSkinThicknessInMillimeters(0);
- returnParameters->SetUseRngSeed(false);
- returnParameters->SetVoxelSpacingInCentimeters(0.06);
- returnParameters->SetXDim(70);
- returnParameters->SetYDim(100);
- returnParameters->SetZDim(100);
- returnParameters->SetMCflag(4);
- return returnParameters;
-}
-
-TissueGeneratorParameters::Pointer CreateSingleVesselHeterogeneousBackground_08_02_18_Parameters()
-{
- auto returnParameters = TissueGeneratorParameters::New();
- returnParameters->SetAirThicknessInMillimeters(1.8);
- returnParameters->SetMinBackgroundAbsorption(0.001);
- returnParameters->SetMaxBackgroundAbsorption(0.2);
- returnParameters->SetBackgroundAnisotropy(0.9);
- returnParameters->SetBackgroundScattering(15);
- returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
- returnParameters->SetDoPartialVolume(true);
- returnParameters->SetMinNumberOfVessels(1);
- returnParameters->SetMaxNumberOfVessels(1);
- returnParameters->SetMinVesselAbsorption(1);
- returnParameters->SetMaxVesselAbsorption(12);
- returnParameters->SetMinVesselAnisotropy(0.9);
- returnParameters->SetMaxVesselAnisotropy(0.9);
- returnParameters->SetMinVesselBending(0);
- returnParameters->SetMaxVesselBending(0.2);
- returnParameters->SetMinVesselRadiusInMillimeters(0.5);
- returnParameters->SetMaxVesselRadiusInMillimeters(6);
- returnParameters->SetMinVesselScattering(15);
- returnParameters->SetMaxVesselScattering(15);
- returnParameters->SetMinVesselZOrigin(1);
- returnParameters->SetMaxVesselZOrigin(3);
- returnParameters->SetVesselBifurcationFrequency(5000);
- returnParameters->SetRandomizePhysicalProperties(false);
- returnParameters->SetSkinThicknessInMillimeters(0);
- returnParameters->SetUseRngSeed(false);
- returnParameters->SetVoxelSpacingInCentimeters(0.06);
- returnParameters->SetXDim(70);
- returnParameters->SetYDim(100);
- returnParameters->SetZDim(100);
- returnParameters->SetMCflag(4);
- return returnParameters;
-}
-
-TissueGeneratorParameters::Pointer CreateMultivessel_19_12_17_Parameters()
-{
- auto returnParameters = TissueGeneratorParameters::New();
- returnParameters->SetAirThicknessInMillimeters(12);
- returnParameters->SetMinBackgroundAbsorption(0.1);
- returnParameters->SetMaxBackgroundAbsorption(0.1);
- returnParameters->SetBackgroundAnisotropy(0.9);
- returnParameters->SetBackgroundScattering(15);
- returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
- returnParameters->SetDoPartialVolume(true);
- returnParameters->SetMinNumberOfVessels(1);
- returnParameters->SetMaxNumberOfVessels(7);
- returnParameters->SetMinVesselAbsorption(2);
- returnParameters->SetMaxVesselAbsorption(8);
- returnParameters->SetMinVesselAnisotropy(0.9);
- returnParameters->SetMaxVesselAnisotropy(0.9);
- returnParameters->SetMinVesselBending(0.1);
- returnParameters->SetMaxVesselBending(0.3);
- returnParameters->SetMinVesselRadiusInMillimeters(0.5);
- returnParameters->SetMaxVesselRadiusInMillimeters(4);
- returnParameters->SetMinVesselScattering(15);
- returnParameters->SetMaxVesselScattering(15);
- returnParameters->SetMinVesselZOrigin(2.2);
- returnParameters->SetMaxVesselZOrigin(4);
- returnParameters->SetVesselBifurcationFrequency(5000);
- returnParameters->SetRandomizePhysicalProperties(false);
- returnParameters->SetSkinThicknessInMillimeters(0);
- returnParameters->SetUseRngSeed(false);
- returnParameters->SetVoxelSpacingInCentimeters(0.06);
- returnParameters->SetXDim(70);
- returnParameters->SetYDim(100);
- returnParameters->SetZDim(100);
- return returnParameters;
-}
-
-TissueGeneratorParameters::Pointer CreateMultivessel_19_10_17_Parameters()
-{
- auto returnParameters = TissueGeneratorParameters::New();
- returnParameters->SetAirThicknessInMillimeters(12);
- returnParameters->SetMinBackgroundAbsorption(0.1);
- returnParameters->SetMaxBackgroundAbsorption(0.1);
- returnParameters->SetBackgroundAnisotropy(0.9);
- returnParameters->SetBackgroundScattering(15);
- returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
- returnParameters->SetDoPartialVolume(true);
- returnParameters->SetMinNumberOfVessels(1);
- returnParameters->SetMaxNumberOfVessels(7);
- returnParameters->SetMinVesselAbsorption(2);
- returnParameters->SetMaxVesselAbsorption(8);
- returnParameters->SetMinVesselAnisotropy(0.9);
- returnParameters->SetMaxVesselAnisotropy(0.9);
- returnParameters->SetMinVesselBending(0.1);
- returnParameters->SetMaxVesselBending(0.3);
- returnParameters->SetMinVesselRadiusInMillimeters(0.5);
- returnParameters->SetMaxVesselRadiusInMillimeters(4);
- returnParameters->SetMinVesselScattering(15);
- returnParameters->SetMaxVesselScattering(15);
- returnParameters->SetMinVesselZOrigin(2.2);
- returnParameters->SetMaxVesselZOrigin(4);
- returnParameters->SetVesselBifurcationFrequency(5000);
- returnParameters->SetRandomizePhysicalProperties(false);
- returnParameters->SetSkinThicknessInMillimeters(0);
- returnParameters->SetUseRngSeed(false);
- returnParameters->SetVoxelSpacingInCentimeters(0.03);
- returnParameters->SetXDim(140);
- returnParameters->SetYDim(200);
- returnParameters->SetZDim(180);
- return returnParameters;
-}
-
-TissueGeneratorParameters::Pointer CreateSinglevessel_19_10_17_Parameters()
-{
- auto returnParameters = TissueGeneratorParameters::New();
- returnParameters->SetAirThicknessInMillimeters(12);
- returnParameters->SetMinBackgroundAbsorption(0.1);
- returnParameters->SetMaxBackgroundAbsorption(0.1);
- returnParameters->SetBackgroundAnisotropy(0.9);
- returnParameters->SetBackgroundScattering(15);
- returnParameters->SetCalculateNewVesselPositionCallback(&VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
- returnParameters->SetDoPartialVolume(true);
- returnParameters->SetMinNumberOfVessels(1);
- returnParameters->SetMaxNumberOfVessels(1);
- returnParameters->SetMinVesselAbsorption(2);
- returnParameters->SetMaxVesselAbsorption(8);
- returnParameters->SetMinVesselAnisotropy(0.9);
- returnParameters->SetMaxVesselAnisotropy(0.9);
- returnParameters->SetMinVesselBending(0.1);
- returnParameters->SetMaxVesselBending(0.3);
- returnParameters->SetMinVesselRadiusInMillimeters(0.5);
- returnParameters->SetMaxVesselRadiusInMillimeters(4);
- returnParameters->SetMinVesselScattering(15);
- returnParameters->SetMaxVesselScattering(15);
- returnParameters->SetMinVesselZOrigin(2.2);
- returnParameters->SetMaxVesselZOrigin(4);
- returnParameters->SetVesselBifurcationFrequency(5000);
- returnParameters->SetRandomizePhysicalProperties(false);
- returnParameters->SetSkinThicknessInMillimeters(0);
- returnParameters->SetUseRngSeed(false);
- returnParameters->SetVoxelSpacingInCentimeters(0.03);
- returnParameters->SetXDim(140);
- returnParameters->SetYDim(200);
- returnParameters->SetZDim(180);
- return returnParameters;
-}
-
-struct InputParameters
-{
- std::string saveFolderPath;
- std::string identifyer;
- std::string exePath;
- std::string probePath;
- bool verbose;
-};
-
-InputParameters parseInput(int argc, char* argv[])
-{
- MITK_INFO << "Paring arguments...";
- mitkCommandLineParser parser;
- // set general information
- parser.setCategory("MITK-Photoacoustics");
- parser.setTitle("Mitk Tissue Batch Generator");
- parser.setDescription("Creates in silico tissue in batch processing and automatically calculates fluence values for the central slice of the volume.");
- parser.setContributor("Computer Assisted Medical Interventions, DKFZ");
-
- // how should arguments be prefixed
- parser.setArgumentPrefix("--", "-");
- // add each argument, unless specified otherwise each argument is optional
- // see mitkCommandLineParser::addArgument for more information
- parser.beginGroup("Required parameters");
- parser.addArgument(
- "savePath", "s", mitkCommandLineParser::Directory,
- "Input save folder (directory)", "input save folder",
- us::Any(), false, false, false, mitkCommandLineParser::Input);
- parser.addArgument(
- "mitkMcxyz", "m", mitkCommandLineParser::File,
- "MitkMcxyz binary (file)", "path to the MitkMcxyz binary",
- us::Any(), false, false, false, mitkCommandLineParser::Output);
- parser.endGroup();
- parser.beginGroup("Optional parameters");
- parser.addArgument(
- "probe", "p", mitkCommandLineParser::File,
- "xml probe file (file)", "file to the definition of the used probe (*.xml)",
- us::Any(), true, false, false, mitkCommandLineParser::Output);
- parser.addArgument(
- "verbose", "v", mitkCommandLineParser::Bool,
- "Verbose Output", "Whether to produce verbose, or rather debug output");
- parser.addArgument(
- "identifyer", "i", mitkCommandLineParser::String,
- "Generator identifyer (string)", "A unique identifyer for the calculation instance");
-
- InputParameters input;
-
- std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
- if (parsedArgs.size() == 0)
- exit(-1);
-
- if (parsedArgs.count("verbose"))
- {
- MITK_INFO << "verbose";
- input.verbose = us::any_cast<bool>(parsedArgs["verbose"]);
- }
- else
- {
- input.verbose = false;
- }
-
- if (parsedArgs.count("savePath"))
- {
- MITK_INFO << "savePath";
- input.saveFolderPath = us::any_cast<std::string>(parsedArgs["savePath"]);
- }
-
- if (parsedArgs.count("mitkMcxyz"))
- {
- MITK_INFO << "mitkMcxyz";
- input.exePath = us::any_cast<std::string>(parsedArgs["mitkMcxyz"]);
- }
-
- if (parsedArgs.count("probe"))
- {
- MITK_INFO << "probe";
- input.probePath = us::any_cast<std::string>(parsedArgs["probe"]);
- }
-
- if (parsedArgs.count("identifyer"))
- {
- MITK_INFO << "identifyer";
- input.identifyer = us::any_cast<std::string>(parsedArgs["identifyer"]);
- }
- else
- {
- MITK_INFO << "generating identifyer";
- input.identifyer = mitk::UIDGenerator().GetUID();
- }
- MITK_INFO << "Paring arguments...[Done]";
- return input;
-}
-
-int main(int argc, char * argv[])
-{
- auto input = parseInput(argc, argv);
- unsigned int iterationNumber = 0;
-
- while (true)
- {
- auto parameters = CreateBaselineHB_13_02_18_Parameters();
- MITK_INFO(input.verbose) << "Generating tissue..";
- auto resultTissue = InSilicoTissueGenerator::GenerateInSilicoData(parameters);
- MITK_INFO(input.verbose) << "Generating tissue..[Done]";
-
- auto inputfolder = std::string(input.saveFolderPath + "input/");
- auto outputfolder = std::string(input.saveFolderPath + "output/");
- if (!itksys::SystemTools::FileIsDirectory(inputfolder))
- {
- itksys::SystemTools::MakeDirectory(inputfolder);
- }
- if (!itksys::SystemTools::FileIsDirectory(outputfolder))
- {
- itksys::SystemTools::MakeDirectory(outputfolder);
- }
-
- std::string savePath = input.saveFolderPath + "input/BaselineHB_" + input.identifyer +
- "_" + std::to_string(iterationNumber) + ".nrrd";
- mitk::IOUtil::Save(resultTissue->ConvertToMitkImage(), savePath);
- std::string outputPath = input.saveFolderPath + "output/BaselineHB_" + input.identifyer +
- "_" + std::to_string(iterationNumber) + "/";
-
- if (!itksys::SystemTools::FileIsDirectory(outputPath))
- {
- itksys::SystemTools::MakeDirectory(outputPath);
- }
-
- outputPath = outputPath + "Fluence_BaselineHB_" + input.identifyer + "_" + std::to_string(iterationNumber);
-
- MITK_INFO(input.verbose) << "Simulating fluence..";
- for(double yo = -1.8; yo <= 1.81; yo=yo+0.12)
- {
- std::string yo_string = std::to_string(round(yo*100)/100.0);
- int result = -4;
- if(!input.probePath.empty())
- result = std::system(std::string(input.exePath + " -i " + savePath + " -o " +
- (outputPath + "_yo" + yo_string + ".nrrd") +
- " -yo " + yo_string + " -p " + input.probePath +
- " -n 100000000").c_str());
- else
- result = std::system(std::string(input.exePath + " -i " + savePath + " -o " +
- (outputPath + "_yo" + yo_string + ".nrrd") +
- " -yo " + yo_string + " -n 100000000").c_str());
- MITK_INFO << "yo: " << yo_string << ": " << result;
- }
-
- MITK_INFO(input.verbose) << "Simulating fluence..[Done]";
-
- iterationNumber++;
- }
-}
diff --git a/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/files.cmake b/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/files.cmake
deleted file mode 100644
index d4e42c83d5..0000000000
--- a/Modules/PhotoacousticsLib/MitkTissueBatchGenerator/files.cmake
+++ /dev/null
@@ -1,3 +0,0 @@
-set(CPP_FILES
- TissueBatchGenerator.cpp
-)
diff --git a/Modules/PhotoacousticsLib/Resources/photoacoustics128x128.png b/Modules/PhotoacousticsLib/Resources/photoacoustics128x128.png
deleted file mode 100644
index 05deecf751..0000000000
Binary files a/Modules/PhotoacousticsLib/Resources/photoacoustics128x128.png and /dev/null differ
diff --git a/Modules/PhotoacousticsLib/Resources/spectralLIB.dat b/Modules/PhotoacousticsLib/Resources/spectralLIB.dat
deleted file mode 100644
index b2e2f59f24..0000000000
--- a/Modules/PhotoacousticsLib/Resources/spectralLIB.dat
+++ /dev/null
@@ -1 +0,0 @@
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0.00374 0.0001 2680 332 541 499 0.00366 0.0001 2660 333 547 505 0.00359 0.0001 2630 334 554 512 0.00351 0.0001 2600 335 558 523 0.00344 0.0001 2580 336 562 534 0.00337 0.0001 2550 337 566 547 0.00329 0.0001 2530 338 570 559 0.00322 0.0001 2500 339 574 570 0.00314 0.0001 2480 340 578 581 0.00307 0.0001 2450 341 581 588 0.003 0.0001 2430 342 584 594 0.00292 0.0001 2410 343 587 601 0.00285 0.0001 2380 344 590 608 0.00277 0.0001 2360 345 587 615 0.0027 0.0001 2340 346 584 621 0.00263 0.0001 2310 347 581 629 0.00255 0.0001 2290 348 578 636 0.00248 0.0001 2270 349 574 645 0.0024 0.0001 2250 350 571 654 0.00233 0.0001 2230 351 567 663 0.00228 0.0001 2210 352 562 672 0.00224 0.0001 2190 353 559 681 0.00219 0.0001 2160 354 555 690 0.00214 0.0001 2140 355 550 699 0.0021 0.0001 2120 356 544 707 0.00205 0.0001 2100 357 534 712 0.00201 0.0001 2090 358 524 716 0.00196 0.0001 2070 359 516 719 0.00191 0.0001 2050 360 507 723 0.00187 0.0001 2030 361 501 726 0.00182 0.0001 2010 362 494 728 0.00177 0.0001 1990 363 488 731 0.00173 0.0001 1970 364 481 733 0.00168 0.0001 1950 365 477 736 0.00163 0.0001 1940 366 474 738 0.00159 0.0001 1920 367 471 741 0.00154 0.0001 1900 368 469 744 0.00149 0.0001 1880 369 470 747 0.00145 0.0001 1870 370 472 750 0.0014 0.0001 1850 371 481 752 0.00136 0.0001 1830 372 490 755 0.00131 0.0001 1820 373 500 758 0.00126 0.0001 1800 374 509 761 0.00122 0.0001 1790 375 520 764 0.00117 0.0001 1770 376 530 767 0.00115 0.0001 1750 377 542 770 0.00112 0.0001 1740 378 554 773 0.0011 0.0001 1720 379 570 776 0.00108 0.0001 1710 380 587 778 0.00105 0.0001 1690 381 607 778 0.00103 0.0001 1680 382 626 778 0.001 0.0001 1660 383 649 787 0.000981 0.0001 1650 384 672 796 0.000958 0.0001 1640 385 698 810 0.000934 0.0001 1620 386 724 824 0.00091 0.0001 1610 387 758 839 0.000887 0.0001 1590 388 793 854 0.000863 0.0001 1580 389 846 876 0.00084 0.0001 1570 390 898 898 0.000816 0.0001 1550 391 957 931 0.000792 0.0001 1540 392 1020 964 0.000769 0.0001 1530 393 1080 995 0.000745 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0.000404 0.0001 1190 423 2160 2390 0.000396 0.0001 1190 424 2010 2470 0.000388 0.0001 1180 425 1880 2520 0.00038 0.0001 1170 426 1750 2580 0.000376 0.0001 1160 427 1630 2630 0.000372 0.0001 1150 428 1520 2680 0.000368 0.0001 1140 429 1420 2760 0.000364 8.28 1130 430 1320 2830 0.00036 8.216 1120 431 1230 2890 0.000356 8.158 1110 432 1150 2960 0.000352 8.069 1110 433 1020 2960 0.000348 7.927 1100 434 885 2960 0.000344 7.832 1090 435 798 2940 0.00034 7.721 1080 436 711 2930 0.000336 7.652 1070 437 675 2810 0.000332 7.623 1060 438 638 2690 0.000328 7.56 1060 439 594 2450 0.000324 7.474 1050 440 549 2210 0.00032 7.383 1040 441 523 2080 0.000316 7.244 1030 442 497 1950 0.000312 7.104 1020 443 466 1730 0.000308 7 1020 444 436 1510 0.000304 6.899 1010 445 422 1390 0.0003 6.811 1000 446 409 1270 0.000296 6.729 994 447 384 1100 0.000292 6.659 986 448 359 928 0.000288 6.571 979 449 348 741 0.000284 6.464 972 450 336 553 0.00028 6.375 965 451 326 444 0.000279 6.291 957 452 315 335 0.000277 6.21 950 453 301 265 0.000276 6.135 943 454 287 194 0.000275 6.049 937 455 276 179 0.000273 5.95 930 456 265 164 0.000272 5.837 923 457 260 152 0.000271 5.751 916 458 254 139 0.000269 5.663 910 459 246 132 0.000268 5.593 903 460 238 125 0.000267 5.523 897 461 230 119 0.000265 5.413 890 462 221 112 0.000264 5.288 884 463 217 108 0.000263 5.144 877 464 213 103 0.000262 4.985 871 465 206 100 0.00026 4.846 865 466 199 97.1 0.000259 4.72 859 467 193 94.2 0.000258 4.594 853 468 187 91.2 0.000256 4.513 846 469 182 88.8 0.000255 4.434 840 470 178 86.5 0.000254 4.327 835 471 174 84.2 0.000252 4.208 829 472 169 82 0.000251 4.084 823 473 165 81.3 0.00025 3.961 817 474 161 80.6 0.000248 3.843 811 475 158 79.9 0.000247 3.732 806 476 154 79.2 0.000247 3.635 800 477 151 78.9 0.000247 3.534 794 478 148 78.5 0.000247 3.452 789 479 146 78.2 0.000247 3.386 783 480 143 77.9 0.000248 3.315 778 481 140 78.8 0.000248 3.261 773 482 138 79.7 0.000248 3.192 767 483 136 80.6 0.000248 3.109 762 484 135 81.5 0.000248 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0.000445 0.785 497 550 230 286 0.00045 0.773 494 551 221 288 0.000464 0.763 491 552 212 290 0.000477 0.76 489 553 205 291 0.000491 0.757 486 554 197 292 0.000504 0.746 483 555 191 292 0.000518 0.733 480 556 185 292 0.000532 0.724 477 557 182 291 0.000545 0.718 474 558 179 290 0.000559 0.71 471 559 177 289 0.000572 0.704 468 560 175 288 0.000586 0.698 466 561 175 284 0.0006 0.69 463 562 175 280 0.000613 0.682 460 563 178 275 0.000627 0.673 457 564 182 271 0.00064 0.662 455 565 189 266 0.000654 0.653 452 566 195 261 0.000668 0.647 449 567 205 256 0.000681 0.641 447 568 215 251 0.000695 0.636 444 569 227 246 0.000708 0.63 442 570 238 241 0.000722 0.629 439 571 251 237 0.000736 0.633 436 572 263 232 0.000749 0.639 434 573 274 228 0.000763 0.632 431 574 285 223 0.000776 0.613 429 575 291 219 0.00079 0.589 426 576 297 215 0.00085 0.573 424 577 295 210 0.000911 0.562 422 578 293 206 0.000971 0.563 419 579 281 202 0.00103 0.566 417 580 268 198 0.00109 0.566 414 581 250 195 0.00115 0.564 412 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0.00314 0.464 289 647 2.06 20.9 0.00315 0.464 288 648 2.03 20.7 0.00317 0.464 286 649 2 20.4 0.00318 0.465 285 650 1.97 20.1 0.0032 0.471 283 651 1.94 19.8 0.00324 0.472 282 652 1.91 19.5 0.00328 0.467 281 653 1.88 19.2 0.00331 0.464 279 654 1.85 18.9 0.00335 0.457 278 655 1.82 18.6 0.00339 0.448 276 656 1.79 18.4 0.00343 0.438 275 657 1.77 18.1 0.00347 0.428 274 658 1.74 17.8 0.0035 0.424 272 659 1.73 17.5 0.00354 0.422 271 660 1.71 17.3 0.00358 0.418 269 661 1.7 17 0.00362 0.414 268 662 1.68 16.8 0.00366 0.413 267 663 1.67 16.6 0.00369 0.414 265 664 1.65 16.4 0.00373 0.419 264 665 1.64 16.1 0.00377 0.428 263 666 1.62 15.9 0.00381 0.439 261 667 1.61 15.7 0.00385 0.447 260 668 1.6 15.4 0.00388 0.452 259 669 1.59 15.2 0.00392 0.453 258 670 1.57 15 0.00396 0.45 256 671 1.56 14.7 0.004 0.452 255 672 1.55 14.5 0.00404 0.457 254 673 1.54 14.3 0.00407 0.462 252 674 1.53 14.1 0.00411 0.463 251 675 1.52 13.9 0.00415 0.457 250 676 1.51 13.7 0.00422 0.446 249 677 1.5 13.5 0.0043 0.433 248 678 1.5 13.3 0.00437 0.422 246 679 1.49 13.1 0.00445 0.413 245 680 1.49 12.9 0.00452 0.406 244 681 1.48 12.7 0.00459 0.398 243 682 1.48 12.5 0.00467 0.387 242 683 1.47 12.3 0.00474 0.375 240 684 1.47 12.1 0.00482 0.37 239 685 1.47 11.9 0.00489 0.369 238 686 1.46 11.7 0.00496 0.366 237 687 1.47 11.5 0.00504 0.361 236 688 1.47 11.3 0.00511 0.354 235 689 1.47 11.2 0.00519 0.348 233 690 1.48 11 0.00526 0.342 232 691 1.48 10.9 0.00533 0.338 231 692 1.49 10.7 0.00541 0.335 230 693 1.49 10.6 0.00548 0.331 229 694 1.5 10.4 0.00556 0.328 228 695 1.5 10.3 0.00563 0.324 227 696 1.51 10.2 0.0057 0.321 226 697 1.52 10 0.00578 0.324 225 698 1.53 9.89 0.00585 0.327 224 699 1.54 9.75 0.00593 0.325 223 700 1.55 9.61 0.006 0.323 221 701 1.56 9.47 0.0064 0.32 220 702 1.57 9.32 0.00679 0.319 219 703 1.59 9.18 0.00719 0.322 218 704 1.6 9.04 0.00758 0.326 217 705 1.61 8.9 0.00798 0.323 216 706 1.62 8.75 0.00838 0.318 215 707 1.64 8.62 0.00877 0.313 214 708 1.65 8.48 0.00917 0.31 213 709 1.67 8.36 0.00956 0.311 212 710 1.68 8.25 0.00996 0.315 211 711 1.7 8.13 0.0104 0.32 210 712 1.71 8.02 0.0108 0.321 209 713 1.73 7.9 0.0111 0.32 208 714 1.74 7.79 0.0115 0.321 207 715 1.76 7.67 0.0119 0.326 206 716 1.78 7.56 0.0123 0.334 205 717 1.8 7.44 0.0127 0.343 204 718 1.82 7.33 0.0131 0.351 204 719 1.84 7.21 0.0135 0.358 203 720 1.86 7.1 0.0139 0.367 202 721 1.88 6.99 0.0143 0.376 201 722 1.91 6.88 0.0147 0.383 200 723 1.93 6.77 0.0151 0.39 199 724 1.95 6.66 0.0155 0.401 198 725 1.97 6.55 0.0159 0.415 197 726 1.99 6.45 0.0163 0.43 196 727 2.02 6.31 0.0167 0.447 195 728 2.04 6.17 0.0171 0.463 194 729 2.06 6.04 0.0175 0.48 193 730 2.09 5.9 0.0179 0.499 193 731 2.11 5.9 0.0183 0.516 192 732 2.14 5.9 0.0187 0.535 191 733 2.16 5.9 0.0191 0.552 190 734 2.18 5.9 0.0195 0.564 189 735 2.21 5.9 0.0199 0.576 188 736 2.24 5.9 0.0203 0.589 187 737 2.28 5.9 0.0207 0.6 187 738 2.32 5.89 0.0212 0.616 186 739 2.35 5.93 0.0216 0.636 185 740 2.39 5.98 0.022 0.654 184 741 2.42 6.1 0.0224 0.68 183 742 2.46 6.22 0.0228 0.707 182 743 2.5 6.34 0.0232 0.735 182 744 2.53 6.47 0.0236 0.768 181 745 2.57 6.62 0.024 0.801 180 746 2.61 6.78 0.0244 0.837 179 747 2.65 6.96 0.0248 0.874 178 748 2.69 7.14 0.0252 0.908 178 749 2.73 7.33 0.0256 0.941 177 750 2.77 7.52 0.026 0.972 176 751 2.81 7.82 0.0259 1.001 175 752 2.86 8.11 0.0258 1.03 174 753 2.9 8.19 0.0258 1.059 174 754 2.94 8.26 0.0257 1.089 173 755 2.97 8.31 0.0256 1.12 172 756 3.01 8.36 0.0255 1.155 171 757 3.04 8.36 0.0254 1.19 171 758 3.07 8.36 0.0254 1.227 170 759 3.11 8.32 0.0253 1.258 169 760 3.14 8.29 0.0252 1.278 168 761 3.17 8.18 0.0251 1.289 168 762 3.2 8.08 0.025 1.29 167 763 3.23 7.95 0.025 1.273 166 764 3.27 7.82 0.0249 1.249 166 765 3.3 7.68 0.0248 1.206 165 766 3.33 7.55 0.0247 1.153 164 767 3.37 7.42 0.0246 1.089 163 768 3.41 7.29 0.0246 1.021 163 769 3.44 7.16 0.0245 0.948 162 770 3.48 7.02 0.0244 0.871 161 771 3.52 6.89 0.0243 0.793 161 772 3.55 6.76 0.0242 0.719 160 773 3.59 6.63 0.0242 0.653 159 774 3.63 6.5 0.0241 0.596 159 775 3.66 6.36 0.024 0.553 158 776 3.69 6.23 0.0238 0.515 157 777 3.72 6.1 0.0237 0.481 156 778 3.75 5.97 0.0235 0.451 156 779 3.77 5.86 0.0234 0.426 155 780 3.8 5.76 0.0232 0.409 154 781 3.83 5.65 0.023 0.391 154 782 3.86 5.55 0.0229 0.378 153 783 3.89 5.44 0.0227 0.366 153 784 3.91 5.34 0.0226 0.36 152 785 3.94 5.23 0.0224 0.357 151 786 3.96 5.13 0.0222 0.355 151 787 3.98 5.03 0.0221 0.353 150 788 4.01 4.94 0.0219 0.349 149 789 4.03 4.85 0.0218 0.346 149 790 4.05 4.77 0.0216 0.346 148 791 4.07 4.69 0.0214 0.347 147 792 4.09 4.6 0.0213 0.347 147 793 4.11 4.52 0.0211 0.347 146 794 4.13 4.44 0.021 0.352 146 795 4.17 4.37 0.0208 0.359 145 796 4.21 4.3 0.0206 0.369 144 797 4.27 4.24 0.0205 0.379 144 798 4.32 4.19 0.0203 0.387 143 799 4.35 4.13 0.0202 0.393 143 800 4.37 4.08 0.02 0.403 142 801 4.4 4.03 0.02 0.413 141 802 4.43 3.98 0.02 0.424 141 803 4.46 3.97 0.02 0.434 140 804 4.48 3.95 0.0199 0.442 140 805 4.5 3.93 0.0199 0.454 139 806 4.52 3.91 0.0199 0.467 138 807 4.55 3.89 0.0199 0.482 138 808 4.58 3.87 0.0199 0.497 137 809 4.61 3.86 0.0199 0.511 137 810 4.63 3.84 0.0199 0.527 136 811 4.65 3.83 0.0203 0.547 136 812 4.67 3.81 0.0207 0.567 135 813 4.69 3.8 0.0211 0.583 135 814 4.71 3.78 0.0215 0.594 134 815 4.73 3.77 0.0219 0.603 133 816 4.75 3.76 0.0223 0.615 133 817 4.79 3.74 0.0227 0.633 132 818 4.83 3.73 0.0231 0.654 132 819 4.87 3.72 0.0235 0.674 131 820 4.91 3.71 0.0239 0.691 131 821 4.94 3.71 0.0247 0.708 130 822 4.98 3.71 0.0255 0.724 130 823 5.02 3.71 0.0264 0.74 129 824 5.06 3.71 0.0272 0.758 129 825 5.09 3.71 0.028 0.775 128 826 5.12 3.71 0.0282 0.786 128 827 5.14 3.71 0.0284 0.796 127 828 5.17 3.71 0.0286 0.799 127 829 5.19 3.71 0.0289 0.802 126 830 5.22 3.71 0.0291 0.803 126 831 5.24 3.71 0.0296 0.803 125 832 5.26 3.71 0.0302 0.801 125 833 5.29 3.71 0.0308 0.794 124 834 5.31 3.71 0.0313 0.785 124 835 5.34 3.71 0.0319 0.775 123 836 5.36 3.71 0.0325 0.764 123 837 5.39 3.71 0.033 0.757 122 838 5.42 3.71 0.0336 0.751 122 839 5.44 3.71 0.0341 0.739 121 840 5.47 3.71 0.0347 0.726 121 841 5.5 3.71 0.0355 0.715 120 842 5.53 3.71 0.0364 0.703 120 843 5.56 3.71 0.0372 0.692 119 844 5.58 3.71 0.038 0.685 119 845 5.6 3.7 0.0389 0.678 118 846 5.62 3.7 0.0397 0.669 118 847 5.63 3.7 0.0405 0.661 117 848 5.64 3.7 0.0413 0.651 117 849 5.65 3.7 0.0422 0.643 116 850 5.67 3.7 0.043 0.637 116 851 5.68 3.7 0.0434 0.633 116 852 5.69 3.7 0.0438 0.632 115 853 5.7 3.7 0.0441 0.631 115 854 5.71 3.7 0.0445 0.633 114 855 5.73 3.7 0.0449 0.639 114 856 5.74 3.7 0.0453 0.647 113 857 5.77 3.7 0.0456 0.656 113 858 5.8 3.71 0.046 0.662 112 859 5.82 3.71 0.0464 0.666 112 860 5.85 3.72 0.0468 0.674 112 861 5.87 3.72 0.0473 0.68 111 862 5.9 3.73 0.0478 0.69 111 863 5.92 3.73 0.0483 0.705 110 864 5.95 3.74 0.0489 0.724 110 865 5.97 3.74 0.0494 0.751 109 866 5.99 3.75 0.0499 0.786 109 867 6 3.75 0.0504 0.822 109 868 6.01 3.76 0.051 0.86 108 869 6.03 3.77 0.0515 0.899 108 870 6.04 3.78 0.052 0.938 107 871 6.05 3.79 0.0528 0.979 107 872 6.07 3.8 0.0536 1.022 107 873 6.08 3.81 0.0544 1.074 106 874 6.09 3.82 0.0552 1.133 106 875 6.11 3.83 0.056 1.198 105 876 6.12 3.85 0.056 1.264 105 877 6.13 3.86 0.056 1.345 105 878 6.15 3.87 0.056 1.43 104 879 6.16 3.88 0.056 1.527 104 880 6.18 3.89 0.056 1.636 103 881 6.19 3.9 0.0564 1.752 103 882 6.21 3.91 0.0569 1.867 103 883 6.22 3.92 0.0573 1.992 102 884 6.24 3.93 0.0578 2.121 102 885 6.25 3.94 0.0582 2.262 101 886 6.27 3.94 0.0587 2.414 101 887 6.28 3.95 0.0591 2.581 101 888 6.29 3.96 0.0595 2.754 100 889 6.3 3.97 0.06 2.932 99.9 890 6.31 3.98 0.0604 3.116 99.6 891 6.32 3.99 0.0612 3.305 99.2 892 6.33 4 0.0619 3.491 98.8 893 6.34 4.01 0.0627 3.674 98.4 894 6.35 4.02 0.0635 3.833 98.1 895 6.36 4.03 0.0642 3.983 97.7 896 6.37 4.04 0.065 4.121 97.4 897 6.38 4.05 0.0657 4.256 97 898 6.39 4.06 0.0665 4.384 96.6 899 6.4 4.07 0.0672 4.506 96.3 900 6.42 4.08 0.068 4.633 95.9 901 6.43 4.09 0.0685 4.766 95.6 902 6.44 4.1 0.069 4.915 95.2 903 6.45 4.1 0.0695 5.078 94.9 904 6.46 4.11 0.07 5.267 94.5 905 6.47 4.12 0.0705 5.472 94.2 906 6.48 4.12 0.0709 5.721 93.8 907 6.48 4.13 0.0714 5.994 93.5 908 6.49 4.13 0.0719 6.316 93.1 909 6.49 4.14 0.0724 6.663 92.8 910 6.5 4.15 0.0729 7.046 92.5 911 6.51 4.15 0.0765 7.438 92.1 912 6.51 4.16 0.0802 7.837 91.8 913 6.52 4.16 0.0838 8.234 91.4 914 6.53 4.17 0.0875 8.621 91.1 915 6.53 4.17 0.0911 8.994 90.8 916 6.54 4.17 0.0947 9.354 90.5 917 6.54 4.17 0.0984 9.683 90.1 918 6.55 4.16 0.102 10 89.8 919 6.55 4.16 0.106 10.32 89.5 920 6.55 4.16 0.109 10.65 89.2 921 6.56 4.16 0.116 10.99 88.8 922 6.56 4.16 0.123 11.33 88.5 923 6.57 4.16 0.13 11.67 88.2 924 6.57 4.16 0.137 12 87.9 925 6.57 4.15 0.144 12.31 87.6 926 6.57 4.14 0.15 12.6 87.2 927 6.56 4.12 0.156 12.82 86.9 928 6.56 4.11 0.161 12.99 86.6 929 6.55 4.1 0.167 13.07 86.3 930 6.54 4.09 0.173 13.1 86 931 6.54 4.06 0.182 12.99 85.7 932 6.53 4.03 0.192 12.83 85.4 933 6.52 3.99 0.201 12.53 85.1 934 6.52 3.95 0.211 12.18 84.8 935 6.51 3.91 0.22 11.75 84.5 936 6.51 3.87 0.23 11.26 84.2 937 6.51 3.83 0.239 10.7 83.9 938 6.51 3.79 0.248 10.08 83.6 939 6.5 3.75 0.258 9.433 83.3 940 6.5 3.71 0.267 8.754 83 941 6.5 3.67 0.28 8.088 82.7 942 6.5 3.63 0.292 7.446 82.4 943 6.49 3.59 0.304 6.822 82.1 944 6.49 3.54 0.316 6.25 81.8 945 6.49 3.48 0.329 5.704 81.5 946 6.48 3.43 0.341 5.234 81.3 947 6.47 3.38 0.353 4.802 81 948 6.46 3.33 0.365 4.445 80.7 949 6.46 3.28 0.378 4.109 80.4 950 6.45 3.22 0.39 3.799 80.1 951 6.44 3.17 0.393 3.519 79.8 952 6.43 3.12 0.396 3.274 79.6 953 6.42 3.09 0.399 3.046 79.3 954 6.41 3.05 0.402 2.852 79 955 6.4 3.01 0.405 2.666 78.7 956 6.39 2.97 0.408 2.504 78.5 957 6.38 2.93 0.411 2.358 78.2 958 6.37 2.89 0.414 2.242 77.9 959 6.36 2.85 0.417 2.133 77.6 960 6.35 2.81 0.42 2.047 77.4 961 6.34 2.78 0.423 1.975 77.1 962 6.33 2.74 0.426 1.917 76.8 963 6.32 2.69 0.429 1.86 76.6 964 6.31 2.65 0.432 1.808 76.3 965 6.3 2.59 0.435 1.753 76 966 6.28 2.53 0.438 1.693 75.8 967 6.27 2.48 0.441 1.639 75.5 968 6.25 2.42 0.444 1.589 75.3 969 6.24 2.36 0.447 1.554 75 970 6.22 2.3 0.45 1.528 74.7 971 6.21 2.26 0.45 1.51 74.5 972 6.19 2.22 0.45 1.491 74.2 973 6.18 2.19 0.45 1.463 74 974 6.16 2.15 0.45 1.431 73.7 975 6.14 2.12 0.45 1.413 73.5 976 6.13 2.08 0.446 1.408 73.2 977 6.1 2.05 0.442 1.414 73 978 6.08 2.01 0.438 1.421 72.7 979 6.06 1.97 0.434 1.423 72.5 980 6.04 1.93 0.43 1.417 72.2 981 6.02 1.88 0.428 1.407 72 982 6 1.84 0.426 1.406 71.7 983 5.98 1.8 0.424 1.42 71.5 984 5.95 1.76 0.422 1.441 71.3 985 5.93 1.72 0.42 1.481 71 986 5.9 1.68 0.418 1.524 70.8 987 5.87 1.64 0.416 1.564 70.5 988 5.84 1.6 0.414 1.607 70.3 989 5.81 1.56 0.412 1.652 70.1 990 5.78 1.52 0.41 1.716 69.8 991 5.75 1.48 0.405 1.793 69.6 992 5.72 1.43 0.4 1.891 69.4 993 5.69 1.39 0.395 1.994 69.1 994 5.66 1.35 0.39 2.087 68.9 995 5.63 1.31 0.385 2.178 68.7 996 5.6 1.27 0.38 2.272 68.4 997 5.57 1.23 0.375 2.366 68.2 998 5.54 1.19 0.37 2.464 68 999 5.51 1.15 0.365 2.56 67.8 1000 5.48 1.11 0.36 2.654 67.5
diff --git a/Modules/PhotoacousticsLib/files.cmake b/Modules/PhotoacousticsLib/files.cmake
deleted file mode 100644
index 5bc7c84dfc..0000000000
--- a/Modules/PhotoacousticsLib/files.cmake
+++ /dev/null
@@ -1,65 +0,0 @@
-SET(H_FILES
- include/mitkPAPropertyCalculator.h
- include/mitkPAVector.h
- include/mitkPATissueGeneratorParameters.h
- include/mitkPAInSilicoTissueVolume.h
- include/mitkPATissueGenerator.h
- include/mitkPAVesselTree.h
- include/mitkPAVessel.h
- include/mitkPAVesselMeanderStrategy.h
- include/mitkPANoiseGenerator.h
- include/mitkPAVolume.h
- include/mitkPAComposedVolume.h
- include/mitkPASlicedVolumeGenerator.h
- include/mitkPAProbe.h
- include/mitkPALightSource.h
- include/mitkPAIOUtil.h
- include/mitkPAMonteCarloThreadHandler.h
- include/mitkPASimulationBatchGenerator.h
- include/mitkPAFluenceYOffsetPair.h
- include/mitkPAVolumeManipulator.h
- include/mitkPAVesselProperties.h
- include/mitkPASimulationBatchGeneratorParameters.h
- include/mitkPAExceptions.h
- include/mitkPASpectralUnmixingFilterBase.h
- include/mitkPALinearSpectralUnmixingFilter.h
- include/mitkPASpectralUnmixingSO2.h
- include/mitkPASpectralUnmixingFilterLagrange.h
- include/mitkPASpectralUnmixingFilterSimplex.h
- include/mitkPASpectralUnmixingFilterVigra.h
-)
-
-set(CPP_FILES
- Domain/Vessel/mitkPAVesselTree.cpp
- Domain/Vessel/mitkPAVessel.cpp
- Domain/Vessel/mitkPAVesselMeanderStrategy.cpp
- Domain/Vessel/mitkPAVesselProperties.cpp
- Domain/Volume/mitkPAInSilicoTissueVolume.cpp
- Domain/Volume/mitkPAVolume.cpp
- Domain/Volume/mitkPAComposedVolume.cpp
- Domain/Volume/mitkPAFluenceYOffsetPair.cpp
- Generator/mitkPATissueGenerator.cpp
- Generator/mitkPANoiseGenerator.cpp
- Generator/mitkPASlicedVolumeGenerator.cpp
- Generator/mitkPASimulationBatchGenerator.cpp
- Generator/mitkPASimulationBatchGeneratorParameters.cpp
- IO/mitkPAIOUtil.cpp
- Utils/mitkPAPropertyCalculator.cpp
- Utils/mitkPAVector.cpp
- Utils/mitkPATissueGeneratorParameters.cpp
- Utils/mitkPAVolumeManipulator.cpp
- Utils/ProbeDesign/mitkPAProbe.cpp
- Utils/ProbeDesign/mitkPALightSource.cpp
- Utils/Thread/mitkPAMonteCarloThreadHandler.cpp
- SUFilter/mitkPASpectralUnmixingFilterBase.cpp
- SUFilter/mitkPALinearSpectralUnmixingFilter.cpp
- SUFilter/mitkPASpectralUnmixingSO2.cpp
- SUFilter/mitkPASpectralUnmixingFilterSimplex.cpp
- SUFilter/mitkPASpectralUnmixingFilterVigra.cpp
- SUFilter/mitkPASpectralUnmixingFilterLagrange.cpp
- Utils/mitkPAVesselDrawer.cpp
-)
-
-set(RESOURCE_FILES
- spectralLIB.dat
-)
diff --git a/Modules/PhotoacousticsLib/include/mitkPAComposedVolume.h b/Modules/PhotoacousticsLib/include/mitkPAComposedVolume.h
deleted file mode 100644
index da76c63790..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAComposedVolume.h
+++ /dev/null
@@ -1,86 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICCOMPOSEDVOLUME_H
-#define MITKPHOTOACOUSTICCOMPOSEDVOLUME_H
-
-#include <MitkPhotoacousticsLibExports.h>
-
-#include <mitkPAInSilicoTissueVolume.h>
-#include <mitkPAFluenceYOffsetPair.h>
-#include <vector>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- /**
- * @brief The ComposedVolume class provides the means to systematically collect nrrd files that correspond to
- * different simulation slices of the same InSilicoTissueVolume.
- *
- * An instance of this class is needed for the SlicedVolumeGenerator
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT ComposedVolume : public itk::Object
- {
- public:
- mitkClassMacroItkParent(ComposedVolume, itk::Object);
- mitkNewMacro1Param(Self, InSilicoTissueVolume::Pointer);
-
- /**
- * @brief fluenceYOffsetPair
- *
- * @param fluenceYOffsetPair
- */
- void AddSlice(mitk::pa::FluenceYOffsetPair::Pointer fluenceYOffsetPair);
-
- /**
- * @brief GetNumberOfFluenceComponents
- * @return the number of fluence components encapsuled by this ComposedVolume.
- */
- int GetNumberOfFluenceComponents();
-
- /**
- * @brief GetFluenceValue
- * @param fluenceComponent
- * @param x
- * @param y
- * @param z
- * @return the fluence value for a specific fluence component index at the given 3D location.
- */
- double GetFluenceValue(int fluenceComponent, int x, int y, int z);
-
- /**
- * @brief GetYOffsetForFluenceComponentInPixels
- * @param fluenceComponent
- * @return the y-offset value for a given fluence component index.
- */
- int GetYOffsetForFluenceComponentInPixels(int fluenceComponent);
-
- void Sort();
-
- itkGetMacro(GroundTruthVolume, InSilicoTissueVolume::Pointer);
-
- protected:
- ComposedVolume(InSilicoTissueVolume::Pointer groundTruthVolume);
- ~ComposedVolume() override;
-
- private:
- int m_FluenceComponents;
- InSilicoTissueVolume::Pointer m_GroundTruthVolume;
- std::vector<mitk::pa::FluenceYOffsetPair::Pointer> m_FluenceValues;
- };
- }
-}
-
-#endif // MITKPHOTOACOUSTICCOMPOSEDVOLUME_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAExceptions.h b/Modules/PhotoacousticsLib/include/mitkPAExceptions.h
deleted file mode 100644
index 5eb8da3baa..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAExceptions.h
+++ /dev/null
@@ -1,66 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKEXCEPTIONS_H
-#define MITKEXCEPTIONS_H
-
-#include <MitkPhotoacousticsLibExports.h>
-
-#include <mitkCommon.h>
-
-//std
-#include <string>
-#include <exception>
-
-namespace mitk {
- namespace pa {
- /**
- *@brief this exception is thrown if an invalid input occurs
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT InvalidInputException : public std::exception
- {
- std::string m_InvalidParameter;
- public:
- InvalidInputException(std::string invalidparameter)
- {
- m_InvalidParameter = invalidparameter;
- MITK_ERROR << GetFullMessage();
- }
-
- const std::string GetFullMessage() const throw()
- {
- return "InvalidInputException: " + m_InvalidParameter;
- }
- };
-
- /**
- *@brief this exception is thrown if an invalid value is supposed to be processed
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT InvalidValueException : public std::exception
- {
- std::string m_ValueType;
- public:
- InvalidValueException(std::string valueType)
- {
- m_ValueType = valueType;
- MITK_ERROR << GetFullMessage();
- }
-
- const std::string GetFullMessage() const throw()
- {
- return "InvalidValueException: " + m_ValueType;
- }
- };
- }
-}
-
-#endif // MITKEXCEPTIONS_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAFluenceYOffsetPair.h b/Modules/PhotoacousticsLib/include/mitkPAFluenceYOffsetPair.h
deleted file mode 100644
index 1d73fd4d94..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAFluenceYOffsetPair.h
+++ /dev/null
@@ -1,59 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPAFLUENCEYOFFSETPAIR_H
-#define MITKPAFLUENCEYOFFSETPAIR_H
-
-#include <MitkPhotoacousticsLibExports.h>
-#include <itkMacro.h>
-
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-#include <mitkPAVolume.h>
-
-namespace mitk
-{
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT FluenceYOffsetPair : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(FluenceYOffsetPair, itk::LightObject);
- mitkNewMacro2Param(Self, mitk::pa::Volume::Pointer, double);
-
- FluenceYOffsetPair(const FluenceYOffsetPair::Pointer other);
-
- const FluenceYOffsetPair &operator=(const FluenceYOffsetPair::Pointer other)
- {
- if (this == other)
- return *this;
-
- m_FluenceValue = other->GetFluenceValue();
- m_YOffsetInCentimeters = other->GetYOffsetInCentimeters();
-
- return *this;
- }
-
- mitk::pa::Volume::Pointer GetFluenceValue() const;
- double GetYOffsetInCentimeters() const;
-
- private:
- FluenceYOffsetPair(mitk::pa::Volume::Pointer fluenceValue, double yOffset);
-
- ~FluenceYOffsetPair() override;
-
- mitk::pa::Volume::Pointer m_FluenceValue;
- double m_YOffsetInCentimeters;
- };
- }
-}
-
-#endif // MITKPHOTOACOUSTICCOMPOSEDVOLUME_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAIOUtil.h b/Modules/PhotoacousticsLib/include/mitkPAIOUtil.h
deleted file mode 100644
index d2a5d01b19..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAIOUtil.h
+++ /dev/null
@@ -1,120 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICIO_H
-#define MITKPHOTOACOUSTICIO_H
-
-#include "MitkPhotoacousticsLibExports.h"
-
-#include <map>
-#include <mutex>
-#include <thread>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-#include "mitkPAVolume.h"
-#include <mitkPAInSilicoTissueVolume.h>
-#include <mitkPAFluenceYOffsetPair.h>
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT IOUtil final
- {
- public:
-
- struct Position
- {
- int x, z;
-
- bool operator <(const Position& rhs) const
- {
- return (x < rhs.x || ((x == rhs.x) && z < rhs.z));
- }
- };
-
- /**
- * @brief LoadFluenceContributionMaps loads multiple nrrd files from a given folder
- * and sorts them into a position map if such meta information is available in
- * the filename.
- *
- * As this method was specifically designed to load many fluence files, the
- * naming convention for the position values is:
- *
- * <b>*_pN,N,NFluence*.nrrd</b>
- *
- * @param foldername
- * @param blur
- * @param progress
- * @param log10
- *
- * @return
- */
- static std::map<Position, Volume::Pointer> LoadFluenceContributionMaps(
- std::string foldername, double blur, int* progress, bool log10 = false);
-
- /**
- * @brief loads a nrrd file from a given filename.
- * @param filename
- * @param sigma
- * @return nullptr if the given filename was invalid.
- */
- static Volume::Pointer LoadNrrd(std::string filename, double sigma = 0);
-
- /**
- *@brief returns the number of .nrrd files in a given directory
- */
- static int GetNumberOfNrrdFilesInDirectory(std::string directory);
-
- /**
- *@brief returns a list of all .nrrd files in a given directory
- */
- static std::vector<std::string> GetListOfAllNrrdFilesInDirectory(
- std::string directory, bool keepFileFormat = false);
-
- /**
- *@brief convenience method to check wether a given strings ends on a given substring.
- *@return false if the substring is longer than the string or if the strings are empty.
- */
- static bool DoesFileHaveEnding(std::string const &fullString, std::string const &ending);
-
- /**
- *@brief returns all child folders from a folder if there is no .nrrd file in the folder
- * If there IS a .nrrd file in the folder this method will return the given folder path.
- */
- static std::vector<std::string> GetAllChildfoldersFromFolder(std::string folderPath);
-
- /**
- *@brief loads an in silico tissue volume from a saved nrrd file.
- */
- static InSilicoTissueVolume::Pointer LoadInSilicoTissueVolumeFromNrrdFile(std::string filePath);
-
- /**
- * @brief LoadFluenceSimulation
- * Adds a MC Simulation nrrd file to this composed volume.
- * The given file needs to contain the meta information "y-offset".
- * This method ensures that all added slices are in the correct order
- * corresponding to their y-offset.
- *
- * @param fluenceSimulation path to the nrrd file on hard drive
- */
- static FluenceYOffsetPair::Pointer LoadFluenceSimulation(std::string fluenceSimulation);
-
- private:
-
- IOUtil();
- ~IOUtil();
- };
- }
-}
-#endif // MITKPHOTOACOUSTICIO_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAInSilicoTissueVolume.h b/Modules/PhotoacousticsLib/include/mitkPAInSilicoTissueVolume.h
deleted file mode 100644
index f72151ada8..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAInSilicoTissueVolume.h
+++ /dev/null
@@ -1,160 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICVOLUME_H
-#define MITKPHOTOACOUSTICVOLUME_H
-
-#include <MitkPhotoacousticsLibExports.h>
-#include <mitkImage.h>
-#include <mitkProperties.h>
-#include <mitkPATissueGeneratorParameters.h>
-#include <mitkPAVolume.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT InSilicoTissueVolume : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(InSilicoTissueVolume, itk::LightObject);
- mitkNewMacro2Param(Self, TissueGeneratorParameters::Pointer, std::mt19937*);
-
- enum SegmentationType
- {
- AIR = -1,
- BACKGROUND = 0,
- VESSEL = 1,
- FAT = 2,
- SKIN = 3
- };
-
- /**
- * @brief ConvertToMitkImage
- * @return a pointer to an mitk image containing this volume.
- */
- mitk::Image::Pointer ConvertToMitkImage();
-
- /**
- * @brief SetVolumeValues sets the values for aborption, scattering and anisotropy at the specified voxel location.
- *
- * @param x
- * @param y
- * @param z
- * @param absorption
- * @param scattering
- * @param anisotropy
- * @param segmentType
- */
- void SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy, SegmentationType segmentType);
-
- /**
- * @brief SetVolumeValues sets the values for aborption, scattering and anisotropy at the specified voxel location.
- *
- * @param x
- * @param y
- * @param z
- * @param absorption
- * @param scattering
- * @param anisotropy
- */
- void SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy);
-
- /**
- * @brief IsInsideVolume
- *
- * @param x
- * @param y
- * @param z
- * @return true if the voxel location is inside the volume
- */
- bool IsInsideVolume(int x, int y, int z);
-
- /**
- * @brief AddDoubleProperty adds a persistent property to the volume, which will be exported to the mitk image.
- *
- * @param label
- * @param value
- */
- void AddDoubleProperty(std::string label, double value);
-
- /**
- * @brief AddIntProperty adds a persistent property to the volume, which will be exported to the mitk image.
- *
- * @param label
- * @param value
- */
- void AddIntProperty(std::string label, int value);
-
- Volume::Pointer GetAbsorptionVolume();
- Volume::Pointer GetScatteringVolume();
- Volume::Pointer GetAnisotropyVolume();
- Volume::Pointer GetSegmentationVolume();
-
- void SetAbsorptionVolume(Volume::Pointer volume);
- void SetScatteringVolume(Volume::Pointer volume);
- void SetAnisotropyVolume(Volume::Pointer volume);
- void SetSegmentationVolume(Volume::Pointer volume);
-
- double GetSpacing();
- void SetSpacing(double spacing);
-
- void FinalizeVolume();
- itkGetMacro(TissueParameters, TissueGeneratorParameters::Pointer);
- itkGetMacro(TDim, unsigned int);
-
- static InSilicoTissueVolume::Pointer New(mitk::pa::Volume::Pointer absorptionVolume,
- Volume::Pointer scatteringVolume,
- Volume::Pointer anisotropyVolume,
- Volume::Pointer segmentationVolume,
- TissueGeneratorParameters::Pointer tissueParameters,
- mitk::PropertyList::Pointer propertyList);
-
- protected:
- InSilicoTissueVolume(TissueGeneratorParameters::Pointer parameters, std::mt19937* rng);
- InSilicoTissueVolume(Volume::Pointer absorptionVolume,
- Volume::Pointer scatteringVolume,
- Volume::Pointer anisotropyVolume,
- Volume::Pointer segmentationVolume,
- TissueGeneratorParameters::Pointer tissueParameters,
- mitk::PropertyList::Pointer propertyList);
- ~InSilicoTissueVolume() override;
-
- mitk::pa::Volume::Pointer m_AbsorptionVolume;
- mitk::pa::Volume::Pointer m_ScatteringVolume;
- mitk::pa::Volume::Pointer m_AnisotropyVolume;
- mitk::pa::Volume::Pointer m_SegmentationVolume;
-
- TissueGeneratorParameters::Pointer m_TissueParameters;
-
- unsigned int m_TDim;
-
- double m_InitialBackgroundAbsorption;
-
- std::mt19937* m_Rng;
-
- void RandomizeTissueCoefficients(long rngSeed, bool useRngSeed, double percentage);
-
- mitk::PropertyList::Pointer m_PropertyList;
-
- private:
- void FillZLayer(int x, int y, double startIdx, double endIdx,
- double absorption, double scattering, double anisotropy,
- SegmentationType segmentationType);
- void AddSkinAndAirLayers();
- void UpdatePropertyList();
- };
- }
-}
-#endif // MITKPHOTOACOUSTICVOLUME_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPALightSource.h b/Modules/PhotoacousticsLib/include/mitkPALightSource.h
deleted file mode 100644
index b45d72f0b8..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPALightSource.h
+++ /dev/null
@@ -1,179 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICLIGHTSOURCE_H
-#define MITKPHOTOACOUSTICLIGHTSOURCE_H
-
-#include <mitkCommon.h>
-
-#include "MitkPhotoacousticsLibExports.h"
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkObject.h"
-#include "itkMacro.h"
-
-#include <tinyxml.h>
-
-namespace mitk {
- namespace pa {
- /**
- * @brief The LightSource class
- * The representation of a LightSource
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT LightSource : public itk::Object
- {
- public:
-
- mitkClassMacroItkParent(LightSource, itk::Object);
- itkFactorylessNewMacro(Self);
- mitkNewMacro2Param(Self, TiXmlElement*, bool);
-
- const std::string XML_TAG_X_ANGLE = "xAngle";
- const std::string XML_TAG_Y_ANGLE = "yAngle";
- const std::string XML_TAG_PHOTON_DIRECTION = "PhotonDirection";
- const std::string XML_TAG_MINIMUM = "min";
- const std::string XML_TAG_MAXIMUM = "max";
- const std::string XML_TAG_MODE = "mode";
- const std::string XML_TAG_ENERGY = "energy";
- const std::string XML_TAG_SPAWN_TYPE = "SpawnType";
- const std::string XML_TAG_SPAWN_TYPE_POINT = "POINT";
- const std::string XML_TAG_SPAWN_TYPE_RECTANGLE = "RECTANGLE";
- const std::string XML_TAG_SPAWN_TYPE_CIRCLE = "CIRCLE";
- const std::string XML_TAG_X = "x";
- const std::string XML_TAG_Y = "y";
- const std::string XML_TAG_Z = "z";
- const std::string XML_TAG_R = "r";
- const std::string XML_TAG_X_LENGTH = "xLength";
- const std::string XML_TAG_Y_LENGTH = "yLength";
- const std::string XML_TAG_Z_LENGTH = "zLength";
-
- enum SpawnType
- {
- POINT, RECTANGLE, CIRCLE
- };
-
- enum DistributionMode
- {
- UNIFORM, GAUSSIAN
- };
-
- struct PhotonInformation
- {
- double xPosition;
- double yPosition;
- double zPosition;
- double xAngle;
- double yAngle;
- double zAngle;
- };
-
- PhotonInformation GetNextPhoton(double rnd1, double rnd2, double rnd3,
- double rnd4, double rnd5, double gau1, double gau2);
-
- bool IsValid();
-
- LightSource(TiXmlElement* element, bool verbose);
- LightSource();
- ~LightSource() override;
-
- void ParseAngle(TiXmlElement* direction, std::string angle);
-
- itkGetMacro(SpawnType, SpawnType);
-
- itkSetMacro(SpawnType, SpawnType);
-
- itkGetMacro(SpawnLocationX, double);
-
- itkSetMacro(SpawnLocationX, double);
- itkGetMacro(SpawnLocationY, double);
- itkSetMacro(SpawnLocationY, double);
- itkGetMacro(SpawnLocationZ, double);
-
- itkSetMacro(SpawnLocationZ, double);
-
- itkGetMacro(SpawnLocationXLength, double);
-
- itkSetMacro(SpawnLocationXLength, double);
- itkGetMacro(SpawnLocationYLength, double);
- itkSetMacro(SpawnLocationYLength, double);
- itkGetMacro(SpawnLocationZLength, double);
-
- itkSetMacro(SpawnLocationZLength, double);
-
- itkGetMacro(SpawnLocationRadius, double);
-
- itkSetMacro(SpawnLocationRadius, double);
- itkGetMacro(Energy, double);
- itkSetMacro(Energy, double);
- itkGetMacro(AngleXMinimum, double);
-
- itkSetMacro(AngleXMinimum, double);
-
- itkGetMacro(AngleXMaximum, double);
-
- itkSetMacro(AngleXMaximum, double);
- itkGetMacro(AngleYMinimum, double);
- itkSetMacro(AngleYMinimum, double);
- itkGetMacro(AngleYMaximum, double);
-
- itkSetMacro(AngleYMaximum, double);
-
- itkGetMacro(AngleXMode, DistributionMode);
-
- itkSetMacro(AngleXMode, DistributionMode);
- itkGetMacro(AngleYMode, DistributionMode);
- itkSetMacro(AngleYMode, DistributionMode);
- itkGetMacro(Verbose, bool);
-
- itkSetMacro(Verbose, bool);
-
- protected:
-
- const double TWO_PI = 2.0*3.14159265358979323846;
-
- SpawnType m_SpawnType;
- double m_SpawnLocationX;
- double m_SpawnLocationY;
- double m_SpawnLocationZ;
- double m_SpawnLocationXLength;
- double m_SpawnLocationYLength;
- double m_SpawnLocationZLength;
- double m_SpawnLocationRadius;
-
- double m_Energy;
-
- double m_AngleXMinimum;
- double m_AngleXMaximum;
- double m_AngleYMinimum;
- double m_AngleYMaximum;
- DistributionMode m_AngleXMode;
- DistributionMode m_AngleYMode;
-
- bool m_IsValid;
- bool m_Verbose;
-
- struct TransformResult
- {
- double z0;
- double z1;
- };
-
- void ParsePhotonDirection(TiXmlElement* element);
- void ParseEnergy(TiXmlElement* element);
- void ParsePhotonSpawnArea(TiXmlElement* element);
-
- TransformResult BoxMuellerTransform(double u1, double u2, double mu, double sigma);
- };
- }
-}
-#endif // MITKPHOTOACOUSTICLIGHTSOURCE_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h b/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h
deleted file mode 100644
index c62b88d87b..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPALinearSpectralUnmixingFilter.h
+++ /dev/null
@@ -1,100 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKLINEARPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H
-#define MITKLINEARPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H
-
-#include <mitkPASpectralUnmixingFilterBase.h>
-#include <MitkPhotoacousticsLibExports.h>
-
-namespace mitk {
- namespace pa {
- /**
- * \brief This filter is subclass of the spectral unmixing filter base. All algorithms in this class are
- * based on the Eigen open source c++ library. It takes a multispectral pixel as input and returns a vector
- * with the unmixing result.
- *
- * Input:
- * - endmemberMatrix Eigen Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains
- * the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method.
- * - inputVector Eigen Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece)
- * so the pixelvalue of the first wavelength is stored in inputVector[0] and so on.
- *
- * Output:
- * - Eigen vector with unmixing result of one multispectral pixel. The ith element of the vector corresponds to the ith entry of the
- * m_Chromophore vector.
- *
- * Algorithms (see AlgortihmType enum):
- * - HOUSEHOLDERQR computes the solution by QR decomposition
- * - COLPIVHOUSEHOLDERQR computes the solution by QR decomposition
- * - FULLPIVHOUSEHOLDERQR computes the solution by QR decomposition
- * - LDLT computes the solution by Cholesky decomposition
- * - LLT computes the solution by Cholesky decomposition
- * - JACOBISVD computes the solution by singular value decomposition uses least square solver
- *
- * Possible exceptions:
- * - "algorithm not working": doesn't work now (2018/06/19)
- * - "404 VIGRA ALGORITHM NOT FOUND": Algorithm not implemented
- */
-
- class MITKPHOTOACOUSTICSLIB_EXPORT LinearSpectralUnmixingFilter : public SpectralUnmixingFilterBase
- {
- public:
-
- mitkClassMacro(LinearSpectralUnmixingFilter, SpectralUnmixingFilterBase);
-
- itkFactorylessNewMacro(Self);
-
- /**
- * \brief Contains all implemented Eigen algorithms for spectral unmixing. For detailed information of the algorithms look at the
- * mitkPALinearSpectralUnmixingFilter.h documentation (section Algorithms).
- */
- enum AlgortihmType
- {
- HOUSEHOLDERQR,
- LDLT,
- LLT,
- COLPIVHOUSEHOLDERQR,
- JACOBISVD,
- FULLPIVLU,
- FULLPIVHOUSEHOLDERQR
- };
-
- /**
- * \brief Takes a mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType and fix it for usage at the "SpectralUnmixingAlgorithm" method.
- * @param inputAlgorithmName has to be a mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType
- */
- void SetAlgorithm(AlgortihmType inputAlgorithmName);
-
- protected:
- LinearSpectralUnmixingFilter();
- ~LinearSpectralUnmixingFilter() override;
-
- /**
- * \brief overrides the baseclass method with a mehtod to calculate the spectral unmixing result vector. Herain the class performs the
- * algorithm set by the "SetAlgorithm" method and writes the result into a Eigen vector which is the return value.
- * @param endmemberMatrix Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains
- * the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method.
- * @param inputVector Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece)
- * so the pixelvalue of the first wavelength is stored in inputVector[0] and so on.
- * @throws if the algorithmName is not a member of the enum VigraAlgortihmType
- * @throws if one chooses the ldlt/llt solver which doens't work yet
- */
- Eigen::VectorXf SpectralUnmixingAlgorithm(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> endmemberMatrix,
- Eigen::VectorXf inputVector) override;
-
- private:
- AlgortihmType algorithmName;
- };
- }
-}
-#endif // MITKLINEARPHOTOACOUSTICSPECTRALUNMIXINGFILTER_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAMonteCarloThreadHandler.h b/Modules/PhotoacousticsLib/include/mitkPAMonteCarloThreadHandler.h
deleted file mode 100644
index 0c8e02f381..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAMonteCarloThreadHandler.h
+++ /dev/null
@@ -1,91 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKMONTECARLOTHREADHANDLER_H
-#define MITKMONTECARLOTHREADHANDLER_H
-
-#include <mitkCommon.h>
-#include <MitkPhotoacousticsLibExports.h>
-#include <mutex>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- /**
- * @brief The PhotoacousticStatefulObject class
- * Designed for inheritence. Provides a state member variable and convenience methods to check
- * for the state.
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT MonteCarloThreadHandler : public itk::LightObject
- {
- public:
-
- mitkClassMacroItkParent(MonteCarloThreadHandler, itk::LightObject);
- mitkNewMacro2Param(MonteCarloThreadHandler, long, bool);
- mitkNewMacro3Param(MonteCarloThreadHandler, long, bool, bool);
-
- long GetNextWorkPackage();
-
- void SetPackageSize(long sizeInMilliseconsOrNumberOfPhotons);
-
- itkGetMacro(NumberPhotonsToSimulate, long);
- itkGetMacro(NumberPhotonsRemaining, long);
- itkGetMacro(WorkPackageSize, long);
- itkGetMacro(SimulationTime, long);
- itkGetMacro(SimulateOnTimeBasis, bool);
- itkGetMacro(Verbose, bool);
-
- protected:
- long m_NumberPhotonsToSimulate;
- long m_NumberPhotonsRemaining;
- long m_WorkPackageSize;
- long m_SimulationTime;
- long m_Time;
- bool m_SimulateOnTimeBasis;
- bool m_Verbose;
- std::mutex m_MutexRemainingPhotonsManipulation;
-
- /**
- * @brief PhotoacousticThreadhandler
- * @param timInMilliseconsOrNumberofPhotons
- * @param simulateOnTimeBasis
- */
- MonteCarloThreadHandler(long timInMilliseconsOrNumberofPhotons, bool simulateOnTimeBasis);
-
- /**
- * @brief PhotoacousticThreadhandler
- * @param timInMilliseconsOrNumberofPhotons
- * @param simulateOnTimeBasis
- * @param verbose
- */
- MonteCarloThreadHandler(long timInMilliseconsOrNumberofPhotons, bool simulateOnTimeBasis, bool verbose);
- ~MonteCarloThreadHandler() override;
- };
-
- /**
- * @brief Equal A function comparing two thread handlers for beeing equal
- *
- * @param rightHandSide A object to be compared
- * @param leftHandSide A object to be compared
- * @param eps tolarence for comparison. You can use mitk::eps in most cases.
- * @param verbose flag indicating if the user wants detailed console output or not.
- * @return true, if all subsequent comparisons are true, false otherwise
- */
- MITKPHOTOACOUSTICSLIB_EXPORT bool Equal(const MonteCarloThreadHandler::Pointer leftHandSide,
- const MonteCarloThreadHandler::Pointer rightHandSide, double eps, bool verbose);
- }
-}
-
-#endif // MITKMONTECARLOTHREADHANDLER_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPANoiseGenerator.h b/Modules/PhotoacousticsLib/include/mitkPANoiseGenerator.h
deleted file mode 100644
index 07a7fa3523..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPANoiseGenerator.h
+++ /dev/null
@@ -1,42 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICNOISEGENERATOR_H
-#define MITKPHOTOACOUSTICNOISEGENERATOR_H
-
-#include "MitkPhotoacousticsLibExports.h"
-
-#include "mitkPAVolume.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT NoiseGenerator final
- {
- public:
-
- /**
- * @brief ApplyNoiseModel
- * Applies noise to an image.
- * @param image the image to apply the noise to
- * @param detectorNoise >= 0
- * @param speckleNoise >= 1
- */
- static void ApplyNoiseModel(mitk::pa::Volume::Pointer image, double detectorNoise, double speckleNoise);
-
- private:
- NoiseGenerator();
- ~NoiseGenerator() {};
- };
- }
-}
-
-#endif // MITKPHOTOACOUSTICNOISEGENERATOR_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAPhantomTissueGenerator.h b/Modules/PhotoacousticsLib/include/mitkPAPhantomTissueGenerator.h
deleted file mode 100644
index 1c57151de6..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAPhantomTissueGenerator.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef mitkPhotoacousticPhantomTissueGenerator_h
-#define mitkPhotoacousticPhantomTissueGenerator_h
-
-#include <mitkBaseData.h>
-#include <vector>
-#include <random>
-#include <chrono>
-
-#include <MitkPhotoacousticsLibExports.h>
-#include <mitkPATissueGeneratorParameters.h>
-
-#include "mitkPAVesselTree.h"
-#include "mitkPAInSilicoTissueVolume.h"
-
-#include "mitkCommon.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT PhantomTissueGenerator final
- {
- public:
-
- /**
- * @brief GenerateInSilicoData This method will return a InSilicoTissueVolume created in terms of the given parameters.
- * @param parameters
- * @return
- */
- static InSilicoTissueVolume::Pointer GeneratePhantomData(TissueGeneratorParameters::Pointer parameters);
-
- private:
- PhantomTissueGenerator();
- virtual ~PhantomTissueGenerator();
- };
- }
-}
-#endif
diff --git a/Modules/PhotoacousticsLib/include/mitkPAProbe.h b/Modules/PhotoacousticsLib/include/mitkPAProbe.h
deleted file mode 100644
index 711af98b47..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAProbe.h
+++ /dev/null
@@ -1,65 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICPROBE_H
-#define MITKPHOTOACOUSTICPROBE_H
-
-#include <MitkPhotoacousticsLibExports.h>
-
-#include <mitkCommon.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-#include "mitkPALightSource.h"
-#include <vector>
-#include <tinyxml.h>
-
-namespace mitk {
- namespace pa {
- /**
- * @brief The Probe class
- * The representation of a Probe
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT Probe : public itk::LightObject
- {
- public:
-
- mitkClassMacroItkParent(Probe, itk::LightObject);
- mitkNewMacro2Param(Self, std::string, bool);
- mitkNewMacro2Param(Self, const char*, bool);
-
- const std::string XML_TAG_PROBE = "Probe";
- const std::string XML_TAG_LIGHT_SOURCE = "LightSource";
-
- LightSource::PhotonInformation GetNextPhoton(double rng1, double rnd2, double rnd3, double rnd4,
- double rnd5, double rnd6, double rnd7, double rnd8);
-
- bool IsValid();
-
- Probe(std::string xmlFile, bool verbose);
- Probe(const char* fileStream, bool verbose);
- ~Probe() override;
-
- protected:
-
- std::vector<LightSource::Pointer> m_LightSources;
- bool m_IsValid;
- double m_TotalEnergy;
- bool m_Verbose;
-
- void InitProbe(TiXmlDocument document);
- };
- }
-}
-#endif // MITKPHOTOACOUSTICPROBE_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAPropertyCalculator.h b/Modules/PhotoacousticsLib/include/mitkPAPropertyCalculator.h
deleted file mode 100644
index a83738b207..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAPropertyCalculator.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICPROPERTYCALCULATOR_H
-#define MITKPHOTOACOUSTICPROPERTYCALCULATOR_H
-
-#include "MitkPhotoacousticsLibExports.h"
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT PropertyCalculator : public itk::LightObject
- {
- public:
-
- mitkClassMacroItkParent(PropertyCalculator, itk::LightObject);
- itkFactorylessNewMacro(Self);
-
- struct Properties
- {
- double mua;
- double mus;
- double g;
- };
-
- enum TissueType
- {
- AIR = 1,
- BLOOD = 2,
- EPIDERMIS = 3,
- FAT = 4,
- STANDARD_TISSUE = 5
- };
-
- enum ChromophoreType
- {
- OXYGENATED = 1,
- DEOXYGENATED = 2,
- WATER = 3,
- FATTY = 4,
- MELANIN = 5,
- ONEENDMEMBER = 6
- };
-
- double GetAbsorptionForWavelength(
- ChromophoreType chromophoreType, int wavelength);
-
- Properties CalculatePropertyForSpecificWavelength(
- TissueType tissueType, int wavelength, double oxygenSaturatonInFraction = 0);
-
- protected:
- PropertyCalculator();
- ~PropertyCalculator() override;
-
- bool m_Valid = false;
-
- std::map<int, std::map<int, double>> m_SpectralLibMap;
-
- };
- }
-}
-
-#endif // MITKPHOTOACOUSTICPROPERTYCALCULATOR_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPASimulationBatchGenerator.h b/Modules/PhotoacousticsLib/include/mitkPASimulationBatchGenerator.h
deleted file mode 100644
index 1f48abfe47..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASimulationBatchGenerator.h
+++ /dev/null
@@ -1,45 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSIMULATIONBATCHGENERATOR_H
-#define MITKPHOTOACOUSTICSIMULATIONBATCHGENERATOR_H
-
-#include <MitkPhotoacousticsLibExports.h>
-#include <mitkCommon.h>
-#include <mitkImage.h>
-
-#include <mitkPASimulationBatchGeneratorParameters.h>
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT SimulationBatchGenerator
- {
- public:
- static void WriteBatchFileAndSaveTissueVolume(
- SimulationBatchGeneratorParameters::Pointer parameters,
- mitk::Image::Pointer tissueVolume);
-
- static std::string CreateBatchSimulationString(
- SimulationBatchGeneratorParameters::Pointer parameter);
- protected:
- SimulationBatchGenerator();
- virtual ~SimulationBatchGenerator();
-
- static std::string GetVolumeNumber(
- SimulationBatchGeneratorParameters::Pointer parameters);
-
- static std::string GetOutputFolderName(
- SimulationBatchGeneratorParameters::Pointer parameter);
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSIMULATIONBATCHGENERATOR_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPASimulationBatchGeneratorParameters.h b/Modules/PhotoacousticsLib/include/mitkPASimulationBatchGeneratorParameters.h
deleted file mode 100644
index d17c010833..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASimulationBatchGeneratorParameters.h
+++ /dev/null
@@ -1,67 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSimulationBatchGENERATORPARAMETERS_H
-#define MITKPHOTOACOUSTICSimulationBatchGENERATORPARAMETERS_H
-
-#include <MitkPhotoacousticsLibExports.h>
-#include <mitkPAVesselMeanderStrategy.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT SimulationBatchGeneratorParameters : public itk::Object
- {
- public:
- mitkClassMacroItkParent(SimulationBatchGeneratorParameters, itk::Object);
- itkFactorylessNewMacro(Self);
- itkSetMacro(VolumeIndex, unsigned int);
- itkSetMacro(NrrdFilePath, std::string);
- itkSetMacro(TissueName, std::string);
- itkSetMacro(BinaryPath, std::string);
- itkSetMacro(NumberOfPhotons, long);
- itkSetMacro(YOffsetLowerThresholdInCentimeters, double);
- itkSetMacro(YOffsetUpperThresholdInCentimeters, double);
- itkSetMacro(YOffsetStepInCentimeters, double);
- itkGetMacro(VolumeIndex, unsigned int);
-
- itkGetMacro(NrrdFilePath, std::string);
-
- itkGetMacro(TissueName, std::string);
-
- itkGetMacro(BinaryPath, std::string);
- itkGetMacro(NumberOfPhotons, long);
- itkGetMacro(YOffsetLowerThresholdInCentimeters, double);
- itkGetMacro(YOffsetUpperThresholdInCentimeters, double);
- itkGetMacro(YOffsetStepInCentimeters, double);
-
- protected:
- SimulationBatchGeneratorParameters();
- ~SimulationBatchGeneratorParameters() override;
-
- private:
-
- unsigned int m_VolumeIndex;
- std::string m_NrrdFilePath;
- std::string m_TissueName;
- std::string m_BinaryPath;
- long m_NumberOfPhotons;
- double m_YOffsetLowerThresholdInCentimeters;
- double m_YOffsetUpperThresholdInCentimeters;
- double m_YOffsetStepInCentimeters;
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSimulationBatchGENERATORPARAMETERS_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPASlicedVolumeGenerator.h b/Modules/PhotoacousticsLib/include/mitkPASlicedVolumeGenerator.h
deleted file mode 100644
index 1316fab25b..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASlicedVolumeGenerator.h
+++ /dev/null
@@ -1,56 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSLICEDVOLUMEGENERATOR_H
-#define MITKPHOTOACOUSTICSLICEDVOLUMEGENERATOR_H
-
-#include <MitkPhotoacousticsLibExports.h>
-
-#include <mitkPAComposedVolume.h>
-#include <mitkPAVolume.h>
-#include <mitkImage.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT SlicedVolumeGenerator : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(SlicedVolumeGenerator, itk::LightObject);
- mitkNewMacro4Param(Self, int, bool,
- mitk::pa::Volume::Pointer, bool);
-
- mitk::pa::Volume::Pointer GetSlicedFluenceImageFromComposedVolume(
- mitk::pa::ComposedVolume::Pointer composedVolume);
-
- mitk::pa::Volume::Pointer GetSlicedSignalImageFromComposedVolume(
- mitk::pa::ComposedVolume::Pointer composedVolume);
-
- mitk::pa::Volume::Pointer GetSlicedGroundTruthImageFromComposedVolume(
- mitk::pa::ComposedVolume::Pointer composedVolume);
-
- protected:
- SlicedVolumeGenerator(int centralYSlice, bool precorrect,
- mitk::pa::Volume::Pointer precorrectionVolume, bool inverse);
- ~SlicedVolumeGenerator() override;
-
- int m_CentralYSlice;
- bool m_Precorrect;
- bool m_Inverse;
- mitk::pa::Volume::Pointer m_PrecorrectionVolume;
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSLICEDVOLUMEGENERATOR_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h
deleted file mode 100644
index dce6a5d2ce..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterBase.h
+++ /dev/null
@@ -1,194 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERBASE_H
-#define MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERBASE_H
-
-#include "mitkImageToImageFilter.h"
-#include <MitkPhotoacousticsLibExports.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-// Includes for AddEnmemberMatrix
-#include "mitkPAPropertyCalculator.h"
-#include <eigen3/Eigen/Dense>
-
-namespace mitk {
- namespace pa {
- /**
- * \brief The spectral unmixing filter base is designed as superclass for several spectral unmixing filter eg. Eigen- or Vigrabased ones.
- * One can add wavelengths and chromophores and get a unmixed output images out of one MITK input image using algorithms from the subclasses.
- *
- * Input:
- * The unmixing input has to be a 3D MITK image where the XY-plane is a image and the Z-direction represents recordings for different
- * wavelengths. Herein a XY-plane for a specific Z-direction will be called "image". Every image has to be assigned to a certain wavelength.
- * The "AddWavelength" uses "push_back" to write float values into a vector. The first wavelength will correspond to the first image!!!
- * If there a more input images 'I' then added wavelengths 'w' the filter base interprets the next x images as repetition sequence of the same
- * wavelengths. If I % w !=0 the surplus image(s) will be dropped.
- * Addtionaly one has to add chromophores from the property calculator class enum "ChromophoreType" with the "AddChromophore" method.
- * This method as well uses "push_back" but the chosen (arbitary) order will be the order of the outputs.
- *
- * Output:
- * The output will be one MITK image per chosen chromophore. Where the XY-plane is a image and the Z-direction represents recordings for different
- * sequences. Furthermore it is possible to creat an output image that contains the information about the relative error between unmixing result
- * and the input image.
- *
- * Subclasses:
- * - mitkPASpectralUnmixingFilterVigra
- * - mitkPALinearSpectralUnmixingFilter (uses Eigen algorithms)
- * - mitkPASpectralUnmixingFilterSimplex
- *
- * Possible exceptions:
- * - "PIXELTYPE ERROR! FLOAT 32 REQUIRED": The MITK input image has to consist out of floats.
- * - "ERROR! REMOVE WAVELENGTHS!": One needs at least the same amount of images (z-dimension) then added wavelengths.
- * - "ADD MORE WAVELENGTHS!": One needs at least the same amount of wavelengths then added chromophores.
- * - "WAVELENGTH XXX nm NOT SUPPORTED!": The wavelength is not part of the proptery calculater data base. The data base can be found @
- * [...]/mitk/Modules/PhotoacousticsLib/Resources/spectralLIB.dat
- * - "ADD OUTPUTS HAS TO BE LARGER THEN ZERO!"
- * - "NO WAVELENGHTS/CHROMOPHORES SELECZED!
- * - "INDEX ERROR! NUMBER OF OUTPUTS DOESN'T FIT TO OTHER SETTIGNS!"
- */
-
- class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingFilterBase : public mitk::ImageToImageFilter
- {
- public:
- mitkClassMacro(SpectralUnmixingFilterBase, mitk::ImageToImageFilter);
-
- /**
- * \brief AddChromophore takes mitk::pa::PropertyCalculator::ChromophoreType and writes them at the end of the m_Chromophore vector.
- * The call of the method sets the order of the GetOutput method!
- *
- * @param chromophore has to be element of porperty calculater enum chromophore type
- * @return for wavelength smaller then 300nm and larger then 1000nm the return will be 0, because not at the data base (2018/06/19)
- */
- void AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType chromophore);
-
- /**
- * \brief AddWavelength takes integers and writes them at the end of the m_Wavelength vector. The first call of the method then
- * corresponds to the first input image and so on.
- * @param wavelength database supports integers between 300 and 1000 nm
- */
- void AddWavelength(int wavelength);
-
- /*
- * \brief Verbose gives more information to the console. Default value is false.
- * @param verbose is the boolian to activate the MITK_INFO logged to the console
- */
- virtual void Verbose(bool verbose);
-
- /**
- * \brief AddOutputs takes an integer and sets indexed outputs
- * @param outputs integer correponds to the number of output images
- * @throws if outputs == 0
- */
- virtual void AddOutputs(unsigned int outputs);
-
- /*
- * \brief RelativeError returns a image which compare the L2 norm of the input vector with the unmixing result
- * @param relativeError is the boolian to activate this tool
- */
- virtual void RelativeError(bool relativeError);
-
- /**
- * \brief AddRelativeErrorSettings takes integers and writes them at the end of the m_RelativeErrorSettings vector.
- * @param value has to be a integer
- */
- virtual void AddRelativeErrorSettings(int value);
-
- std::ofstream myfile; // just for testing purposes; has to be removeed
-
- protected:
- /**
- * \brief Constructor creats proptery calculater smart pointer new()
- */
- SpectralUnmixingFilterBase();
- ~SpectralUnmixingFilterBase() override;
-
- /**
- * \brief The subclasses will override the mehtod to calculate the spectral unmixing result vector.
- * @param endmemberMatrix Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains
- * the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method.
- * @param inputVector Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece)
- * so the pixelvalue of the first wavelength is stored in inputVector[0] and so on.
- * @throws if algorithm implementiation fails (implemented for the algorithms with critical requirements)
- */
- virtual Eigen::VectorXf SpectralUnmixingAlgorithm(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> endmemberMatrix,
- Eigen::VectorXf inputVector) = 0;
-
- bool m_Verbose = false;
- bool m_RelativeError = false;
-
- std::vector<mitk::pa::PropertyCalculator::ChromophoreType> m_Chromophore;
- std::vector<int> m_Wavelength;
- std::vector<int> m_RelativeErrorSettings;
-
- private:
- /*
- * \brief Initialized output images with the same XY-plane size like the input image and total size in z-direction equals number of sequences.
- * The pixel type is set to float.
- * @param totalNumberOfSequences = (unsigned int) (numberOfInputImages / numberOfWavelength) >= 1
- */
- virtual void InitializeOutputs(unsigned int totalNumberOfSequences);
-
- /*
- * \brief Checks if there are a suitable amount of wavelengths and if the input image consists of floats.
- * @param input pointer on the MITK input image
- * @throws if there are more wavelength then images
- * @throws if there are more chromophores then wavelengths
- * @throws if the pixel type is not float 32
- * @throws if no chromophores or wavelengths selected as input
- * @throws if the number of indexed outputs does'nt fit to the expected number
- */
- virtual void CheckPreConditions(mitk::Image::Pointer input);
-
- /*
- * \brief Inherit from the "ImageToImageFilter" Superclass. Herain it calls InitializeOutputs, CalculateEndmemberMatrix and
- * CheckPreConditions methods and enables pixelwise access to do spectral unmixing with the "SpectralUnmixingAlgorithm"
- * method. In the end the method writes the results into the new MITK output images.
- */
- void GenerateData() override;
-
- /*
- * \brief Creats a Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains
- * the absorbtion of chromophore j @ wavelength i. The absorbtion values are taken from the "PropertyElement" method.
- * @param m_Chromophore is a vector of "PropertyCalculator::ChromophoreType" containing all selected chromophores for the unmixing
- * @param m_Wavelength is a vector of integers containing all wavelengths of one sequence
- */
- virtual Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> CalculateEndmemberMatrix(
- std::vector<mitk::pa::PropertyCalculator::ChromophoreType> m_Chromophore, std::vector<int> m_Wavelength);
-
- /*
- * \brief "PropertyElement" is the tool to access the absorbtion values out of the database using mitk::pa::PropertyCalculator::GetAbsorptionForWavelengt
- * and checks if the requested wavelength is part of the database (not zero values). The "ONEENDMEMBER" is a pseudo absorber with static absorbtion 1
- * at every wavelength and is therefor not part of the database. If this one is the selected chromophore the return value is 1 for every wavelength.
- * @param wavelength has to be integer between 300 and 1000 nm
- * @param chromophore has to be a mitk::pa::PropertyCalculator::ChromophoreType
- * @throws if mitk::pa::PropertyCalculator::GetAbsorptionForWavelengt returns 0, because this means that the delivered wavelength is not in the database.
- */
- virtual float PropertyElement(mitk::pa::PropertyCalculator::ChromophoreType, int wavelength);
-
- /*
- * \brief calculates the relative error between the input image and the unmixing result in the L2 norm
- * @param endmemberMatrix is a Eigen matrix containing the endmember information
- * @param inputVector is a Eigen vector containing the multispectral information of one pixel
- * @param resultVector is a Eigen vector containing the spectral unmmixing result
- */
- float CalculateRelativeError(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> endmemberMatrix,
- Eigen::VectorXf inputVector, Eigen::VectorXf resultVector);
-
- PropertyCalculator::Pointer m_PropertyCalculatorEigen;
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERBASE_
diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterLagrange.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterLagrange.h
deleted file mode 100644
index d99e73e310..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterLagrange.h
+++ /dev/null
@@ -1,36 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERLAGRANGE_H
-#define MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERLAGRANGE_H
-
-#include <mitkPASpectralUnmixingFilterBase.h>
-#include <MitkPhotoacousticsLibExports.h>
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingFilterLagrange : public SpectralUnmixingFilterBase
- {
- public:
-
- mitkClassMacro(SpectralUnmixingFilterLagrange, SpectralUnmixingFilterBase);
-
- protected:
- SpectralUnmixingFilterLagrange();
- ~SpectralUnmixingFilterLagrange() override;
-
- private:
-
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERLAGRANGE_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterSimplex.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterSimplex.h
deleted file mode 100644
index c5ca41dbe3..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterSimplex.h
+++ /dev/null
@@ -1,50 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERSIMPLEX_H
-#define MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERSIMPLEX_H
-
-#include <mitkPASpectralUnmixingFilterBase.h>
-#include <MitkPhotoacousticsLibExports.h>
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingFilterSimplex : public SpectralUnmixingFilterBase
- {
- public:
-
- mitkClassMacro(SpectralUnmixingFilterSimplex, SpectralUnmixingFilterBase);
-
- itkFactorylessNewMacro(Self);
-
- protected:
- SpectralUnmixingFilterSimplex();
- ~SpectralUnmixingFilterSimplex() override;
-
- private:
-
- Eigen::VectorXf SpectralUnmixingAlgorithm(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> EndmemberMatrix,
- Eigen::VectorXf inputVector) override;
-
- int factorial(int n);
- virtual Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> GenerateA(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> EndmemberMatrix,
- Eigen::VectorXf inputVector, int i);
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> GenerateD2(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> A);
- float simplexVolume(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> Matrix);
-
- virtual Eigen::VectorXf Normalization(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> EndmemberMatrix,
- Eigen::VectorXf inputVector);
-
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERSIMPLEX_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterVigra.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterVigra.h
deleted file mode 100644
index f6d8f638b3..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingFilterVigra.h
+++ /dev/null
@@ -1,104 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERVIGRA_H
-#define MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERVIGRA_H
-
-#include <mitkPASpectralUnmixingFilterBase.h>
-#include <MitkPhotoacousticsLibExports.h>
-#include <mitkPALinearSpectralUnmixingFilter.h>
-
-
-
-namespace mitk {
- namespace pa {
- /**
- * \brief This filter is subclass of the spectral unmixing filter base. All algorithms in this class are
- * based on the vigra open source c++ library. It takes a multispectral pixel as input and returns a vector
- * with the unmixing result.
- *
- * Input:
- * - endmemberMatrix Eigen Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains
- * the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method.
- * - inputVector Eigen Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece)
- * so the pixelvalue of the first wavelength is stored in inputVector[0] and so on.
- *
- * Output:
- * - Eigen vector with unmixing result of one multispectral pixel. The ith element of the vector corresponds to the ith entry of the
- * m_Chromophore vector.
- *
- * Algorithms (see VigraAlgortihmType enum):
- * - LARS algorithm minimizes (A*x-b)^2 s.t. x>=0 using least angle regression
- * - GOLDFARB minimizes (A*x-b)^2 s.t. x>=0 using the Goldfarb-Idnani algorithm
- * - WEIGHTED minimizes transpose(A*x-b)*diag(weights)*(A*x-b) using QR decomposition
- * - LS minimizes (A*x-b)^2 using QR decomposition
- *
- * Possible exceptions:
- * - "404 VIGRA ALGORITHM NOT FOUND": Algorithm not implemented
- */
-
- class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingFilterVigra : public SpectralUnmixingFilterBase
- {
- public:
- mitkClassMacro(SpectralUnmixingFilterVigra, SpectralUnmixingFilterBase);
- itkFactorylessNewMacro(Self);
-
- /**
- * \brief Contains all implemented Vigra algorithms for spectral unmixing. For detailed information of the algorithms look at the
- * mitkPASpectralUnmixingFilterVigra.h documentation (section Algorithms).
- */
- enum VigraAlgortihmType
- {
- LARS,
- GOLDFARB,
- WEIGHTED,
- LS
- };
-
- /**
- * \brief AddWeight takes integers and writes them at the end of the weightsvec vector. The first call of the method then
- * corresponds to the first input image/wavelength and so on.
- * @param weight is a percentage (integer) between 1 and 100
- */
- void AddWeight(unsigned int weight);
-
- /**
- * \brief Takes a mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType and fix it for usage at the "SpectralUnmixingAlgorithm"
- * method.
- * @param inputAlgorithmName has to be a mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType
- */
- void SetAlgorithm(VigraAlgortihmType inputAlgorithmName);
-
- protected:
- SpectralUnmixingFilterVigra();
- ~SpectralUnmixingFilterVigra() override;
-
- /**
- * \brief overrides the baseclass method with a mehtod to calculate the spectral unmixing result vector. Herain it first converts the
- * Eigen inputs to the Vigra class. Afterwards the class performs the algorithm set by the "SetAlgorithm" method and writes the result
- * into a Eigen vector which is the return value.
- * @param EndmemberMatrix Matrix with number of chromophores colums and number of wavelengths rows so matrix element (i,j) contains
- * the absorbtion of chromophore j @ wavelength i taken from the database by PropertyElement method.
- * @param inputVector Vector containing values of one pixel of XY-plane image with number of wavelength rows (z-dimension of a sequenece)
- * so the pixelvalue of the first wavelength is stored in inputVector[0] and so on.
- * @throws if the algorithmName is not a member of the enum VigraAlgortihmType
- */
- Eigen::VectorXf SpectralUnmixingAlgorithm(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> EndmemberMatrix,
- Eigen::VectorXf inputVector) override;
-
- private:
- std::vector<double> weightsvec;
- SpectralUnmixingFilterVigra::VigraAlgortihmType algorithmName;
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGFILTERVIGRA_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h b/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h
deleted file mode 100644
index a1b90efcf6..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPASpectralUnmixingSO2.h
+++ /dev/null
@@ -1,112 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_H
-#define MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_H
-
-#include "mitkImageToImageFilter.h"
-#include <MitkPhotoacousticsLibExports.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-
-namespace mitk {
- namespace pa {
- /**
- * \brief derives out of two identical sized MITK images the oxygen saturation and return one MITK image as result. Furthermore
- * it is possible to set settings that the result shows just SO2 values above a threshold, or above a input value for Hb, HbO2 to
- * get just a oxygen saturation image of interessting structures.
- *
- * Input:
- * The input has to be two 3D MITK images. The order of the inputs matter! The first input has to be the Hb image the second input
- * has to be the HbO2 image. The settings are integer values. The SO2 threshold therefore is percentage value.
- *
- * Output:
- * The output will be one MITK image. Where one can see the oxygen saturation of all pixels above the set threholds. If a pixel is
- * below a threhold or NAN then the value will be set to zero.
- *
- * UPDATE: SO2 Filter will get an second output, the total hemoglobin value with ->GetOutput(1).
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT SpectralUnmixingSO2 : public mitk::ImageToImageFilter
- {
- public:
- mitkClassMacro(SpectralUnmixingSO2, mitk::ImageToImageFilter);
- itkFactorylessNewMacro(Self);
-
- /**
- * \brief AddSO2Settings takes integers and writes them at the end of the m_SO2Settings vector.
- * @param value of the Setting
- */
- virtual void AddSO2Settings(int value);
-
- /**
- * \brief Verbose gives more information to the console. Default value is false.
- * @param verbose is the boolian to activate the MITK_INFO logged to the console
- */
- virtual void Verbose(bool verbose);
-
- protected:
- /**
- * \brief Constructor sets number of input images to two and number of output images to one, respectively.
- */
- SpectralUnmixingSO2();
- ~SpectralUnmixingSO2() override;
-
- std::vector<int> m_SO2Settings;
- bool m_Verbose = false;
-
- private:
- /**
- * \brief Inherit from the "ImageToImageFilter" Superclass. Herain it calls InitializeOutputs and the CheckPreConditions
- * methods and enables pixelwise access to the inputs to calculate the oxygen saturation via the "calculate SO2" method.
- */
- void GenerateData() override;
-
- /**
- * \brief Initialized output images with the same size like the input image. The pixel type is set to float.
- */
- virtual void InitializeOutputs();
-
- /**
- * \brief Checks if the dimensions of the input images are equal and made out of floating poinhts.
- * @throws if the inputs don't have the same size
- * @throws if input images don't consist of floats
- */
- virtual void CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb);
-
- /**
- * \brief calculates HbO2 / (Hb + HbO2) and afterwards checks if the result is significant (SO2ValueNotSiginificant method).
- * If not the method returns zero otherwise it returns the calculated result.
- * @param pixelHb is the pixel value of the Hb input.
- * @param pixelHb is the pixel value of the Hb input.
- * @warn if the sO2 value is NAN (in patricular if Hb == -HbO2), but result will be set to zero
- */
- float CalculateSO2(float pixelHb, float pixelHbO2);
-
- /**
- * \brief calculates (Hb + HbO2).
- * @param pixelHb is the pixel value of the Hb input.
- * @param pixelHb is the pixel value of the Hb input.
- * @warn if the tHb value is NAN (in patricular if Hb == -HbO2), but result will be set to zero
- */
- float CalculateTHb(float pixelHb, float pixelHbO2);
-
- /**
- * \brief return true if SO2 result is not significant by checking if the input values are above the threshold of the settings
- */
- bool SO2ValueNotSiginificant(float Hb, float HbO2, float result);
- };
- }
-}
-#endif // MITKPHOTOACOUSTICSPECTRALUNMIXINGSO2_
diff --git a/Modules/PhotoacousticsLib/include/mitkPATissueGenerator.h b/Modules/PhotoacousticsLib/include/mitkPATissueGenerator.h
deleted file mode 100644
index eb4c4450f7..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPATissueGenerator.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef mitkPhotoacousticTissueGenerator_h
-#define mitkPhotoacousticTissueGenerator_h
-
-#include <mitkBaseData.h>
-#include <vector>
-#include <random>
-#include <chrono>
-
-#include <MitkPhotoacousticsLibExports.h>
-#include <mitkPATissueGeneratorParameters.h>
-
-#include "mitkPAVesselTree.h"
-#include "mitkPAInSilicoTissueVolume.h"
-
-#include "mitkCommon.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT InSilicoTissueGenerator final
- {
- public:
-
- /**
- * @brief GenerateInSilicoData This method will return a InSilicoTissueVolume created in terms of the given parameters.
- * @param parameters
- * @return
- */
- static InSilicoTissueVolume::Pointer GenerateInSilicoData(TissueGeneratorParameters::Pointer parameters);
-
- private:
- InSilicoTissueGenerator();
- virtual ~InSilicoTissueGenerator();
- };
- }
-}
-#endif
diff --git a/Modules/PhotoacousticsLib/include/mitkPATissueGeneratorParameters.h b/Modules/PhotoacousticsLib/include/mitkPATissueGeneratorParameters.h
deleted file mode 100644
index 6e249f2b06..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPATissueGeneratorParameters.h
+++ /dev/null
@@ -1,212 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTICTISSUEGENERATORPARAMETERS_H
-#define MITKPHOTOACOUSTICTISSUEGENERATORPARAMETERS_H
-
-#include <MitkPhotoacousticsLibExports.h>
-#include <mitkPAVesselMeanderStrategy.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT TissueGeneratorParameters : public itk::Object
- {
- public:
- mitkClassMacroItkParent(TissueGeneratorParameters, itk::Object);
- itkFactorylessNewMacro(Self);
-
- /**
- * Callback function definition of a VesselMeanderStrategy
- */
- typedef void (VesselMeanderStrategy::*CalculateNewVesselPositionCallback)
- (Vector::Pointer, double, std::mt19937*);
-
- itkGetMacro(XDim, int);
-
- itkGetMacro(YDim, int);
-
- itkGetMacro(ZDim, int);
-
- itkGetMacro(VoxelSpacingInCentimeters, double);
- itkGetMacro(DoPartialVolume, bool);
- itkGetMacro(UseRngSeed, bool);
- itkGetMacro(RngSeed, long);
- itkGetMacro(RandomizePhysicalProperties, bool);
- itkGetMacro(RandomizePhysicalPropertiesPercentage, double);
- itkGetMacro(ForceVesselsMoveAlongYDirection, bool);
- itkGetMacro(MinBackgroundAbsorption, double);
- itkGetMacro(MaxBackgroundAbsorption, double);
- itkGetMacro(BackgroundScattering, double);
- itkGetMacro(BackgroundAnisotropy, double);
- itkGetMacro(AirAbsorption, double);
- itkGetMacro(AirScattering, double);
- itkGetMacro(AirAnisotropy, double);
- itkGetMacro(AirThicknessInMillimeters, double);
- itkGetMacro(SkinAbsorption, double);
- itkGetMacro(SkinScattering, double);
- itkGetMacro(SkinAnisotropy, double);
- itkGetMacro(SkinThicknessInMillimeters, double);
- itkGetMacro(CalculateNewVesselPositionCallback, CalculateNewVesselPositionCallback);
- itkGetMacro(MinNumberOfVessels, int);
- itkGetMacro(MaxNumberOfVessels, int);
- itkGetMacro(MinVesselBending, double);
- itkGetMacro(MaxVesselBending, double);
- itkGetMacro(MinVesselAbsorption, double);
- itkGetMacro(MaxVesselAbsorption, double);
- itkGetMacro(MinVesselRadiusInMillimeters, double);
- itkGetMacro(MaxVesselRadiusInMillimeters, double);
- itkGetMacro(VesselBifurcationFrequency, int);
- itkGetMacro(MinVesselScattering, double);
- itkGetMacro(MaxVesselScattering, double);
- itkGetMacro(MinVesselAnisotropy, double);
- itkGetMacro(MaxVesselAnisotropy, double);
- itkGetMacro(MinVesselZOrigin, double);
- itkGetMacro(MaxVesselZOrigin, double);
- itkGetMacro(MCflag, double);
- itkGetMacro(MCLaunchflag, double);
- itkGetMacro(MCBoundaryflag, double);
- itkGetMacro(MCLaunchPointX, double);
- itkGetMacro(MCLaunchPointY, double);
- itkGetMacro(MCLaunchPointZ, double);
- itkGetMacro(MCFocusPointX, double);
- itkGetMacro(MCFocusPointY, double);
- itkGetMacro(MCFocusPointZ, double);
- itkGetMacro(MCTrajectoryVectorX, double);
- itkGetMacro(MCTrajectoryVectorY, double);
- itkGetMacro(MCTrajectoryVectorZ, double);
- itkGetMacro(MCRadius, double);
- itkGetMacro(MCWaist, double);
- itkSetMacro(XDim, int);
- itkSetMacro(YDim, int);
- itkSetMacro(ZDim, int);
- itkSetMacro(VoxelSpacingInCentimeters, double);
- itkSetMacro(DoPartialVolume, bool);
- itkSetMacro(UseRngSeed, bool);
- itkSetMacro(RngSeed, long);
- itkSetMacro(RandomizePhysicalProperties, bool);
- itkSetMacro(RandomizePhysicalPropertiesPercentage, double);
- itkSetMacro(ForceVesselsMoveAlongYDirection, bool);
- itkSetMacro(MinBackgroundAbsorption, double);
- itkSetMacro(MaxBackgroundAbsorption, double);
- itkSetMacro(BackgroundScattering, double);
- itkSetMacro(BackgroundAnisotropy, double);
- itkSetMacro(AirAbsorption, double);
- itkSetMacro(AirScattering, double);
- itkSetMacro(AirAnisotropy, double);
- itkSetMacro(AirThicknessInMillimeters, double);
- itkSetMacro(SkinAbsorption, double);
- itkSetMacro(SkinScattering, double);
- itkSetMacro(SkinAnisotropy, double);
- itkSetMacro(SkinThicknessInMillimeters, double);
- itkSetMacro(CalculateNewVesselPositionCallback, CalculateNewVesselPositionCallback);
- itkSetMacro(MinNumberOfVessels, int);
- itkSetMacro(MaxNumberOfVessels, int);
- itkSetMacro(MinVesselBending, double);
- itkSetMacro(MaxVesselBending, double);
- itkSetMacro(MinVesselAbsorption, double);
- itkSetMacro(MaxVesselAbsorption, double);
- itkSetMacro(MinVesselRadiusInMillimeters, double);
- itkSetMacro(MaxVesselRadiusInMillimeters, double);
- itkSetMacro(VesselBifurcationFrequency, int);
- itkSetMacro(MinVesselScattering, double);
- itkSetMacro(MaxVesselScattering, double);
- itkSetMacro(MinVesselAnisotropy, double);
- itkSetMacro(MaxVesselAnisotropy, double);
- itkSetMacro(MinVesselZOrigin, double);
- itkSetMacro(MaxVesselZOrigin, double);
- itkSetMacro(MCflag, double);
-
- itkSetMacro(MCLaunchflag, double);
-
- itkSetMacro(MCBoundaryflag, double);
-
- itkSetMacro(MCLaunchPointX, double);
- itkSetMacro(MCLaunchPointY, double);
- itkSetMacro(MCLaunchPointZ, double);
- itkSetMacro(MCFocusPointX, double);
- itkSetMacro(MCFocusPointY, double);
- itkSetMacro(MCFocusPointZ, double);
- itkSetMacro(MCTrajectoryVectorX, double);
- itkSetMacro(MCTrajectoryVectorY, double);
- itkSetMacro(MCTrajectoryVectorZ, double);
- itkSetMacro(MCRadius, double);
- itkSetMacro(MCWaist, double);
-
- protected:
- TissueGeneratorParameters();
- ~TissueGeneratorParameters() override;
-
- private:
-
- int m_XDim;
- int m_YDim;
- int m_ZDim;
- double m_VoxelSpacingInCentimeters;
- bool m_DoPartialVolume;
- bool m_UseRngSeed;
- long m_RngSeed;
- bool m_RandomizePhysicalProperties;
- double m_RandomizePhysicalPropertiesPercentage;
- bool m_ForceVesselsMoveAlongYDirection;
-
- double m_MinBackgroundAbsorption;
- double m_MaxBackgroundAbsorption;
- double m_BackgroundScattering;
- double m_BackgroundAnisotropy;
- double m_AirAbsorption;
- double m_AirScattering;
- double m_AirAnisotropy;
- double m_AirThicknessInMillimeters;
- double m_SkinAbsorption;
- double m_SkinScattering;
- double m_SkinAnisotropy;
- double m_SkinThicknessInMillimeters;
-
- CalculateNewVesselPositionCallback m_CalculateNewVesselPositionCallback;
- int m_MinNumberOfVessels;
- int m_MaxNumberOfVessels;
- double m_MinVesselBending;
- double m_MaxVesselBending;
- double m_MinVesselAbsorption;
- double m_MaxVesselAbsorption;
- double m_MinVesselRadiusInMillimeters;
- double m_MaxVesselRadiusInMillimeters;
- int m_VesselBifurcationFrequency;
- double m_MinVesselScattering;
- double m_MaxVesselScattering;
- double m_MinVesselAnisotropy;
- double m_MaxVesselAnisotropy;
- double m_MinVesselZOrigin;
- double m_MaxVesselZOrigin;
-
- double m_MCflag;
- double m_MCLaunchflag;
- double m_MCBoundaryflag;
- double m_MCLaunchPointX;
- double m_MCLaunchPointY;
- double m_MCLaunchPointZ;
- double m_MCFocusPointX;
- double m_MCFocusPointY;
- double m_MCFocusPointZ;
- double m_MCTrajectoryVectorX;
- double m_MCTrajectoryVectorY;
- double m_MCTrajectoryVectorZ;
- double m_MCRadius;
- double m_MCWaist;
- };
- }
-}
-#endif // MITKPHOTOACOUSTICTISSUEGENERATORPARAMETERS_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVector.h b/Modules/PhotoacousticsLib/include/mitkPAVector.h
deleted file mode 100644
index 3b25bf6b1c..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVector.h
+++ /dev/null
@@ -1,137 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKSMARTVECTOR_H
-#define MITKSMARTVECTOR_H
-
-#include <mitkVector.h>
-#include <random>
-
-#include <MitkPhotoacousticsLibExports.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT Vector : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(Vector, itk::LightObject);
- itkFactorylessNewMacro(Self);
-
- /**
- * @brief GetNorm calculates the length of this vector.
- * @return the euclidean norm
- */
- double GetNorm();
-
- double GetElement(unsigned short index);
- void SetElement(unsigned short index, double value);
-
- /**
- * @brief Normalize normalizes this vector. After calling this GetNorm() will return 1.
- */
- void Normalize();
- void SetValue(Vector::Pointer value);
-
- /**
- * @brief RandomizeByPercentage alters this vector randomly by [-percentage, percentage] of the bendingFactor.
- *
- * @param percentage
- * @param bendingFactor
- * @param rng
- */
- void RandomizeByPercentage(double percentage, double bendingFactor, std::mt19937* rng);
-
- /**
- * @brief Randomize randomizes this vector to be [lowerLimit, upperLimit] in each element
- *
- * @param xLowerLimit
- * @param xUpperLimit
- * @param yLowerLimit
- * @param yUpperLimit
- * @param zLowerLimit
- * @param zUpperLimit
- * @param rng
- */
- void Randomize(double xLowerLimit, double xUpperLimit, double yLowerLimit, double yUpperLimit, double zLowerLimit, double zUpperLimit, std::mt19937* rng);
-
- /**
- * @brief Randomize randomizes this vector to be [0, limit] in each element
- *
- * @param xLimit
- * @param yLimit
- * @param zLimit
- * @param rng
- */
- void Randomize(double xLimit, double yLimit, double zLimit, std::mt19937* rng);
-
- /**
- * @brief Randomize randomizes this vector to be [-1, 1] in each element
- *
- * @param rng
- */
- void Randomize(std::mt19937* rng);
-
- /**
- * @brief Rotate rotates this Vector around the x, y and z axis with the given angles in radians
- *
- * @param xAngle rotation of the inclination angle in radians
- * @param yAngle rotation of the azimuthal angle in radians
- */
- void Rotate(double xAngle, double yAngle);
-
- /**
- * @brief Scale scales this Vector with the given factor
- *
- * @param factor the scaling factor
- *
- * If a negative number is provided, the direction of the vector will be inverted.
- */
- void Scale(double factor);
-
- /**
- * @brief Clone create a deep copy of this vector
- *
- * @return a new vector with the same values.
- */
- Vector::Pointer Clone();
-
- void Subtract(Vector::Pointer other);
-
- void Add(Vector::Pointer other);
-
- protected:
- Vector();
- ~Vector() override;
-
- void PrintSelf(std::ostream& os, itk::Indent indent) const override;
-
- private:
- mitk::Vector3D m_Vector;
- };
-
- /**
- * @brief Equal A function comparing two vectors for beeing equal
- *
- * @param rightHandSide A Vector to be compared
- * @param leftHandSide A Vector to be compared
- * @param eps tolarence for comparison. You can use mitk::eps in most cases.
- * @param verbose flag indicating if the user wants detailed console output or not.
- * @return true, if all subsequent comparisons are true, false otherwise
- */
- MITKPHOTOACOUSTICSLIB_EXPORT bool Equal(const Vector::Pointer leftHandSide, const Vector::Pointer rightHandSide, double eps, bool verbose);
- }
-}
-#endif // MITKSMARTVECTOR_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVessel.h b/Modules/PhotoacousticsLib/include/mitkPAVessel.h
deleted file mode 100644
index d75d0ed68c..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVessel.h
+++ /dev/null
@@ -1,114 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKVESSEL_H
-#define MITKVESSEL_H
-
-#include "mitkVector.h"
-#include "mitkPAVesselMeanderStrategy.h"
-#include "mitkPAInSilicoTissueVolume.h"
-#include "mitkPAVector.h"
-#include "mitkPAVesselProperties.h"
-#include "mitkPAVesselDrawer.h"
-
-#include <MitkPhotoacousticsLibExports.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT Vessel : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(Vessel, itk::LightObject);
- mitkNewMacro1Param(Self, VesselProperties::Pointer);
-
- /**
- * Callback function definition of a VesselMeanderStrategy
- */
- typedef void (VesselMeanderStrategy::*CalculateNewVesselPositionCallback)
- (Vector::Pointer, double, std::mt19937*);
-
- /**
- * @brief ExpandVessel makes this Vessel expand one step in its current direction.
- * After expanding, the vessel will draw itself into the given InSilicoTissueVolume.
- *
- * @param volume volume for the vessel to draw itself in
- * @param calculateNewPosition a callback function of the VesselMeanderStrategy class.
- * It is used to calculate the final position after taking the step.
- * @param bendingFactor a metric of how much the Vessel should bend. If set to 0 the vessel will go in a straight line.
- * @param rng
- */
- void ExpandVessel(mitk::pa::InSilicoTissueVolume::Pointer volume,
- CalculateNewVesselPositionCallback calculateNewPosition, double bendingFactor, std::mt19937* rng);
-
- /**
- * @brief CanBifurcate
- * @return true if the Vessel is ready to Bifurcate()
- */
- bool CanBifurcate();
-
- /**
- * @brief Bifurcate bifurcates this vessel into two new ones. Makes sure that the volume of the vessels stays the same.
- *
- * @return a new vessel split up from the current one.
- */
- Vessel::Pointer Bifurcate(std::mt19937* rng);
-
- /**
- * @brief IsFinished
- * @return true if the vessel cannot expand any further
- */
- bool IsFinished();
-
- itkGetConstMacro(VesselProperties, VesselProperties::Pointer);
-
- protected:
- Vessel(VesselProperties::Pointer parameters);
- ~Vessel() override;
-
- private:
-
- const double MINIMUM_VESSEL_RADIUS = 0.1;
- const double NEW_RADIUS_MINIMUM_RELATIVE_SIZE = 0.6;
- const double NEW_RADIUS_MAXIMUM_RELATIVE_SIZE = 0.8;
-
- VesselMeanderStrategy::Pointer m_VesselMeanderStrategy;
- bool m_Finished;
- double m_WalkedDistance;
-
- std::uniform_real_distribution<> m_RangeDistribution;
- std::uniform_real_distribution<> m_SignDistribution;
- std::uniform_real_distribution<> m_RadiusRangeDistribution;
-
- int GetSign(std::mt19937* rng);
-
- VesselProperties::Pointer m_VesselProperties;
-
- VesselDrawer::Pointer m_VesselDrawer;
- };
-
- /**
- * @brief Equal A function comparing two vessels for beeing equal
- *
- * @param rightHandSide A vessel to be compared
- * @param leftHandSide A vessel to be compared
- * @param eps tolarence for comparison. You can use mitk::eps in most cases.
- * @param verbose flag indicating if the user wants detailed console output or not.
- * @return true, if all subsequent comparisons are true, false otherwise
- */
- MITKPHOTOACOUSTICSLIB_EXPORT bool Equal(const Vessel::Pointer leftHandSide, const Vessel::Pointer rightHandSide, double eps, bool verbose);
- }
-}
-#endif // MITKVESSEL_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVesselDrawer.h b/Modules/PhotoacousticsLib/include/mitkPAVesselDrawer.h
deleted file mode 100644
index 03453e9453..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVesselDrawer.h
+++ /dev/null
@@ -1,49 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKVESSELDRAWER_H
-#define MITKVESSELDRAWER_H
-
-#include "mitkVector.h"
-#include "mitkPAVesselMeanderStrategy.h"
-#include "mitkPAInSilicoTissueVolume.h"
-#include "mitkPAVector.h"
-#include "mitkPAVesselProperties.h"
-
-#include <MitkPhotoacousticsLibExports.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT VesselDrawer : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(VesselDrawer, itk::LightObject);
- itkFactorylessNewMacro(Self);
-
- void ExpandAndDrawVesselInVolume(
- VesselProperties::Pointer properties,
- InSilicoTissueVolume::Pointer volume);
-
- protected:
- VesselDrawer();
- ~VesselDrawer() override;
-
- private:
- };
-
- }
-}
-#endif // MITKVESSELDRAWER_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVesselMeanderStrategy.h b/Modules/PhotoacousticsLib/include/mitkPAVesselMeanderStrategy.h
deleted file mode 100644
index f8f551ba83..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVesselMeanderStrategy.h
+++ /dev/null
@@ -1,60 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKVESSELMEANDERSTRATEGY_H
-#define MITKVESSELMEANDERSTRATEGY_H
-
-#include "mitkVector.h"
-#include "mitkPAVector.h"
-
-#include <MitkPhotoacousticsLibExports.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT VesselMeanderStrategy : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(VesselMeanderStrategy, itk::LightObject);
- itkFactorylessNewMacro(Self);
-
- /**
- * @brief CalculateNewPositionInStraightLine calculates the new position by just following the direction vector.
- * @param direction
- * @param bendingFactor
- * @param rng
- */
- void CalculateNewDirectionVectorInStraightLine(Vector::Pointer direction, double bendingFactor, std::mt19937* rng);
-
- /**
- * @brief CalculateRandomlyDivergingPosition calculates the new position by modifying the direction vector randomly,
- * proportional to the selected bendingFactor. This means, that the vessels will bend in each expansion step,
- * if bendingFactor > 0.
- *
- * @param direction
- * @param bendingFactor
- * @param rng
- */
- void CalculateNewRandomlyDivergingDirectionVector(Vector::Pointer direction, double bendingFactor, std::mt19937* rng);
-
- protected:
- VesselMeanderStrategy();
- ~VesselMeanderStrategy() override;
-
- const double RANDOMIZATION_PERCENTAGE = 0.4;
- };
- }
-}
-#endif // MITKVESSELMEANDERSTRATEGY_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVesselProperties.h b/Modules/PhotoacousticsLib/include/mitkPAVesselProperties.h
deleted file mode 100644
index 00bbaaf2ee..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVesselProperties.h
+++ /dev/null
@@ -1,79 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPhotoacousticVesselParameters_H
-#define MITKPhotoacousticVesselParameters_H
-
-#include <MitkPhotoacousticsLibExports.h>
-
-#include <mitkPAVector.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT VesselProperties : public itk::Object
- {
- public:
- mitkClassMacroItkParent(VesselProperties, itk::Object);
- itkFactorylessNewMacro(Self);
- mitkNewMacro1Param(Self, Self::Pointer);
-
- itkGetMacro(PositionVector, Vector::Pointer);
- itkGetMacro(DirectionVector, Vector::Pointer);
- itkGetMacro(RadiusInVoxel, double);
- itkGetMacro(AbsorptionCoefficient, double);
- itkGetMacro(ScatteringCoefficient, double);
- itkGetMacro(AnisotopyCoefficient, double);
- itkGetMacro(BifurcationFrequency, double);
- itkGetMacro(DoPartialVolume, bool);
-
- itkSetMacro(PositionVector, Vector::Pointer);
- itkSetMacro(DirectionVector, Vector::Pointer);
- itkSetMacro(RadiusInVoxel, double);
- itkSetMacro(AbsorptionCoefficient, double);
- itkSetMacro(ScatteringCoefficient, double);
- itkSetMacro(AnisotopyCoefficient, double);
- itkSetMacro(BifurcationFrequency, double);
- itkSetMacro(DoPartialVolume, bool);
-
- protected:
- VesselProperties();
- VesselProperties(Self::Pointer other);
- ~VesselProperties() override;
-
- private:
- Vector::Pointer m_PositionVector;
- Vector::Pointer m_DirectionVector;
- double m_RadiusInVoxel;
- double m_AbsorptionCoefficient;
- double m_ScatteringCoefficient;
- double m_AnisotopyCoefficient;
- double m_BifurcationFrequency;
- bool m_DoPartialVolume;
- };
-
- /**
- * @brief Equal A function comparing two VesselProperty instances for beeing equal
- *
- * @param rightHandSide A VesselProperty to be compared
- * @param leftHandSide A Vesselproperty to be compared
- * @param eps tolarence for comparison. You can use mitk::eps in most cases.
- * @param verbose flag indicating if the user wants detailed console output or not.
- * @return true, if all subsequent comparisons are true, false otherwise
- */
- MITKPHOTOACOUSTICSLIB_EXPORT bool Equal(const VesselProperties::Pointer leftHandSide, const VesselProperties::Pointer rightHandSide, double eps, bool verbose);
- }
-}
-#endif // MITKPhotoacousticVesselParameters_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVesselTree.h b/Modules/PhotoacousticsLib/include/mitkPAVesselTree.h
deleted file mode 100644
index dbef42e6d9..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVesselTree.h
+++ /dev/null
@@ -1,67 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKVESSELSTRUCTURE_H
-#define MITKVESSELSTRUCTURE_H
-
-//std includes
-#include <vector>
-
-//mitk includes
-#include "mitkPAVessel.h"
-#include "mitkPAInSilicoTissueVolume.h"
-#include <MitkPhotoacousticsLibExports.h>
-
-//Includes for smart pointer usage
-#include "mitkCommon.h"
-#include "itkLightObject.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT VesselTree : public itk::LightObject
- {
- public:
- mitkClassMacroItkParent(VesselTree, itk::LightObject);
- mitkNewMacro1Param(Self, VesselProperties::Pointer);
-
- /**
- * @brief Step Performs a simulation step, in which all subvessels of this VesselTree are expanded.
- *
- * @param volume
- * @param calculateNewPosition
- * @param bendingFactor
- * @param rng
- */
- void Step(InSilicoTissueVolume::Pointer volume,
- Vessel::CalculateNewVesselPositionCallback calculateNewPosition,
- double bendingFactor, std::mt19937* rng);
-
- /**
- * @brief IsFinished
- * @return true if no subvessel can be expanded.
- */
- bool IsFinished();
-
- itkGetConstMacro(CurrentSubvessels, std::vector<Vessel::Pointer>*);
-
- protected:
- VesselTree(VesselProperties::Pointer initialProperties);
- ~VesselTree() override;
-
- private:
- std::vector<Vessel::Pointer>* m_CurrentSubvessels;
- };
-
- MITKPHOTOACOUSTICSLIB_EXPORT bool Equal(const VesselTree::Pointer leftHandSide, const VesselTree::Pointer rightHandSide, double eps, bool verbose);
- }
-}
-#endif // MITKVESSELSTRUCTURE_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVolume.h b/Modules/PhotoacousticsLib/include/mitkPAVolume.h
deleted file mode 100644
index 059b4df280..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVolume.h
+++ /dev/null
@@ -1,147 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTIC3dVOLUME_H
-#define MITKPHOTOACOUSTIC3dVOLUME_H
-
-#include "MitkPhotoacousticsLibExports.h"
-
-//Includes for smart pointer usage
-#include <mitkImage.h>
-#include <itkLightObject.h>
-
-namespace mitk
-{
- namespace pa
- {
- /**
- * @brief The Volume class is designed to encapsulate volumetric information and to provide convenience methods
- * for data access and image conversions.
- */
- class MITKPHOTOACOUSTICSLIB_EXPORT Volume : public itk::LightObject
- {
- public:
-
- mitkClassMacroItkParent(Volume, itk::LightObject);
-
- /**
- *@brief returns smartpointer reference to a new instance of this objects.
- * The given data array will be freed upon calling this constructor.
- *@param data
- *@param xDim
- *@param yDim
- *@param zDim
- *@param spacing
- *@return smartpointer reference to a new instance of this object
- */
- static Volume::Pointer New(double* data, unsigned int xDim, unsigned int yDim, unsigned int zDim, double spacing);
-
- static Volume::Pointer New(mitk::Image::Pointer image);
-
- /**
- * @brief GetData. Returns data at wanted position. For performance reasons, this method will not check,
- * if the specified position it within the array. Please use the GetXDim(), GetYDim() and GetZDim() methods
- * to check for yourself if necessary.
- *
- * @param x
- * @param y
- * @param z
- * @return the data contained within the data array held by this Volume at
- * positon x|y|z.
- */
- double GetData(unsigned int x, unsigned int y, unsigned int z);
-
- /**
- * Returns a const reference to the data encapsuled by this class.
- */
- double* GetData() const;
-
- /**
- * @brief SetData
- * @param data
- * @param x
- * @param y
- * @param z
- */
- void SetData(double data, unsigned int x, unsigned int y, unsigned int z);
-
- /**
- * @brief GetXDim
- * @return size of x dimension of this Volume
- */
- unsigned int GetXDim();
-
- /**
- * @brief GetYDim
- * @return size of y dimension of this Volume
- */
- unsigned int GetYDim();
-
- /**
- * @brief GetZDim
- * @return size of z dimension of this Volume
- */
- unsigned int GetZDim();
-
- /**
- *@brief returns the Volume instance as an mitk image
- */
- Image::Pointer AsMitkImage();
-
- /**
- * @brief DeepCopy
- * @return a deep copy of this Volume. the old volume remains intact and memory is NOT shared
- * between the objects.
- */
- Volume::Pointer DeepCopy();
-
- /**
- *@brief convenience method to enable consistent access to the dat array
- *@return a 1d index from 3d pixel coordinates
- */
- long long GetIndex(unsigned int x, unsigned int y, unsigned int z);
-
- double GetSpacing();
-
- void SetSpacing(double spacing);
-
- protected:
- /**
- * @brief Initialize initializes this volume with the given pointer to the data array.
- * It is assumed, that the array is of dimension xDim|yDim|zDim.
- * The Photoacoustic3DVolume will handle memory management of the array and delete it on
- * constructor call.
- *
- * @param data a pointer to the data array
- * @param xDim x dimension of the data
- * @param yDim y dimension of the data
- * @param zDim z dimension of the data
- * @param spacing spacing of the data
- */
- Volume(double* data, unsigned int xDim, unsigned int yDim, unsigned int zDim, double spacing);
- Volume(mitk::Image::Pointer image);
- ~Volume() override;
-
- const int NUMBER_OF_SPATIAL_DIMENSIONS = 3;
-
- Image::Pointer m_InternalMitkImage;
-
- // this data is kept to enable fast access
- unsigned int m_XDim;
- unsigned int m_YDim;
- unsigned int m_ZDim;
- double* m_FastAccessDataPointer;
- };
- }
-}
-
-#endif // MITKPHOTOACOUSTIC3dVOLUME_H
diff --git a/Modules/PhotoacousticsLib/include/mitkPAVolumeManipulator.h b/Modules/PhotoacousticsLib/include/mitkPAVolumeManipulator.h
deleted file mode 100644
index 950a0ac28c..0000000000
--- a/Modules/PhotoacousticsLib/include/mitkPAVolumeManipulator.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKPHOTOACOUSTIC3DVOLUMEMANIPULATOR_H
-#define MITKPHOTOACOUSTIC3DVOLUMEMANIPULATOR_H
-
-#include <mitkCommon.h>
-#include <MitkPhotoacousticsLibExports.h>
-#include "mitkPAVolume.h"
-#include "mitkPAInSilicoTissueVolume.h"
-
-namespace mitk {
- namespace pa {
- class MITKPHOTOACOUSTICSLIB_EXPORT VolumeManipulator final
- {
- public:
-
- /**
- * @brief ThresholdImage applies a binary threshold filter to this image.
- * @param threshold
- * @param image
- */
- static void ThresholdImage(Volume::Pointer image, double threshold);
-
- /**
- * @brief Multiplies the image with a given factor
- * @param factor
- * @param image
- */
- static void MultiplyImage(Volume::Pointer image, double factor);
-
- /**
- * @brief applies a Gaussian blur to an image
- * @param sigma
- * @param paVolume
- */
- static void GaussianBlur3D(Volume::Pointer paVolume, double sigma);
-
- static void Log10Image(Volume::Pointer image);
-
- static void RescaleImage(InSilicoTissueVolume::Pointer image, double ratio);
-
- static Volume::Pointer RescaleImage(Volume::Pointer image, double ratio, double sigma);
-
- private:
- VolumeManipulator();
- virtual ~VolumeManipulator();
- };
- }
-}
-
-#endif // MITKPHOTOACOUSTIC3DVOLUMEMANIPULATOR_H
diff --git a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVessel.cpp b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVessel.cpp
deleted file mode 100644
index 3d2612927e..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVessel.cpp
+++ /dev/null
@@ -1,111 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVessel.h"
-#include <chrono>
-#include <thread>
-
-mitk::pa::Vessel::Vessel(VesselProperties::Pointer initialProperties) :
- m_RangeDistribution(itk::Math::pi / 16, itk::Math::pi / 8),
- m_SignDistribution(-1, 1)
-{
- m_Finished = false;
- //Copy this so it may be reused for other vessels.
- m_VesselProperties = VesselProperties::New(initialProperties);
- m_RadiusRangeDistribution = std::uniform_real_distribution<>(NEW_RADIUS_MINIMUM_RELATIVE_SIZE,
- NEW_RADIUS_MAXIMUM_RELATIVE_SIZE);
- m_VesselMeanderStrategy = VesselMeanderStrategy::New();
- m_WalkedDistance = 0;
- m_VesselDrawer = VesselDrawer::New();
-}
-
-mitk::pa::Vessel::~Vessel()
-{
- m_VesselProperties = nullptr;
- m_VesselMeanderStrategy = nullptr;
-}
-
-void mitk::pa::Vessel::ExpandVessel(InSilicoTissueVolume::Pointer volume,
- CalculateNewVesselPositionCallback calculateNewPosition, double bendingFactor, std::mt19937* rng)
-{
- m_VesselDrawer->ExpandAndDrawVesselInVolume(m_VesselProperties, volume);
- (m_VesselMeanderStrategy->*calculateNewPosition)(m_VesselProperties->GetDirectionVector(), bendingFactor, rng);
- m_WalkedDistance += (m_VesselProperties->GetDirectionVector()->GetNorm() / volume->GetSpacing());
-}
-
-bool mitk::pa::Vessel::CanBifurcate()
-{
- return m_VesselProperties->GetBifurcationFrequency() < m_WalkedDistance;
-}
-
-int mitk::pa::Vessel::GetSign(std::mt19937 *rng)
-{
- if (m_SignDistribution(*rng) < 0)
- return -1;
-
- return 1;
-}
-
-mitk::pa::Vessel::Pointer mitk::pa::Vessel::Bifurcate(std::mt19937* rng)
-{
- VesselProperties::Pointer vesselParams = VesselProperties::New(m_VesselProperties);
- double thetaChange = m_RangeDistribution(*rng) * GetSign(rng);
- double phiChange = m_RangeDistribution(*rng) * GetSign(rng);
-
- vesselParams->GetDirectionVector()->Rotate(thetaChange, phiChange);
- m_VesselProperties->GetDirectionVector()->Rotate(-thetaChange, -phiChange);
-
- double newRadius = m_RadiusRangeDistribution(*rng)*m_VesselProperties->GetRadiusInVoxel();
- vesselParams->SetRadiusInVoxel(newRadius);
- m_VesselProperties->SetRadiusInVoxel(
- sqrt(m_VesselProperties->GetRadiusInVoxel()*m_VesselProperties->GetRadiusInVoxel() - newRadius*newRadius));
-
- m_WalkedDistance = 0;
-
- return Vessel::New(vesselParams);
-}
-
-bool mitk::pa::Vessel::IsFinished()
-{
- return m_VesselProperties->GetRadiusInVoxel() < MINIMUM_VESSEL_RADIUS;
-}
-
-bool mitk::pa::Equal(const Vessel::Pointer leftHandSide, const Vessel::Pointer rightHandSide, double eps, bool verbose)
-{
- MITK_INFO(verbose) << "=== mitk::pa::Vessel Equal ===";
-
- if (rightHandSide.IsNull() || leftHandSide.IsNull())
- {
- MITK_INFO(verbose) << "Cannot compare nullpointers";
- return false;
- }
-
- if (leftHandSide->IsFinished() != rightHandSide->IsFinished())
- {
- MITK_INFO(verbose) << "Not same finished state.";
- return false;
- }
-
- if (leftHandSide->CanBifurcate() != rightHandSide->CanBifurcate())
- {
- MITK_INFO(verbose) << "Not same bifurcation state.";
- return false;
- }
-
- if (!Equal(leftHandSide->GetVesselProperties(), rightHandSide->GetVesselProperties(), eps, verbose))
- {
- MITK_INFO(verbose) << "Vesselproperties not equal";
- return false;
- }
-
- return true;
-}
diff --git a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselMeanderStrategy.cpp b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselMeanderStrategy.cpp
deleted file mode 100644
index fdd10f8cda..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselMeanderStrategy.cpp
+++ /dev/null
@@ -1,41 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVesselMeanderStrategy.h"
-
-mitk::pa::VesselMeanderStrategy::VesselMeanderStrategy()
-{
-}
-
-mitk::pa::VesselMeanderStrategy::~VesselMeanderStrategy()
-{
-}
-
-void mitk::pa::VesselMeanderStrategy::CalculateNewDirectionVectorInStraightLine(Vector::Pointer direction, double /*bendingFactor*/, std::mt19937* rng)
-{
- if (direction->GetNorm() <= mitk::eps)
- {
- direction->Randomize(rng);
- }
-}
-
-void mitk::pa::VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector(Vector::Pointer direction, double bendingFactor, std::mt19937* rng)
-{
- if (direction->GetNorm() <= mitk::eps)
- {
- direction->Randomize(rng);
- }
-
- direction->RandomizeByPercentage(RANDOMIZATION_PERCENTAGE, bendingFactor, rng);
-
- direction->Normalize();
-}
diff --git a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselProperties.cpp b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselProperties.cpp
deleted file mode 100644
index fca82cfe7b..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselProperties.cpp
+++ /dev/null
@@ -1,105 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVesselProperties.h"
-
-mitk::pa::VesselProperties::VesselProperties()
-{
- m_PositionVector = Vector::New();
- m_DirectionVector = Vector::New();
- m_RadiusInVoxel = 0;
- m_AbsorptionCoefficient = 0;
- m_ScatteringCoefficient = 0;
- m_AnisotopyCoefficient = 0;
- m_BifurcationFrequency = 0;
- m_DoPartialVolume = false;
-}
-
-mitk::pa::VesselProperties::VesselProperties(Self::Pointer other)
-{
- m_PositionVector = other->GetPositionVector()->Clone();
- m_DirectionVector = other->GetDirectionVector()->Clone();
- m_RadiusInVoxel = other->GetRadiusInVoxel();
- m_AbsorptionCoefficient = other->GetAbsorptionCoefficient();
- m_ScatteringCoefficient = other->GetScatteringCoefficient();
- m_AnisotopyCoefficient = other->GetAnisotopyCoefficient();
- m_BifurcationFrequency = other->GetBifurcationFrequency();
- m_DoPartialVolume = other->GetDoPartialVolume();
-}
-
-mitk::pa::VesselProperties::~VesselProperties()
-{
- m_PositionVector = nullptr;
- m_DirectionVector = nullptr;
-}
-
-bool mitk::pa::Equal(const VesselProperties::Pointer leftHandSide, const VesselProperties::Pointer rightHandSide,
- double eps, bool verbose)
-{
- MITK_INFO(verbose) << "=== mitk::pa::VesselProperties Equal ===";
-
- if (rightHandSide.IsNull() || leftHandSide.IsNull())
- {
- MITK_INFO(verbose) << "Cannot compare nullpointers";
- return false;
- }
-
- if (leftHandSide->GetAbsorptionCoefficient() - rightHandSide->GetAbsorptionCoefficient() > eps)
- {
- MITK_INFO(verbose) << "Not the same AbsorptionCoefficient.";
- return false;
- }
-
- if (leftHandSide->GetAnisotopyCoefficient() - rightHandSide->GetAnisotopyCoefficient() > eps)
- {
- MITK_INFO(verbose) << "Not the same AnisotropyCoefficient.";
- return false;
- }
-
- if (leftHandSide->GetBifurcationFrequency() - rightHandSide->GetBifurcationFrequency() > eps)
- {
- MITK_INFO(verbose) << "Not the same BifurcationFrequency.";
- return false;
- }
-
- if (leftHandSide->GetRadiusInVoxel() - rightHandSide->GetRadiusInVoxel() > eps)
- {
- MITK_INFO(verbose) << "Not the same RadiusInVoxel.";
- return false;
- }
-
- if (leftHandSide->GetScatteringCoefficient() - rightHandSide->GetScatteringCoefficient() > eps)
- {
- MITK_INFO(verbose) << "Not the same ScatteringCoefficient.";
- return false;
- }
-
- if (!Equal(leftHandSide->GetPositionVector(), rightHandSide->GetPositionVector(), eps, verbose))
- {
- MITK_INFO(verbose) << "PositionVector not equal";
- return false;
- }
-
- if (!Equal(leftHandSide->GetDirectionVector(), rightHandSide->GetDirectionVector(), eps, verbose))
- {
- MITK_INFO(verbose) << "DirectionVector not equal";
- return false;
- }
-
- if (!(leftHandSide->GetDoPartialVolume() == rightHandSide->GetDoPartialVolume()))
- {
- MITK_INFO(verbose) << "GetDoPartialVolume not equal";
- return false;
- }
-
- return true;
-}
diff --git a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselTree.cpp b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselTree.cpp
deleted file mode 100644
index 31650d26de..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselTree.cpp
+++ /dev/null
@@ -1,96 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVesselTree.h"
-#include "thread"
-
-mitk::pa::VesselTree::VesselTree(VesselProperties::Pointer initialProperties)
-{
- m_CurrentSubvessels = new std::vector<Vessel::Pointer>();
- Vessel::Pointer tmpVessel = Vessel::New(initialProperties);
- m_CurrentSubvessels->push_back(tmpVessel);
-}
-
-mitk::pa::VesselTree::~VesselTree()
-{
- m_CurrentSubvessels->clear();
- delete m_CurrentSubvessels;
- m_CurrentSubvessels = nullptr;
-}
-
-void mitk::pa::VesselTree::Step(mitk::pa::InSilicoTissueVolume::Pointer volume,
- Vessel::CalculateNewVesselPositionCallback calculateNewPosition, double bendingFactor, std::mt19937* rng)
-{
- std::vector<Vessel::Pointer> newVessels;
-
- for (unsigned int vesselTreeIndex = 0; vesselTreeIndex < m_CurrentSubvessels->size(); vesselTreeIndex++)
- {
- Vessel::Pointer currentVessel = m_CurrentSubvessels->at(vesselTreeIndex);
- if (!currentVessel->IsFinished())
- {
- currentVessel->ExpandVessel(volume, calculateNewPosition, bendingFactor, rng);
- if (currentVessel->CanBifurcate())
- {
- newVessels.push_back(currentVessel->Bifurcate(rng));
- }
- }
- }
-
- for (unsigned int newVesselsIndex = 0; newVesselsIndex < newVessels.size(); newVesselsIndex++)
- {
- m_CurrentSubvessels->push_back(newVessels.at(newVesselsIndex));
- }
-}
-
-bool mitk::pa::VesselTree::IsFinished()
-{
- for (unsigned int vesselTreeIndex = 0; vesselTreeIndex < m_CurrentSubvessels->size(); vesselTreeIndex++)
- {
- if (!m_CurrentSubvessels->at(vesselTreeIndex)->IsFinished())
- return false;
- }
- return true;
-}
-
-bool mitk::pa::Equal(const VesselTree::Pointer leftHandSide, const VesselTree::Pointer rightHandSide, double eps, bool verbose)
-{
- MITK_INFO(verbose) << "=== mitk::pa::Vessel Equal ===";
-
- if (rightHandSide.IsNull() || leftHandSide.IsNull())
- {
- MITK_INFO(verbose) << "Cannot compare nullpointers";
- return false;
- }
-
- if (leftHandSide->IsFinished() != rightHandSide->IsFinished())
- {
- MITK_INFO(verbose) << "Not same finished state.";
- return false;
- }
-
- if (leftHandSide->GetCurrentSubvessels()->size() != rightHandSide->GetCurrentSubvessels()->size())
- {
- MITK_INFO(verbose) << "Not same number of subvessels in the vesseltree.";
- return false;
- }
-
- for (unsigned int vesselIdx = 0, numVessels = leftHandSide->GetCurrentSubvessels()->size(); vesselIdx < numVessels; ++vesselIdx)
- {
- if (!Equal(leftHandSide->GetCurrentSubvessels()->at(vesselIdx), rightHandSide->GetCurrentSubvessels()->at(vesselIdx), eps, verbose))
- {
- MITK_INFO(verbose) << "At least one vessel was not equal or the vessel list were not in order.";
- return false;
- }
- }
-
- return true;
-}
diff --git a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAComposedVolume.cpp b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAComposedVolume.cpp
deleted file mode 100644
index f515bc9f17..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAComposedVolume.cpp
+++ /dev/null
@@ -1,64 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include "mitkPAComposedVolume.h"
-#include "mitkIOUtil.h"
-#include "mitkImageReadAccessor.h"
-#include <string>
-
-mitk::pa::ComposedVolume::ComposedVolume(InSilicoTissueVolume::Pointer groundTruthVolume)
-{
- m_GroundTruthVolume = groundTruthVolume;
- m_FluenceComponents = 0;
- m_FluenceValues.clear();
-}
-
-mitk::pa::ComposedVolume::~ComposedVolume()
-{
- m_FluenceValues.clear();
-}
-
-int mitk::pa::ComposedVolume::GetNumberOfFluenceComponents()
-{
- return m_FluenceComponents;
-}
-
-int mitk::pa::ComposedVolume::GetYOffsetForFluenceComponentInPixels(int fluenceComponent)
-{
- if (fluenceComponent >= m_FluenceComponents)
- mitkThrow() << "Index out of bounds exception: There were less fluence components in the composed volume than the number you tried to access.";
-
- return (int)(m_FluenceValues.at(fluenceComponent)->GetYOffsetInCentimeters() /
- m_GroundTruthVolume->GetTissueParameters()->GetVoxelSpacingInCentimeters());
-}
-
-double mitk::pa::ComposedVolume::GetFluenceValue(int fluenceComponent, int x, int y, int z)
-{
- if (fluenceComponent >= m_FluenceComponents)
- mitkThrow() << "Index out of bounds exception: There were less fluence components in the composed volume than the number you tried to access.";
-
- return m_FluenceValues.at(fluenceComponent)->GetFluenceValue()->GetData(x, y + GetYOffsetForFluenceComponentInPixels(fluenceComponent), z);
-}
-
-void mitk::pa::ComposedVolume::AddSlice(mitk::pa::FluenceYOffsetPair::Pointer pairToAdd)
-{
- m_FluenceValues.push_back(pairToAdd);
- m_FluenceComponents++;
-}
-
-void mitk::pa::ComposedVolume::Sort()
-{
- std::sort(m_FluenceValues.begin(), m_FluenceValues.end(), [](const mitk::pa::FluenceYOffsetPair::Pointer& struct1,
- const mitk::pa::FluenceYOffsetPair::Pointer& struct2)
- {
- return (struct1->GetYOffsetInCentimeters() < struct2->GetYOffsetInCentimeters());
- });
-}
diff --git a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAFluenceYOffsetPair.cpp b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAFluenceYOffsetPair.cpp
deleted file mode 100644
index 73cc7edfb6..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAFluenceYOffsetPair.cpp
+++ /dev/null
@@ -1,39 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include "mitkPAFluenceYOffsetPair.h"
-
-mitk::pa::FluenceYOffsetPair::FluenceYOffsetPair(mitk::pa::Volume::Pointer fluenceValue, double yOffset)
-{
- m_FluenceValue = fluenceValue;
- m_YOffsetInCentimeters = yOffset;
-}
-
-mitk::pa::FluenceYOffsetPair::~FluenceYOffsetPair()
-{
- m_FluenceValue = nullptr;
-}
-
-mitk::pa::FluenceYOffsetPair::FluenceYOffsetPair(const mitk::pa::FluenceYOffsetPair::Pointer other)
-{
- m_FluenceValue = other->GetFluenceValue();
- m_YOffsetInCentimeters = other->GetYOffsetInCentimeters();
-}
-
-mitk::pa::Volume::Pointer mitk::pa::FluenceYOffsetPair::GetFluenceValue() const
-{
- return m_FluenceValue;
-}
-
-double mitk::pa::FluenceYOffsetPair::GetYOffsetInCentimeters() const
-{
- return m_YOffsetInCentimeters;
-}
diff --git a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp
deleted file mode 100644
index 331c90c03b..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp
+++ /dev/null
@@ -1,398 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkPAInSilicoTissueVolume.h>
-#include <mitkProperties.h>
-#include <mitkCoreServices.h>
-#include <mitkIPropertyPersistence.h>
-#include <itkImage.h>
-#include <itkDiscreteGaussianImageFilter.h>
-#include <mitkImageCast.h>
-#include <mitkImageToItk.h>
-#include <chrono>
-
-mitk::pa::InSilicoTissueVolume::InSilicoTissueVolume(TissueGeneratorParameters::Pointer parameters, std::mt19937* rng)
-{
- {
- unsigned int xDim = parameters->GetXDim();
- unsigned int yDim = parameters->GetYDim();
- unsigned int zDim = parameters->GetZDim();
- m_TDim = 4;
- unsigned int size = xDim * yDim * zDim;
- auto* absorptionArray = new double[size];
- auto* scatteringArray = new double[size];
- auto* anisotropyArray = new double[size];
- auto* segmentationArray = new double[size];
-
- m_InitialBackgroundAbsorption = (parameters->GetMinBackgroundAbsorption() + parameters->GetMaxBackgroundAbsorption()) / 2;
- m_Rng = rng;
-
- for (unsigned int index = 0; index < size; index++)
- {
- absorptionArray[index] = m_InitialBackgroundAbsorption;
- scatteringArray[index] = parameters->GetBackgroundScattering();
- anisotropyArray[index] = parameters->GetBackgroundAnisotropy();
- segmentationArray[index] = SegmentationType::BACKGROUND;
- }
-
- m_AbsorptionVolume = Volume::New(absorptionArray, xDim, yDim, zDim, parameters->GetVoxelSpacingInCentimeters());
- m_ScatteringVolume = Volume::New(scatteringArray, xDim, yDim, zDim, parameters->GetVoxelSpacingInCentimeters());
- m_AnisotropyVolume = Volume::New(anisotropyArray, xDim, yDim, zDim, parameters->GetVoxelSpacingInCentimeters());
- m_SegmentationVolume = Volume::New(segmentationArray, xDim, yDim, zDim, parameters->GetVoxelSpacingInCentimeters());
- }
-
- m_TissueParameters = parameters;
- m_PropertyList = mitk::PropertyList::New();
- UpdatePropertyList();
-}
-
-void mitk::pa::InSilicoTissueVolume::UpdatePropertyList()
-{
- //Set properties
- AddIntProperty("mcflag", m_TissueParameters->GetMCflag());
- AddIntProperty("launchflag", m_TissueParameters->GetMCLaunchflag());
- AddIntProperty("boundaryflag", m_TissueParameters->GetMCBoundaryflag());
- AddDoubleProperty("launchPointX", m_TissueParameters->GetMCLaunchPointX());
- AddDoubleProperty("launchPointY", m_TissueParameters->GetMCLaunchPointY());
- AddDoubleProperty("launchPointZ", m_TissueParameters->GetMCLaunchPointZ());
- AddDoubleProperty("focusPointX", m_TissueParameters->GetMCFocusPointX());
- AddDoubleProperty("focusPointY", m_TissueParameters->GetMCFocusPointY());
- AddDoubleProperty("focusPointZ", m_TissueParameters->GetMCFocusPointZ());
- AddDoubleProperty("trajectoryVectorX", m_TissueParameters->GetMCTrajectoryVectorX());
- AddDoubleProperty("trajectoryVectorY", m_TissueParameters->GetMCTrajectoryVectorY());
- AddDoubleProperty("trajectoryVectorZ", m_TissueParameters->GetMCTrajectoryVectorZ());
- AddDoubleProperty("radius", m_TissueParameters->GetMCRadius());
- AddDoubleProperty("waist", m_TissueParameters->GetMCWaist());
- AddDoubleProperty("partialVolume", m_TissueParameters->GetDoPartialVolume());
- AddDoubleProperty("standardTissueAbsorptionMin", m_TissueParameters->GetMinBackgroundAbsorption());
- AddDoubleProperty("standardTissueAbsorptionMax", m_TissueParameters->GetMaxBackgroundAbsorption());
- AddDoubleProperty("standardTissueScattering", m_TissueParameters->GetBackgroundScattering());
- AddDoubleProperty("standardTissueAnisotropy", m_TissueParameters->GetBackgroundAnisotropy());
- AddDoubleProperty("airThickness", m_TissueParameters->GetAirThicknessInMillimeters());
- AddDoubleProperty("skinThickness", m_TissueParameters->GetSkinThicknessInMillimeters());
-}
-
-mitk::pa::InSilicoTissueVolume::InSilicoTissueVolume(
- Volume::Pointer absorptionVolume,
- Volume::Pointer scatteringVolume,
- Volume::Pointer anisotropyVolume,
- Volume::Pointer segmentationVolume,
- TissueGeneratorParameters::Pointer tissueParameters,
- mitk::PropertyList::Pointer propertyList)
-{
- m_AbsorptionVolume = absorptionVolume;
- m_ScatteringVolume = scatteringVolume;
- m_AnisotropyVolume = anisotropyVolume;
- m_SegmentationVolume = segmentationVolume;
- m_TissueParameters = tissueParameters;
- m_PropertyList = propertyList;
- if (m_SegmentationVolume.IsNotNull())
- m_TDim = 4;
- else
- m_TDim = 3;
-}
-
-double mitk::pa::InSilicoTissueVolume::GetSpacing()
-{
- return m_AbsorptionVolume->GetSpacing();
-}
-
-void mitk::pa::InSilicoTissueVolume::SetSpacing(double spacing)
-{
- m_AbsorptionVolume->SetSpacing(spacing);
- m_ScatteringVolume->SetSpacing(spacing);
- m_AnisotropyVolume->SetSpacing(spacing);
- if (m_SegmentationVolume.IsNotNull())
- {
- m_SegmentationVolume->SetSpacing(spacing);
- }
-}
-
-void mitk::pa::InSilicoTissueVolume::AddDoubleProperty(std::string label, double value)
-{
- m_PropertyList->SetDoubleProperty(label.c_str(), value);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New(label));
-}
-
-void mitk::pa::InSilicoTissueVolume::AddIntProperty(std::string label, int value)
-{
- m_PropertyList->SetIntProperty(label.c_str(), value);
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New(label));
-}
-
-mitk::Image::Pointer mitk::pa::InSilicoTissueVolume::ConvertToMitkImage()
-{
- mitk::Image::Pointer resultImage = mitk::Image::New();
- mitk::PixelType TPixel = mitk::MakeScalarPixelType<double>();
- auto* dimensionsOfImage = new unsigned int[4];
-
- // Copy dimensions
- dimensionsOfImage[0] = m_TissueParameters->GetYDim();
- dimensionsOfImage[1] = m_TissueParameters->GetXDim();
- dimensionsOfImage[2] = m_TissueParameters->GetZDim();
- dimensionsOfImage[3] = m_TDim;
-
- resultImage->Initialize(TPixel, 4, dimensionsOfImage, 1);
-
- mitk::Vector3D spacing;
- spacing.Fill(m_TissueParameters->GetVoxelSpacingInCentimeters());
- resultImage->SetSpacing(spacing);
-
- resultImage->SetImportVolume(m_AbsorptionVolume->GetData(), 0, 0, mitk::Image::CopyMemory);
- resultImage->SetImportVolume(m_ScatteringVolume->GetData(), 1, 0, mitk::Image::CopyMemory);
- resultImage->SetImportVolume(m_AnisotropyVolume->GetData(), 2, 0, mitk::Image::CopyMemory);
- if (m_TDim > 3)
- {
- resultImage->SetImportVolume(m_SegmentationVolume->GetData(), 3, 0, mitk::Image::CopyMemory);
- }
-
- resultImage->SetPropertyList(m_PropertyList);
-
- return resultImage;
-}
-
-mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::InSilicoTissueVolume::New(
- Volume::Pointer absorptionVolume,
- Volume::Pointer scatteringVolume,
- Volume::Pointer anisotropyVolume,
- Volume::Pointer segmentationVolume,
- TissueGeneratorParameters::Pointer tissueParameters,
- mitk::PropertyList::Pointer propertyList)
-{
- InSilicoTissueVolume::Pointer smartPtr = new InSilicoTissueVolume(
- absorptionVolume, scatteringVolume, anisotropyVolume, segmentationVolume,
- tissueParameters, propertyList);
- smartPtr->UnRegister();
- return smartPtr;
-}
-
-mitk::pa::InSilicoTissueVolume::~InSilicoTissueVolume()
-{
- m_AbsorptionVolume = nullptr;
- m_ScatteringVolume = nullptr;
- m_AnisotropyVolume = nullptr;
- m_SegmentationVolume = nullptr;
- m_TissueParameters = nullptr;
- m_PropertyList = nullptr;
-}
-
-void mitk::pa::InSilicoTissueVolume::SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy)
-{
- if (IsInsideVolume(x, y, z))
- {
- m_AbsorptionVolume->SetData(absorption, x, y, z);
- m_ScatteringVolume->SetData(scattering, x, y, z);
- m_AnisotropyVolume->SetData(anisotropy, x, y, z);
- }
-}
-
-void mitk::pa::InSilicoTissueVolume::SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy, SegmentationType segmentType)
-{
- if (IsInsideVolume(x, y, z))
- {
- m_AbsorptionVolume->SetData(absorption, x, y, z);
- m_ScatteringVolume->SetData(scattering, x, y, z);
- m_AnisotropyVolume->SetData(anisotropy, x, y, z);
- if (m_SegmentationVolume.IsNotNull())
- {
- m_SegmentationVolume->SetData(segmentType, x, y, z);
- }
- }
-}
-
-bool mitk::pa::InSilicoTissueVolume::IsInsideVolume(int x, int y, int z)
-{
- return x >= 0 && x < m_TissueParameters->GetXDim() &&
- y >= 0 && y < m_TissueParameters->GetYDim() &&
- z >= 0 && z < m_TissueParameters->GetZDim();
-}
-
-mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetAbsorptionVolume()
-{
- return m_AbsorptionVolume;
-}
-
-mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetSegmentationVolume()
-{
- return m_SegmentationVolume;
-}
-
-void mitk::pa::InSilicoTissueVolume::FinalizeVolume()
-{
- AddSkinAndAirLayers();
-
- // If specified, randomize all tissue parameters
- if (m_TissueParameters->GetRandomizePhysicalProperties())
- {
- RandomizeTissueCoefficients(m_TissueParameters->GetUseRngSeed(),
- m_TissueParameters->GetRngSeed(),
- m_TissueParameters->GetRandomizePhysicalPropertiesPercentage());
- }
-
- unsigned int xDim = m_TissueParameters->GetXDim();
- unsigned int yDim = m_TissueParameters->GetYDim();
- unsigned int zDim = m_TissueParameters->GetZDim();
-
- std::uniform_real_distribution<double> randomBackgroundAbsorptionDistribution(
- m_TissueParameters->GetMinBackgroundAbsorption(), m_TissueParameters->GetMaxBackgroundAbsorption());
-
- for (unsigned int z = 0; z < zDim; z++)
- {
- for (unsigned int y = 0; y < yDim; y++)
- {
- for (unsigned int x = 0; x < xDim; x++)
- {
- if (fabs(m_AbsorptionVolume->GetData(x, y, z) - m_InitialBackgroundAbsorption) < mitk::eps)
- {
- m_AbsorptionVolume->SetData(randomBackgroundAbsorptionDistribution(*m_Rng), x, y, z);
- }
- }
- }
- }
-}
-
-void mitk::pa::InSilicoTissueVolume::AddSkinAndAirLayers()
-{
- //Calculate the index location according to thickness in cm
- double airvoxel = (m_TissueParameters->GetAirThicknessInMillimeters() / m_TissueParameters->GetVoxelSpacingInCentimeters()) / 10;
- double skinvoxel = airvoxel + (m_TissueParameters->GetSkinThicknessInMillimeters() / m_TissueParameters->GetVoxelSpacingInCentimeters()) / 10;
-
- for (int y = 0; y < m_TissueParameters->GetYDim(); y++)
- {
- for (int x = 0; x < m_TissueParameters->GetXDim(); x++)
- {
- // Add air from index 0 to airvoxel
- if (m_TissueParameters->GetAirThicknessInMillimeters() > mitk::eps)
- {
- FillZLayer(x, y, 0, airvoxel,
- m_TissueParameters->GetAirAbsorption(),
- m_TissueParameters->GetAirScattering(),
- m_TissueParameters->GetAirAnisotropy(),
- SegmentationType::AIR);
- }
-
- //Add skin from index airvoxel to skinvoxel
- if (m_TissueParameters->GetSkinThicknessInMillimeters() > mitk::eps)
- {
- FillZLayer(x, y, airvoxel, skinvoxel,
- m_TissueParameters->GetSkinAbsorption(),
- m_TissueParameters->GetSkinScattering(),
- m_TissueParameters->GetSkinAnisotropy(),
- SegmentationType::SKIN);
- }
- }
- }
-}
-
-void mitk::pa::InSilicoTissueVolume::FillZLayer(int x, int y, double startIdx, double endIdx,
- double absorption, double scattering, double anisotropy,
- SegmentationType segmentationType)
-{
- for (int z = startIdx; z < endIdx; z++)
- {
- if (IsInsideVolume(x, y, z))
- {
- if (endIdx - z < 1)
- {
- //Simulate partial volume effects
- m_AbsorptionVolume->SetData((1 - (endIdx - z)) *
- m_AbsorptionVolume->GetData(x, y, z) + (endIdx - z) * absorption, x, y, z);
- m_ScatteringVolume->SetData((1 - (endIdx - z)) *
- m_ScatteringVolume->GetData(x, y, z) + (endIdx - z) * scattering, x, y, z);
- m_AnisotropyVolume->SetData((1 - (endIdx - z)) *
- m_AnisotropyVolume->GetData(x, y, z) + (endIdx - z) * anisotropy, x, y, z);
- if (endIdx - z > 0.5)
- {
- //Only put the segmentation label if more than half of the partial volume is the wanted tissue type
- if (m_SegmentationVolume.IsNotNull())
- {
- m_SegmentationVolume->SetData(segmentationType, x, y, z);
- }
- }
- }
- else
- {
- m_AbsorptionVolume->SetData(absorption, x, y, z);
- m_ScatteringVolume->SetData(scattering, x, y, z);
- m_AnisotropyVolume->SetData(anisotropy, x, y, z);
- if (m_SegmentationVolume.IsNotNull())
- {
- m_SegmentationVolume->SetData(segmentationType, x, y, z);
- }
- }
- }
- }
-}
-
-void mitk::pa::InSilicoTissueVolume::RandomizeTissueCoefficients(long rngSeed, bool useRngSeed, double percentage)
-{
- std::mt19937 rng;
- std::random_device randomDevice;
- if (useRngSeed)
- {
- rng.seed(rngSeed);
- }
- else
- {
- if (randomDevice.entropy() > 0.1)
- {
- rng.seed(randomDevice());
- }
- else
- {
- rng.seed(std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::now().time_since_epoch()).count());
- }
- }
- std::normal_distribution<> percentageDistribution(1, percentage / 100);
-
- for (int y = 0; y < m_TissueParameters->GetYDim(); y++)
- {
- for (int x = 0; x < m_TissueParameters->GetXDim(); x++)
- {
- for (int z = 0; z < m_TissueParameters->GetZDim(); z++)
- {
- m_AbsorptionVolume->SetData(m_AbsorptionVolume->GetData(x, y, z) * percentageDistribution(rng), x, y, z);
- m_ScatteringVolume->SetData(m_ScatteringVolume->GetData(x, y, z) * percentageDistribution(rng), x, y, z);
- }
- }
- }
-}
-
-mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetScatteringVolume()
-{
- return m_ScatteringVolume;
-}
-
-mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetAnisotropyVolume()
-{
- return m_AnisotropyVolume;
-}
-
-void mitk::pa::InSilicoTissueVolume::SetAbsorptionVolume(Volume::Pointer volume)
-{
- m_AbsorptionVolume = volume;
-}
-
-void mitk::pa::InSilicoTissueVolume::SetScatteringVolume(Volume::Pointer volume)
-{
- m_ScatteringVolume = volume;
-}
-
-void mitk::pa::InSilicoTissueVolume::SetAnisotropyVolume(Volume::Pointer volume)
-{
- m_AnisotropyVolume = volume;
-}
-
-void mitk::pa::InSilicoTissueVolume::SetSegmentationVolume(Volume::Pointer volume)
-{
- m_SegmentationVolume = volume;
-}
diff --git a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAVolume.cpp b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAVolume.cpp
deleted file mode 100644
index 93fade9690..0000000000
--- a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAVolume.cpp
+++ /dev/null
@@ -1,149 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVolume.h"
-#include <mitkImageWriteAccessor.h>
-#include <mitkImageReadAccessor.h>
-#include <mutex>
-
-mitk::pa::Volume::Volume(double* data,
- unsigned int xDim, unsigned int yDim, unsigned int zDim, double spacing)
-{
- MITK_INFO << "Initialized by data*";
- if (data == nullptr)
- mitkThrow() << "You may not initialize a mitk::Volume with a nullptr";
- m_InternalMitkImage = mitk::Image::New();
-
- auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS];
- dimensions[0] = yDim;
- dimensions[1] = xDim;
- dimensions[2] = zDim;
- m_XDim = xDim;
- m_YDim = yDim;
- m_ZDim = zDim;
- mitk::PixelType pixelType = mitk::MakeScalarPixelType<double>();
-
- m_InternalMitkImage->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions);
- m_InternalMitkImage->SetImportVolume(data, Image::ImportMemoryManagementType::CopyMemory);
-
- SetSpacing(spacing);
-
- m_FastAccessDataPointer = GetData();
-
- delete data;
-}
-
-mitk::pa::Volume::Volume(mitk::Image::Pointer image)
-{
- MITK_INFO << "Initialized by mitk::Image";
-
- if (image.IsNull())
- mitkThrow() << "You may not initialize a mitk::Volume with a null reference to an mitk image";
-
- unsigned int* dimensions = image->GetDimensions();
- m_YDim = dimensions[0];
- m_XDim = dimensions[1];
- m_ZDim = dimensions[2];
-
- m_InternalMitkImage = image;
-
- m_FastAccessDataPointer = GetData();
-}
-
-double mitk::pa::Volume::GetSpacing()
-{
- return m_InternalMitkImage->GetGeometry()->GetSpacing()[0];
-}
-
-void mitk::pa::Volume::SetSpacing(double spacing)
-{
- const mitk::ScalarType spacingArray[]{ spacing, spacing, spacing };
- m_InternalMitkImage->SetSpacing(spacingArray);
-}
-
-mitk::pa::Volume::~Volume()
-{
- m_InternalMitkImage = nullptr;
-}
-
-mitk::pa::Volume::Pointer mitk::pa::Volume::New(double* data, unsigned int xDim, unsigned int yDim, unsigned int zDim, double spacing)
-{
- mitk::pa::Volume::Pointer smartPtr = new mitk::pa::Volume(data, xDim, yDim, zDim, spacing);
- smartPtr->UnRegister();
- return smartPtr;
-}
-
-mitk::pa::Volume::Pointer mitk::pa::Volume::New(mitk::Image::Pointer image)
-{
- mitk::pa::Volume::Pointer smartPtr = new mitk::pa::Volume(image);
- smartPtr->UnRegister();
- return smartPtr;
-}
-
-mitk::Image::Pointer mitk::pa::Volume::AsMitkImage()
-{
- return m_InternalMitkImage;
-}
-
-mitk::pa::Volume::Pointer mitk::pa::Volume::DeepCopy()
-{
- long length = GetXDim()*GetYDim()*GetZDim();
- auto* data = new double[length];
- memcpy(data, GetData(), length * sizeof(double));
-
- return mitk::pa::Volume::New(data, GetXDim(), GetYDim(), GetZDim(), GetSpacing());
-}
-
-double mitk::pa::Volume::GetData(unsigned int x, unsigned int y, unsigned int z)
-{
- return m_FastAccessDataPointer[GetIndex(x, y, z)];
-}
-
-void mitk::pa::Volume::SetData(double data, unsigned int x, unsigned int y, unsigned int z)
-{
- m_FastAccessDataPointer[GetIndex(x, y, z)] = data;
-}
-
-unsigned int mitk::pa::Volume::GetXDim()
-{
- return m_XDim;
-}
-
-unsigned int mitk::pa::Volume::GetYDim()
-{
- return m_YDim;
-}
-
-unsigned int mitk::pa::Volume::GetZDim()
-{
- return m_ZDim;
-}
-
-double* mitk::pa::Volume::GetData() const
-{
- mitk::ImageWriteAccessor imgRead(m_InternalMitkImage, m_InternalMitkImage->GetVolumeData());
- return (double*)imgRead.GetData();
-}
-
-long long mitk::pa::Volume::GetIndex(unsigned int x, unsigned int y, unsigned int z)
-{
-#ifdef _DEBUG
-
- if (x < 0 || x >(GetXDim() - 1) || y < 0 || y >(GetYDim() - 1) || z < 0 || z >(GetZDim() - 1))
- {
- MITK_ERROR << "Index out of bounds at " << x << "|" << y << "|" << z;
- mitkThrow() << "Index out of bounds exception!";
- }
-
-#endif
- return ((long long)z) * m_XDim * m_YDim + ((long long)x) * m_YDim + ((long long)y);
-}
diff --git a/Modules/PhotoacousticsLib/src/Generator/mitkPANoiseGenerator.cpp b/Modules/PhotoacousticsLib/src/Generator/mitkPANoiseGenerator.cpp
deleted file mode 100644
index 1ba0e43613..0000000000
--- a/Modules/PhotoacousticsLib/src/Generator/mitkPANoiseGenerator.cpp
+++ /dev/null
@@ -1,63 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPANoiseGenerator.h"
-#include "mitkPAIOUtil.h"
-#include "mitkPAExceptions.h"
-#include <random>
-#include <chrono>
-#include <mitkCommon.h>
-
-void mitk::pa::NoiseGenerator::ApplyNoiseModel(mitk::pa::Volume::Pointer image, double detectorNoise, double speckleNoise)
-{
- if (detectorNoise < 0 || speckleNoise < 0)
- throw mitk::pa::InvalidInputException("detectorNoise must be >= 0 and speckleNoise must be >= 0");
-
- if (detectorNoise < mitk::eps && speckleNoise < mitk::eps)
- return;
-
- std::mt19937 rng;
- std::random_device randomDevice;
- if (randomDevice.entropy() > mitk::eps)
- {
- rng.seed(randomDevice());
- }
- else
- {
- rng.seed(std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::now().time_since_epoch()).count());
- }
- std::normal_distribution<> detector(detectorNoise / 2, detectorNoise / 2);
- std::normal_distribution<> speckle(1, speckleNoise);
-
- unsigned int negativecounter = 0;
-
- double* data = image->GetData();
-
- for (unsigned int x = 0, xLength = image->GetXDim(); x < xLength; x++)
- for (unsigned int y = 0, yLength = image->GetYDim(); y < yLength; y++)
- for (unsigned int z = 0, zLength = image->GetZDim(); z < zLength; z++)
- {
- double additiveNoise = detector(rng);
-
- double multiplicativeNoise = speckle(rng);
-
- double newSignal = (data[image->GetIndex(x, y, z)] + additiveNoise)*multiplicativeNoise;
-
- if (newSignal <= mitk::eps)
- {
- newSignal = mitk::eps;
- negativecounter++;
- }
-
- data[image->GetIndex(x, y, z)] = newSignal;
- }
-}
diff --git a/Modules/PhotoacousticsLib/src/Generator/mitkPAPhantomTissueGenerator.cpp b/Modules/PhotoacousticsLib/src/Generator/mitkPAPhantomTissueGenerator.cpp
deleted file mode 100644
index e129ec805a..0000000000
--- a/Modules/PhotoacousticsLib/src/Generator/mitkPAPhantomTissueGenerator.cpp
+++ /dev/null
@@ -1,153 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAPhantomTissueGenerator.h"
-#include "mitkPAVector.h"
-#include "mitkPAVolumeManipulator.h"
-
-mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::PhantomTissueGenerator::GeneratePhantomData(
- TissueGeneratorParameters::Pointer parameters)
-{
- MITK_DEBUG << "Initializing Empty Volume";
-
- const double RESAMPLING_FACTOR = 2;
-
- if (parameters->GetDoPartialVolume())
- {
- parameters->SetXDim(parameters->GetXDim() * RESAMPLING_FACTOR);
- parameters->SetYDim(parameters->GetYDim() * RESAMPLING_FACTOR);
- parameters->SetZDim(parameters->GetZDim() * RESAMPLING_FACTOR);
- parameters->SetVesselBifurcationFrequency(parameters->GetVesselBifurcationFrequency() * RESAMPLING_FACTOR);
- parameters->SetVoxelSpacingInCentimeters(parameters->GetVoxelSpacingInCentimeters() / RESAMPLING_FACTOR);
- }
-
- parameters->SetVesselBifurcationFrequency(10000);
-
- std::mt19937 randomNumberGenerator;
- std::random_device randomDevice;
- if (parameters->GetUseRngSeed())
- {
- randomNumberGenerator.seed(parameters->GetRngSeed());
- }
- else
- {
- if (randomDevice.entropy() > 0.1)
- {
- randomNumberGenerator.seed(randomDevice());
- }
- else
- {
- randomNumberGenerator.seed(std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::now().time_since_epoch()).count());
- }
- }
-
- auto generatedVolume = mitk::pa::InSilicoTissueVolume::New(parameters, &randomNumberGenerator);
-
- const unsigned int NUMER_OF_VESSELS = 5;
- const double START_DEPTH_IN_CM = 2.10;
- const double START_X_IN_CM = 0.76;
- const double RADIUS_IN_MM = 0.5;
- const double INCREMENT_XZ_IN_CM = 0.50;
- double ABSORPTION_PER_CM = parameters->GetMinVesselAbsorption();
-
- generatedVolume->AddIntProperty("numberOfVessels", NUMER_OF_VESSELS);
- generatedVolume->AddIntProperty("bifurcationFrequency", parameters->GetVesselBifurcationFrequency());
-
- for (unsigned int vesselNumber = 0; vesselNumber < NUMER_OF_VESSELS; vesselNumber++)
- {
- Vector::Pointer initialPosition = Vector::New();
- Vector::Pointer initialDirection = Vector::New();
-
- double initialRadius = RADIUS_IN_MM / parameters->GetVoxelSpacingInCentimeters() / 10;
- std::stringstream radiusString;
- radiusString << "vessel_" << vesselNumber + 1 << "_radius";
- generatedVolume->AddDoubleProperty(radiusString.str(), initialRadius);
-
- double absorptionCoefficient = ABSORPTION_PER_CM;
- std::stringstream absorptionString;
- absorptionString << "vessel_" << vesselNumber + 1 << "_absorption";
- generatedVolume->AddDoubleProperty(absorptionString.str(), absorptionCoefficient);
-
- double bendingFactor = 0;
- std::stringstream bendingString;
- bendingString << "vessel_" << vesselNumber + 1 << "_bendingFactor";
- generatedVolume->AddDoubleProperty(bendingString.str(), bendingFactor);
-
- double vesselScattering = 15;
- std::stringstream scatteringString;
- scatteringString << "vessel_" << vesselNumber + 1 << "_scattering";
- generatedVolume->AddDoubleProperty(scatteringString.str(), vesselScattering);
-
- double vesselAnisotropy = 0.9;
- std::stringstream anisotropyString;
- anisotropyString << "vessel_" << vesselNumber + 1 << "_anisotropy";
- generatedVolume->AddDoubleProperty(anisotropyString.str(), vesselAnisotropy);
-
- /*The vessel tree shall start at one of the 4 sides of the volume.
- * The vessels will always be completely contained in the volume
- * when starting to meander.
- * They will meander in a direction perpendicular to the
- * plane they started from (within the limits of the
- * DIRECTION_VECTOR_INITIAL_VARIANCE)
- */
-
- double zposition = (START_DEPTH_IN_CM + (vesselNumber*INCREMENT_XZ_IN_CM)) / parameters->GetVoxelSpacingInCentimeters();
-
- double xposition = (START_X_IN_CM + (vesselNumber*INCREMENT_XZ_IN_CM)) / parameters->GetVoxelSpacingInCentimeters();
-
- initialPosition->Randomize(xposition, xposition, 0, 0, zposition, zposition, &randomNumberGenerator);
- initialDirection->Randomize(0, 0, 1, 1, 0, 0, &randomNumberGenerator);
-
- initialDirection->Normalize();
- MITK_INFO << initialPosition->GetElement(0) << " | " << initialPosition->GetElement(1) << " | " << initialPosition->GetElement(2);
- MITK_INFO << initialDirection->GetElement(0) << " | " << initialDirection->GetElement(1) << " | " << initialDirection->GetElement(2);
-
- VesselProperties::Pointer vesselParams = VesselProperties::New();
- vesselParams->SetDirectionVector(initialDirection);
- vesselParams->SetPositionVector(initialPosition);
- vesselParams->SetRadiusInVoxel(initialRadius);
- vesselParams->SetAbsorptionCoefficient(absorptionCoefficient);
- vesselParams->SetScatteringCoefficient(vesselScattering);
- vesselParams->SetAnisotopyCoefficient(vesselAnisotropy);
- vesselParams->SetBifurcationFrequency(parameters->GetVesselBifurcationFrequency());
- vesselParams->SetDoPartialVolume(parameters->GetDoPartialVolume());
-
- VesselTree::Pointer vesselTree = VesselTree::New(vesselParams);
-
- while (!vesselTree->IsFinished())
- {
- vesselTree->Step(generatedVolume, parameters->GetCalculateNewVesselPositionCallback(), bendingFactor, &randomNumberGenerator);
- }
- }
-
- if (parameters->GetDoPartialVolume())
- {
- VolumeManipulator::RescaleImage(generatedVolume, (1.0 / RESAMPLING_FACTOR));
- parameters->SetXDim(parameters->GetXDim() / RESAMPLING_FACTOR);
- parameters->SetYDim(parameters->GetYDim() / RESAMPLING_FACTOR);
- parameters->SetZDim(parameters->GetZDim() / RESAMPLING_FACTOR);
- parameters->SetVesselBifurcationFrequency(parameters->GetVesselBifurcationFrequency() / RESAMPLING_FACTOR);
- parameters->SetVoxelSpacingInCentimeters(parameters->GetVoxelSpacingInCentimeters() * RESAMPLING_FACTOR);
- }
-
- generatedVolume->FinalizeVolume();
-
- return generatedVolume;
-}
-
-mitk::pa::PhantomTissueGenerator::PhantomTissueGenerator()
-{
-}
-
-mitk::pa::PhantomTissueGenerator::~PhantomTissueGenerator()
-{
-}
diff --git a/Modules/PhotoacousticsLib/src/Generator/mitkPASimulationBatchGenerator.cpp b/Modules/PhotoacousticsLib/src/Generator/mitkPASimulationBatchGenerator.cpp
deleted file mode 100644
index 973fb6730b..0000000000
--- a/Modules/PhotoacousticsLib/src/Generator/mitkPASimulationBatchGenerator.cpp
+++ /dev/null
@@ -1,87 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPASimulationBatchGenerator.h"
-#include <mitkIOUtil.h>
-
-#include <iomanip>
-
-#ifdef _WIN32
-#include <direct.h>
-#else
-#include <sys/types.h>
-#include <sys/stat.h>
-#endif
-
-mitk::pa::SimulationBatchGenerator::SimulationBatchGenerator()
-{
-}
-
-mitk::pa::SimulationBatchGenerator::~SimulationBatchGenerator()
-{
-}
-
-std::string mitk::pa::SimulationBatchGenerator::GetVolumeNumber(
- SimulationBatchGeneratorParameters::Pointer parameters)
-{
- std::string volumeNumber = std::to_string(parameters->GetVolumeIndex());
- volumeNumber = std::string((3 - volumeNumber.length()), '0') + volumeNumber;
- return volumeNumber;
-}
-
-std::string mitk::pa::SimulationBatchGenerator::GetOutputFolderName(
- SimulationBatchGeneratorParameters::Pointer parameters)
-{
- return (parameters->GetTissueName() + GetVolumeNumber(parameters));
-}
-
-std::string mitk::pa::SimulationBatchGenerator::CreateBatchSimulationString(
- SimulationBatchGeneratorParameters::Pointer parameters)
-{
- std::string outputFolderName = GetOutputFolderName(parameters);
- std::string savePath = outputFolderName + ".nrrd";
- std::stringstream batchstring;
- for (double d = parameters->GetYOffsetLowerThresholdInCentimeters();
- d <= parameters->GetYOffsetUpperThresholdInCentimeters() + 1e-5;
- d += parameters->GetYOffsetStepInCentimeters())
- {
- batchstring << parameters->GetBinaryPath() << " -p PROBE_DESIGN.xml -i " << savePath << " -o " << outputFolderName << "/"
- << parameters->GetTissueName() << GetVolumeNumber(parameters) << "_yo" << round(d * 100) / 100 << ".nrrd" << " -yo " << round(d * 100) / 100 << " -n "
- << parameters->GetNumberOfPhotons() << "\n";
- }
- return batchstring.str();
-}
-
-void mitk::pa::SimulationBatchGenerator::WriteBatchFileAndSaveTissueVolume(
- SimulationBatchGeneratorParameters::Pointer parameters,
- mitk::Image::Pointer tissueVolume)
-{
- std::string outputFolderName = parameters->GetNrrdFilePath() + GetOutputFolderName(parameters);
- std::string savePath = outputFolderName + ".nrrd";
- mitk::IOUtil::Save(tissueVolume, savePath);
-
- std::string filenameAllSimulation = "simulate_all";
-#ifdef _WIN32
- mkdir(outputFolderName.c_str());
- filenameAllSimulation += ".bat";
-#else
- mkdir(outputFolderName.c_str(), S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH);
- filenameAllSimulation += ".sh";
-#endif
-
- std::ofstream fileAllSimulation(parameters->GetNrrdFilePath() + "/" + filenameAllSimulation, std::ios_base::app);
- if (fileAllSimulation.is_open())
- {
- fileAllSimulation << CreateBatchSimulationString(parameters);
- fileAllSimulation.close();
- }
-}
diff --git a/Modules/PhotoacousticsLib/src/Generator/mitkPASimulationBatchGeneratorParameters.cpp b/Modules/PhotoacousticsLib/src/Generator/mitkPASimulationBatchGeneratorParameters.cpp
deleted file mode 100644
index 20f78d606f..0000000000
--- a/Modules/PhotoacousticsLib/src/Generator/mitkPASimulationBatchGeneratorParameters.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPASimulationBatchGeneratorParameters.h"
-
-mitk::pa::SimulationBatchGeneratorParameters::SimulationBatchGeneratorParameters()
-{
- m_BinaryPath = "";
- m_NrrdFilePath = "";
- m_NumberOfPhotons = 0;
- m_TissueName = "";
- m_VolumeIndex = 0;
- m_YOffsetLowerThresholdInCentimeters = 0;
- m_YOffsetUpperThresholdInCentimeters = 0;
- m_YOffsetStepInCentimeters = 0;
-}
-
-mitk::pa::SimulationBatchGeneratorParameters::~SimulationBatchGeneratorParameters()
-{
-}
diff --git a/Modules/PhotoacousticsLib/src/Generator/mitkPASlicedVolumeGenerator.cpp b/Modules/PhotoacousticsLib/src/Generator/mitkPASlicedVolumeGenerator.cpp
deleted file mode 100644
index dfa4c659b8..0000000000
--- a/Modules/PhotoacousticsLib/src/Generator/mitkPASlicedVolumeGenerator.cpp
+++ /dev/null
@@ -1,114 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPASlicedVolumeGenerator.h"
-#include <mitkException.h>
-
-mitk::pa::SlicedVolumeGenerator::SlicedVolumeGenerator(int centralYSlice, bool precorrect,
- Volume::Pointer precorrectionVolume, bool inverse)
-{
- m_CentralYSlice = centralYSlice;
- m_Precorrect = precorrect;
- m_Inverse = inverse;
- m_PrecorrectionVolume = nullptr;
-
- if (m_Precorrect)
- {
- m_PrecorrectionVolume = precorrectionVolume;
- }
-}
-
-mitk::pa::SlicedVolumeGenerator::~SlicedVolumeGenerator()
-{
- m_CentralYSlice = -1;
- m_Precorrect = false;
- m_PrecorrectionVolume = nullptr;
-}
-
-mitk::pa::Volume::Pointer mitk::pa::SlicedVolumeGenerator::GetSlicedFluenceImageFromComposedVolume(
- ComposedVolume::Pointer composedVolume)
-{
- int fluenceComponents = composedVolume->GetNumberOfFluenceComponents();
-
- int xDim = composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetXDim();
- int zDim = composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetZDim();
-
- auto* imageArray = new double[xDim*zDim*fluenceComponents];
-
- for (int fluenceComponentIdx = 0; fluenceComponentIdx < fluenceComponents; fluenceComponentIdx++)
- for (int z = 0; z < zDim; z++)
- for (int x = 0; x < xDim; x++)
- {
- int index = z * xDim * fluenceComponents + x * fluenceComponents + fluenceComponentIdx;
- imageArray[index] = composedVolume->GetFluenceValue(fluenceComponentIdx, x, m_CentralYSlice, z);
-
- if (m_Precorrect)
- {
- imageArray[index] = imageArray[index] / m_PrecorrectionVolume->GetData(x, m_CentralYSlice, z);
- }
-
- if (m_Inverse)
- {
- if (std::abs(imageArray[index] - 0) >= mitk::eps)
- imageArray[index] = 1 / imageArray[index];
- else
- imageArray[index] = INFINITY;
- }
- }
-
- return mitk::pa::Volume::New(imageArray, xDim, fluenceComponents, zDim, composedVolume->GetGroundTruthVolume()->GetSpacing());
-}
-
-mitk::pa::Volume::Pointer mitk::pa::SlicedVolumeGenerator::GetSlicedSignalImageFromComposedVolume(
- ComposedVolume::Pointer composedVolume)
-{
- int fluenceComponents = composedVolume->GetNumberOfFluenceComponents();
-
- int xDim = composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetXDim();
- int zDim = composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetZDim();
-
- auto* imageArray = new double[xDim*zDim*fluenceComponents];
-
- for (int fluenceComponentIdx = 0; fluenceComponentIdx < fluenceComponents; fluenceComponentIdx++)
- for (int z = 0; z < zDim; z++)
- for (int x = 0; x < xDim; x++)
- {
- int y = m_CentralYSlice + composedVolume->GetYOffsetForFluenceComponentInPixels(fluenceComponentIdx);
- imageArray[z * xDim * fluenceComponents + x * fluenceComponents + fluenceComponentIdx] =
- composedVolume->GetFluenceValue(fluenceComponentIdx, x, m_CentralYSlice, z)
- * composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetData(x, y, z);
- }
-
- return mitk::pa::Volume::New(imageArray, xDim, fluenceComponents, zDim, composedVolume->GetGroundTruthVolume()->GetSpacing());
-}
-
-mitk::pa::Volume::Pointer mitk::pa::SlicedVolumeGenerator::GetSlicedGroundTruthImageFromComposedVolume(
- ComposedVolume::Pointer composedVolume)
-{
- int fluenceComponents = composedVolume->GetNumberOfFluenceComponents();
-
- int xDim = composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetXDim();
- int zDim = composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetZDim();
-
- auto* imageArray = new double[xDim*zDim*fluenceComponents];
-
- for (int fluenceComponentIdx = 0; fluenceComponentIdx < fluenceComponents; fluenceComponentIdx++)
- for (int z = 0; z < zDim; z++)
- for (int x = 0; x < xDim; x++)
- {
- int y = m_CentralYSlice + composedVolume->GetYOffsetForFluenceComponentInPixels(fluenceComponentIdx);
- imageArray[z * xDim * fluenceComponents + x * fluenceComponents + fluenceComponentIdx] =
- composedVolume->GetGroundTruthVolume()->GetAbsorptionVolume()->GetData(x, y, z);
- }
-
- return mitk::pa::Volume::New(imageArray, xDim, fluenceComponents, zDim, composedVolume->GetGroundTruthVolume()->GetSpacing());
-}
diff --git a/Modules/PhotoacousticsLib/src/Generator/mitkPATissueGenerator.cpp b/Modules/PhotoacousticsLib/src/Generator/mitkPATissueGenerator.cpp
deleted file mode 100644
index 8bca26a705..0000000000
--- a/Modules/PhotoacousticsLib/src/Generator/mitkPATissueGenerator.cpp
+++ /dev/null
@@ -1,195 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPATissueGenerator.h"
-#include "mitkPAVector.h"
-#include "mitkPAVolumeManipulator.h"
-
-mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::InSilicoTissueGenerator::GenerateInSilicoData(
- TissueGeneratorParameters::Pointer parameters)
-{
- MITK_DEBUG << "Initializing Empty Volume";
-
- const double RESAMPLING_FACTOR = 2;
-
- if (parameters->GetDoPartialVolume())
- {
- parameters->SetXDim(parameters->GetXDim() * RESAMPLING_FACTOR);
- parameters->SetYDim(parameters->GetYDim() * RESAMPLING_FACTOR);
- parameters->SetZDim(parameters->GetZDim() * RESAMPLING_FACTOR);
- parameters->SetVesselBifurcationFrequency(parameters->GetVesselBifurcationFrequency() * RESAMPLING_FACTOR);
- parameters->SetVoxelSpacingInCentimeters(parameters->GetVoxelSpacingInCentimeters() / RESAMPLING_FACTOR);
- }
-
- std::mt19937 randomNumberGenerator;
- std::random_device randomDevice;
- if (parameters->GetUseRngSeed())
- {
- randomNumberGenerator.seed(parameters->GetRngSeed());
- }
- else
- {
- if (randomDevice.entropy() > 0.1)
- {
- randomNumberGenerator.seed(randomDevice());
- }
- else
- {
- randomNumberGenerator.seed(std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::now().time_since_epoch()).count());
- }
- }
-
- auto generatedVolume = mitk::pa::InSilicoTissueVolume::New(parameters, &randomNumberGenerator);
-
- double DIRECTION_VECTOR_INITIAL_VARIANCE = 0.2;
-
- if(parameters->GetForceVesselsMoveAlongYDirection())
- DIRECTION_VECTOR_INITIAL_VARIANCE = 0;
-
- std::uniform_int_distribution<int> randomNumVesselDistribution(
- parameters->GetMinNumberOfVessels(), parameters->GetMaxNumberOfVessels());
- std::uniform_real_distribution<double> randomBendingDistribution(
- parameters->GetMinVesselBending(), parameters->GetMaxVesselBending());
- std::uniform_real_distribution<double> randomAbsorptionDistribution(
- parameters->GetMinVesselAbsorption(), parameters->GetMaxVesselAbsorption());
- std::uniform_real_distribution<double> randomRadiusDistribution(
- parameters->GetMinVesselRadiusInMillimeters(), parameters->GetMaxVesselRadiusInMillimeters());
- std::uniform_real_distribution<double> randomScatteringDistribution(
- parameters->GetMinVesselScattering(), parameters->GetMaxVesselScattering());
- std::uniform_real_distribution<double> randomAnisotropyDistribution(
- parameters->GetMinVesselAnisotropy(), parameters->GetMaxVesselAnisotropy());
- std::uniform_int_distribution<int> borderTypeDistribution(0, 3);
-
- int numberOfBloodVessels = randomNumVesselDistribution(randomNumberGenerator);
-
- generatedVolume->AddIntProperty("numberOfVessels", numberOfBloodVessels);
- generatedVolume->AddIntProperty("bifurcationFrequency", parameters->GetVesselBifurcationFrequency());
-
- MITK_INFO << "Simulating " << numberOfBloodVessels << " vessel structures";
- for (int vesselNumber = 0; vesselNumber < numberOfBloodVessels; vesselNumber++)
- {
- Vector::Pointer initialPosition = Vector::New();
- Vector::Pointer initialDirection = Vector::New();
-
- double initialRadius = randomRadiusDistribution(randomNumberGenerator) / parameters->GetVoxelSpacingInCentimeters() / 10;
- std::stringstream radiusString;
- radiusString << "vessel_" << vesselNumber + 1 << "_radius";
- generatedVolume->AddDoubleProperty(radiusString.str(), initialRadius);
-
- double absorptionCoefficient = randomAbsorptionDistribution(randomNumberGenerator);
- std::stringstream absorptionString;
- absorptionString << "vessel_" << vesselNumber + 1 << "_absorption";
- generatedVolume->AddDoubleProperty(absorptionString.str(), absorptionCoefficient);
-
- double bendingFactor = randomBendingDistribution(randomNumberGenerator);
- std::stringstream bendingString;
- bendingString << "vessel_" << vesselNumber + 1 << "_bendingFactor";
- generatedVolume->AddDoubleProperty(bendingString.str(), bendingFactor);
-
- double vesselScattering = randomScatteringDistribution(randomNumberGenerator);
- std::stringstream scatteringString;
- scatteringString << "vessel_" << vesselNumber + 1 << "_scattering";
- generatedVolume->AddDoubleProperty(scatteringString.str(), vesselScattering);
-
- double vesselAnisotropy = randomAnisotropyDistribution(randomNumberGenerator);
- std::stringstream anisotropyString;
- anisotropyString << "vessel_" << vesselNumber + 1 << "_anisotropy";
- generatedVolume->AddDoubleProperty(anisotropyString.str(), vesselAnisotropy);
-
- /*The vessel tree shall start at one of the 4 sides of the volume.
- * The vessels will always be completely contained in the volume
- * when starting to meander.
- * They will meander in a direction perpendicular to the
- * plane they started from (within the limits of the
- * DIRECTION_VECTOR_INITIAL_VARIANCE)
- */
- int borderType = borderTypeDistribution(randomNumberGenerator);
-
- if(parameters->GetForceVesselsMoveAlongYDirection())
- borderType = 2;
-
- switch (borderType)
- {
- case 0:
- initialPosition->Randomize(0, 0, initialRadius, parameters->GetYDim() - initialRadius,
- parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(),
- parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator);
- initialDirection->Randomize(1, 2, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE,
- -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator);
- break;
- case 1:
- initialPosition->Randomize(parameters->GetXDim() - 1, parameters->GetXDim() - 1, initialRadius, parameters->GetYDim() - initialRadius,
- parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(),
- parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator);
- initialDirection->Randomize(-2, -1, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE,
- -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator);
- break;
- case 2:
- initialPosition->Randomize(initialRadius, parameters->GetXDim() - initialRadius, 0, 0,
- parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(),
- parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator);
- initialDirection->Randomize(-DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, 1, 2,
- -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator);
- break;
- case 3:
- initialPosition->Randomize(initialRadius, parameters->GetXDim() - initialRadius, parameters->GetYDim() - 1, parameters->GetYDim() - 1,
- parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(),
- parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator);
- initialDirection->Randomize(-DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, -2, -1,
- -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator);
- break;
- }
-
- initialDirection->Normalize();
- MITK_INFO << initialPosition->GetElement(0) << " | " << initialPosition->GetElement(1) << " | " << initialPosition->GetElement(2);
- MITK_INFO << initialDirection->GetElement(0) << " | " << initialDirection->GetElement(1) << " | " << initialDirection->GetElement(2);
-
- VesselProperties::Pointer vesselParams = VesselProperties::New();
- vesselParams->SetDirectionVector(initialDirection);
- vesselParams->SetPositionVector(initialPosition);
- vesselParams->SetRadiusInVoxel(initialRadius);
- vesselParams->SetAbsorptionCoefficient(absorptionCoefficient);
- vesselParams->SetScatteringCoefficient(vesselScattering);
- vesselParams->SetAnisotopyCoefficient(vesselAnisotropy);
- vesselParams->SetBifurcationFrequency(parameters->GetVesselBifurcationFrequency());
- vesselParams->SetDoPartialVolume(parameters->GetDoPartialVolume());
-
- VesselTree::Pointer vesselTree = VesselTree::New(vesselParams);
-
- while (!vesselTree->IsFinished())
- {
- vesselTree->Step(generatedVolume, parameters->GetCalculateNewVesselPositionCallback(), bendingFactor, &randomNumberGenerator);
- }
- }
-
- if (parameters->GetDoPartialVolume())
- {
- VolumeManipulator::RescaleImage(generatedVolume, (1.0 / RESAMPLING_FACTOR));
- parameters->SetXDim(parameters->GetXDim() / RESAMPLING_FACTOR);
- parameters->SetYDim(parameters->GetYDim() / RESAMPLING_FACTOR);
- parameters->SetZDim(parameters->GetZDim() / RESAMPLING_FACTOR);
- parameters->SetVesselBifurcationFrequency(parameters->GetVesselBifurcationFrequency() / RESAMPLING_FACTOR);
- parameters->SetVoxelSpacingInCentimeters(parameters->GetVoxelSpacingInCentimeters() * RESAMPLING_FACTOR);
- }
-
- generatedVolume->FinalizeVolume();
-
- return generatedVolume;
-}
-
-mitk::pa::InSilicoTissueGenerator::InSilicoTissueGenerator()
-{
-}
-
-mitk::pa::InSilicoTissueGenerator::~InSilicoTissueGenerator()
-{
-}
diff --git a/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp b/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp
deleted file mode 100644
index 3fe9583c7e..0000000000
--- a/Modules/PhotoacousticsLib/src/IO/mitkPAIOUtil.cpp
+++ /dev/null
@@ -1,252 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAIOUtil.h"
-
-#include "mitkIOUtil.h"
-#include "mitkImageReadAccessor.h"
-
-#include <string>
-#include <sstream>
-#include <vector>
-
-#include "mitkPAComposedVolume.h"
-#include "mitkPASlicedVolumeGenerator.h"
-#include "mitkPANoiseGenerator.h"
-#include "mitkPAVolumeManipulator.h"
-#include <mitkProperties.h>
-#include <itkDirectory.h>
-#include <itksys/SystemTools.hxx>
-
-static std::vector<int> splitString(const std::string &s, const char* delim) {
- std::vector<int> elems;
- std::stringstream ss(s);
- std::string item;
- while (std::getline(ss, item, *delim))
- {
- int numb;
- std::stringstream(item) >> numb;
- elems.push_back(numb);
- }
- return elems;
-}
-
-bool mitk::pa::IOUtil::DoesFileHaveEnding(std::string const &fullString, std::string const &ending) {
- if (fullString.length() == 0 || ending.length() == 0 || fullString.length() < ending.length())
- return false;
-
- return (0 == fullString.compare(fullString.length() - ending.length(), ending.length(), ending));
-}
-
-mitk::pa::IOUtil::IOUtil() {}
-
-mitk::pa::IOUtil::~IOUtil() {}
-
-mitk::pa::Volume::Pointer mitk::pa::IOUtil::LoadNrrd(std::string filename, double blur)
-{
- if (filename.empty() || filename == "")
- return nullptr;
-
- mitk::Image::Pointer inputImage = mitk::IOUtil::Load<mitk::Image>(filename);
-
- if (inputImage.IsNull())
- return nullptr;
-
- auto returnImage = Volume::New(inputImage);
-
- VolumeManipulator::GaussianBlur3D(returnImage, blur);
-
- return returnImage;
-}
-
-std::map<mitk::pa::IOUtil::Position, mitk::pa::Volume::Pointer>
-mitk::pa::IOUtil::LoadFluenceContributionMaps(std::string foldername, double blur, int* progress, bool doLog10)
-{
- std::map<IOUtil::Position, Volume::Pointer> resultMap;
-
- itk::Directory::Pointer directoryHandler = itk::Directory::New();
- directoryHandler->Load(foldername.c_str());
- for (unsigned int fileIndex = 0, numFiles = directoryHandler->GetNumberOfFiles(); fileIndex < numFiles; ++fileIndex)
- {
- std::string filename = std::string(directoryHandler->GetFile(fileIndex));
- if (itksys::SystemTools::FileIsDirectory(filename))
- continue;
-
- if (!DoesFileHaveEnding(filename, ".nrrd"))
- continue;
-
- size_t s = filename.find("_p");
- size_t e = filename.find("Fluence", s);
- std::string sub = filename.substr(s + 2, e - s - 2);
- std::vector<int> coords = splitString(sub, ",");
-
- if (coords.size() != 3)
- {
- MITK_ERROR << "Some of the data to read was corrupted or did not match the " <<
- "naming pattern *_pN,N,NFluence*.nrrd";
- mitkThrow() << "Some of the data to read was corrupted or did not match the" <<
- " naming pattern *_pN,N,NFluence*.nrrd";
- }
- else
- {
- MITK_DEBUG << "Extracted coords: " << coords[0] << "|" << coords[1] << "|" << coords[2] << " from string " << sub;
- Volume::Pointer nrrdFile = LoadNrrd(foldername + filename, blur);
- if (doLog10)
- VolumeManipulator::Log10Image(nrrdFile);
- resultMap[Position{ coords[0], coords[2] }] = nrrdFile;
- *progress = *progress + 1;
- }
- }
-
- return resultMap;
-}
-
-int mitk::pa::IOUtil::GetNumberOfNrrdFilesInDirectory(std::string directory)
-{
- return GetListOfAllNrrdFilesInDirectory(directory).size();
-}
-
-std::vector<std::string> mitk::pa::IOUtil::GetListOfAllNrrdFilesInDirectory(std::string directory, bool keepFileFormat)
-{
- std::vector<std::string> filenames;
- itk::Directory::Pointer directoryHandler = itk::Directory::New();
- directoryHandler->Load(directory.c_str());
- for (unsigned int fileIndex = 0, numFiles = directoryHandler->GetNumberOfFiles(); fileIndex < numFiles; ++fileIndex)
- {
- std::string filename = std::string(directoryHandler->GetFile(fileIndex));
- if (itksys::SystemTools::FileIsDirectory(filename))
- continue;
-
- if (!DoesFileHaveEnding(filename, ".nrrd"))
- continue;
-
- if (keepFileFormat)
- {
- filenames.push_back(filename);
- }
- else
- {
- filenames.push_back(filename.substr(0, filename.size() - 5));
- }
- }
-
- return filenames;
-}
-
-std::vector<std::string> mitk::pa::IOUtil::GetAllChildfoldersFromFolder(std::string folderPath)
-{
- std::vector<std::string> returnVector;
-
- itksys::Directory directoryHandler;
- directoryHandler.Load(folderPath.c_str());
- for (unsigned int fileIndex = 0, numFiles = directoryHandler.GetNumberOfFiles(); fileIndex < numFiles; ++fileIndex)
- {
- std::string foldername = std::string(directoryHandler.GetFile(fileIndex));
- std::string filename = folderPath + "/" + foldername;
- if (itksys::SystemTools::FileIsDirectory(filename))
- {
- if (foldername != std::string(".") && foldername != std::string(".."))
- {
- MITK_INFO << filename;
- returnVector.push_back(filename);
- }
- continue;
- }
-
- //If there is a nrrd file in the directory we assume that a bottom level directory was chosen.
- if (DoesFileHaveEnding(filename, ".nrrd"))
- {
- returnVector.clear();
- returnVector.push_back(folderPath);
- return returnVector;
- }
- }
-
- return returnVector;
-}
-
-mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::IOUtil::LoadInSilicoTissueVolumeFromNrrdFile(std::string nrrdFile)
-{
- MITK_INFO << "Initializing ComposedVolume by nrrd...";
- auto inputImage = mitk::IOUtil::Load<mitk::Image>(nrrdFile);
-
- auto tissueParameters = TissueGeneratorParameters::New();
-
- unsigned int xDim = inputImage->GetDimensions()[1];
- unsigned int yDim = inputImage->GetDimensions()[0];
- unsigned int zDim = inputImage->GetDimensions()[2];
- tissueParameters->SetXDim(xDim);
- tissueParameters->SetYDim(yDim);
- tissueParameters->SetZDim(zDim);
-
- double xSpacing = inputImage->GetGeometry(0)->GetSpacing()[1];
- double ySpacing = inputImage->GetGeometry(0)->GetSpacing()[0];
- double zSpacing = inputImage->GetGeometry(0)->GetSpacing()[2];
-
- if ((xSpacing - ySpacing) > mitk::eps || (xSpacing - zSpacing) > mitk::eps || (ySpacing - zSpacing) > mitk::eps)
- {
- throw mitk::Exception("Cannot handle unequal spacing.");
- }
-
- tissueParameters->SetVoxelSpacingInCentimeters(xSpacing);
-
- mitk::PropertyList::Pointer propertyList = inputImage->GetPropertyList();
-
- mitk::ImageReadAccessor readAccess0(inputImage, inputImage->GetVolumeData(0));
- auto* m_AbsorptionArray = new double[xDim*yDim*zDim];
- memcpy(m_AbsorptionArray, readAccess0.GetData(), xDim*yDim*zDim * sizeof(double));
- auto absorptionVolume = Volume::New(m_AbsorptionArray, xDim, yDim, zDim, xSpacing);
-
- mitk::ImageReadAccessor readAccess1(inputImage, inputImage->GetVolumeData(1));
- auto* m_ScatteringArray = new double[xDim*yDim*zDim];
- memcpy(m_ScatteringArray, readAccess1.GetData(), xDim*yDim*zDim * sizeof(double));
- auto scatteringVolume = Volume::New(m_ScatteringArray, xDim, yDim, zDim, xSpacing);
-
- mitk::ImageReadAccessor readAccess2(inputImage, inputImage->GetVolumeData(2));
- auto* m_AnisotropyArray = new double[xDim*yDim*zDim];
- memcpy(m_AnisotropyArray, readAccess2.GetData(), xDim*yDim*zDim * sizeof(double));
- auto anisotropyVolume = Volume::New(m_AnisotropyArray, xDim, yDim, zDim, xSpacing);
-
- Volume::Pointer segmentationVolume;
-
- if (inputImage->GetDimension() == 4)
- {
- mitk::ImageReadAccessor readAccess3(inputImage, inputImage->GetVolumeData(3));
- auto* m_SegmentationArray = new double[xDim*yDim*zDim];
- memcpy(m_SegmentationArray, readAccess3.GetData(), xDim*yDim*zDim * sizeof(double));
- segmentationVolume = Volume::New(m_SegmentationArray, xDim, yDim, zDim, xSpacing);
- }
-
- return mitk::pa::InSilicoTissueVolume::New(absorptionVolume, scatteringVolume,
- anisotropyVolume, segmentationVolume, tissueParameters, propertyList);
-}
-
-mitk::pa::FluenceYOffsetPair::Pointer mitk::pa::IOUtil::LoadFluenceSimulation(std::string fluenceSimulation)
-{
- MITK_INFO << "Adding slice...";
-
- mitk::Image::Pointer inputImage = mitk::IOUtil::Load<mitk::Image>(fluenceSimulation);
-
- auto yOffsetProperty = inputImage->GetProperty("y-offset");
-
- if (yOffsetProperty.IsNull())
- mitkThrow() << "No \"y-offset\" property found in fluence file!";
-
- std::string yOff = yOffsetProperty->GetValueAsString();
- MITK_INFO << "Reading y Offset: " << yOff;
-#ifdef __linux__
- std::replace(yOff.begin(), yOff.end(), '.', ',');
-#endif // __linux__
- double yOffset = std::stod(yOff);
- MITK_INFO << "Converted offset " << yOffset;
- return FluenceYOffsetPair::New(Volume::New(inputImage), yOffset);
-}
diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp
deleted file mode 100644
index 0a83f8faad..0000000000
--- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPALinearSpectralUnmixingFilter.cpp
+++ /dev/null
@@ -1,80 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPALinearSpectralUnmixingFilter.h"
-
-// Testing algorithms
-#include <eigen3/Eigen/src/SVD/JacobiSVD.h>
-
-// ImageAccessor
-#include <mitkImageReadAccessor.h>
-#include <mitkImageWriteAccessor.h>
-
-mitk::pa::LinearSpectralUnmixingFilter::LinearSpectralUnmixingFilter()
-{
-}
-
-mitk::pa::LinearSpectralUnmixingFilter::~LinearSpectralUnmixingFilter()
-{
-}
-
-void mitk::pa::LinearSpectralUnmixingFilter::SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType inputAlgorithmName)
-{
- algorithmName = inputAlgorithmName;
-}
-
-Eigen::VectorXf mitk::pa::LinearSpectralUnmixingFilter::SpectralUnmixingAlgorithm(
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> endmemberMatrix, Eigen::VectorXf inputVector)
-{
- Eigen::VectorXf resultVector;
-
- if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR == algorithmName)
- resultVector = endmemberMatrix.householderQr().solve(inputVector);
-
- else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LDLT == algorithmName)
- {
- Eigen::LLT<Eigen::MatrixXf> lltOfA(endmemberMatrix);
- if (lltOfA.info() == Eigen::NumericalIssue)
- {
- mitkThrow() << "Possibly non semi-positive definitie endmembermatrix!";
- }
- else
- resultVector = endmemberMatrix.ldlt().solve(inputVector);
- }
-
- else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LLT == algorithmName)
- {
- Eigen::LLT<Eigen::MatrixXf> lltOfA(endmemberMatrix);
- if (lltOfA.info() == Eigen::NumericalIssue)
- {
- mitkThrow() << "Possibly non semi-positive definitie endmembermatrix!";
- }
- else
- resultVector = endmemberMatrix.llt().solve(inputVector);
- }
-
- else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::COLPIVHOUSEHOLDERQR == algorithmName)
- resultVector = endmemberMatrix.colPivHouseholderQr().solve(inputVector);
-
- else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD == algorithmName)
- resultVector = endmemberMatrix.jacobiSvd(Eigen::ComputeFullU | Eigen::ComputeFullV).solve(inputVector);
-
- else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU == algorithmName)
- resultVector = endmemberMatrix.fullPivLu().solve(inputVector);
-
- else if (mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVHOUSEHOLDERQR == algorithmName)
- resultVector = endmemberMatrix.fullPivHouseholderQr().solve(inputVector);
- else
- mitkThrow() << "404 VIGRA ALGORITHM NOT FOUND";
-
- return resultVector;
-}
diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp
deleted file mode 100644
index 71d9fc6e14..0000000000
--- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterBase.cpp
+++ /dev/null
@@ -1,235 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPASpectralUnmixingFilterBase.h"
-
-// Includes for AddEnmemberMatrix
-#include "mitkPAPropertyCalculator.h"
-#include <eigen3/Eigen/Dense>
-
-// ImageAccessor
-#include <mitkImageReadAccessor.h>
-#include <mitkImageWriteAccessor.h>
-
-mitk::pa::SpectralUnmixingFilterBase::SpectralUnmixingFilterBase()
-{
- m_PropertyCalculatorEigen = mitk::pa::PropertyCalculator::New();
-}
-
-mitk::pa::SpectralUnmixingFilterBase::~SpectralUnmixingFilterBase()
-{
-
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::AddOutputs(unsigned int outputs)
-{
- if (outputs == 0)
- mitkThrow() << "ADD OUTPUTS HAS TO BE LARGER THEN ZERO!";
- this->SetNumberOfIndexedOutputs(outputs);
- for (unsigned int i = 0; i<GetNumberOfIndexedOutputs(); i++)
- this->SetNthOutput(i, mitk::Image::New());
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::AddWavelength(int wavelength)
-{
- m_Wavelength.push_back(wavelength);
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::AddChromophore(mitk::pa::PropertyCalculator::ChromophoreType chromophore)
-{
- m_Chromophore.push_back(chromophore);
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::Verbose(bool verbose)
-{
- m_Verbose = verbose;
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::RelativeError(bool relativeError)
-{
- m_RelativeError = relativeError;
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::AddRelativeErrorSettings(int value)
-{
- m_RelativeErrorSettings.push_back(value);
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::GenerateData()
-{
- MITK_INFO(m_Verbose) << "GENERATING DATA..";
-
- mitk::Image::Pointer input = GetInput(0);
- CheckPreConditions(input);
-
- unsigned int xDim = input->GetDimensions()[0];
- unsigned int yDim = input->GetDimensions()[1];
- unsigned int numberOfInputImages = input->GetDimensions()[2];
-
- MITK_INFO(m_Verbose) << "x dimension: " << xDim;
- MITK_INFO(m_Verbose) << "y dimension: " << yDim;
- MITK_INFO(m_Verbose) << "z dimension: " << numberOfInputImages;
-
- // Copy input image into array
- mitk::ImageReadAccessor readAccess(input);
- const float* inputDataArray = ((const float*)readAccess.GetData());
-
- unsigned int sequenceSize = m_Wavelength.size();
- unsigned int totalNumberOfSequences = numberOfInputImages / sequenceSize;
- MITK_INFO(m_Verbose) << "TotalNumberOfSequences: " << totalNumberOfSequences;
-
- InitializeOutputs(totalNumberOfSequences);
-
- auto endmemberMatrix = CalculateEndmemberMatrix(m_Chromophore, m_Wavelength);
-
- // test to see pixel values @ txt file
- myfile.open("SimplexNormalisation.txt");
-
- unsigned int outputCounter = GetNumberOfIndexedOutputs();
- std::vector<float*> writteBufferVector;
- for (unsigned int i = 0; i < outputCounter; ++i)
- {
- auto output = GetOutput(i);
- mitk::ImageWriteAccessor writeOutput(output);
- float* writeBuffer = (float *)writeOutput.GetData();
- writteBufferVector.push_back(writeBuffer);
- }
-
- if (m_RelativeError == true)
- {
- // -1 because rel error is output[IndexedOutputs() - 1] and loop over chromophore outputs has to end at [IndexedOutputs() - 2]
- outputCounter -= 1;
- }
-
- for (unsigned int sequenceCounter = 0; sequenceCounter < totalNumberOfSequences; ++sequenceCounter)
- {
- MITK_INFO(m_Verbose) << "SequenceCounter: " << sequenceCounter;
- //loop over every pixel in XY-plane
- for (unsigned int x = 0; x < xDim; x++)
- {
- for (unsigned int y = 0; y < yDim; y++)
- {
- Eigen::VectorXf inputVector(sequenceSize);
- for (unsigned int z = 0; z < sequenceSize; z++)
- {
- /**
- * 'sequenceCounter*sequenceSize' has to be added to 'z' to ensure that one accesses the
- * correct pixel, because the inputDataArray contains the information of all sequences and
- * not just the one of the current sequence.
- */
- unsigned int pixelNumber = (xDim*yDim*(z+sequenceCounter*sequenceSize)) + x * yDim + y;
- auto pixel = inputDataArray[pixelNumber];
-
- inputVector[z] = pixel;
- }
- Eigen::VectorXf resultVector = SpectralUnmixingAlgorithm(endmemberMatrix, inputVector);
-
- if (m_RelativeError == true)
- {
- float relativeError = CalculateRelativeError(endmemberMatrix, inputVector, resultVector);
- writteBufferVector[outputCounter][(xDim*yDim * sequenceCounter) + x * yDim + y] = relativeError;
- }
-
- for (unsigned int outputIdx = 0; outputIdx < outputCounter; ++outputIdx)
- {
- writteBufferVector[outputIdx][(xDim*yDim * sequenceCounter) + x * yDim + y] = resultVector[outputIdx];
- }
- }
- }
- }
- MITK_INFO(m_Verbose) << "GENERATING DATA...[DONE]";
- myfile.close();
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::CheckPreConditions(mitk::Image::Pointer input)
-{
- MITK_INFO(m_Verbose) << "CHECK PRECONDITIONS ...";
-
- if (m_Chromophore.size() == 0 || m_Wavelength.size() == 0)
- mitkThrow() << "NO WAVELENGHTS/CHROMOPHORES SELECTED!";
-
- if (m_Wavelength.size() < input->GetDimensions()[2])
- MITK_WARN(m_Verbose) << "NUMBER OF WAVELENGTHS < NUMBER OF INPUT IMAGES";
-
- if (m_Chromophore.size() > m_Wavelength.size())
- mitkThrow() << "ADD MORE WAVELENGTHS OR REMOVE ENDMEMBERS!";
-
- if (input->GetPixelType() != mitk::MakeScalarPixelType<float>())
- mitkThrow() << "PIXELTYPE ERROR! FLOAT REQUIRED";
-
- if ((m_Chromophore.size()+ m_RelativeError )!= GetNumberOfIndexedOutputs() || input->GetDimensions()[2] < GetNumberOfIndexedOutputs())
- mitkThrow() << "INDEX ERROR! NUMBER OF OUTPUTS DOESN'T FIT TO OTHER SETTIGNS!";
-
- MITK_INFO(m_Verbose) << "...[DONE]";
-}
-
-void mitk::pa::SpectralUnmixingFilterBase::InitializeOutputs(unsigned int totalNumberOfSequences)
-{
- MITK_INFO(m_Verbose) << "Initialize Outputs ...";
-
- unsigned int numberOfInputs = GetNumberOfIndexedInputs();
- unsigned int numberOfOutputs = GetNumberOfIndexedOutputs();
- MITK_INFO(m_Verbose) << "Inputs: " << numberOfInputs << " Outputs: " << numberOfOutputs;
-
- mitk::PixelType pixelType = mitk::MakeScalarPixelType<float>();
- const int NUMBER_OF_SPATIAL_DIMENSIONS = 3;
- auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS];
- for (unsigned int dimIdx = 0; dimIdx < 2; dimIdx++)
- dimensions[dimIdx] = GetInput()->GetDimensions()[dimIdx];
- dimensions[2] = totalNumberOfSequences;
-
- for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++)
- GetOutput(outputIdx)->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions);
- MITK_INFO(m_Verbose) << "...[DONE]";
-}
-
-Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> mitk::pa::SpectralUnmixingFilterBase::CalculateEndmemberMatrix(
- std::vector<mitk::pa::PropertyCalculator::ChromophoreType> m_Chromophore, std::vector<int> m_Wavelength)
-{
- unsigned int numberOfChromophores = m_Chromophore.size(); //columns
- unsigned int numberOfWavelengths = m_Wavelength.size(); //rows
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> endmemberMatrixEigen(numberOfWavelengths, numberOfChromophores);
-
- for (unsigned int j = 0; j < numberOfChromophores; ++j)
- {
- for (unsigned int i = 0; i < numberOfWavelengths; ++i)
- endmemberMatrixEigen(i, j) = PropertyElement(m_Chromophore[j], m_Wavelength[i]);
- }
- MITK_INFO(m_Verbose) << "GENERATING ENMEMBERMATRIX [DONE]";
- return endmemberMatrixEigen;
-}
-
-float mitk::pa::SpectralUnmixingFilterBase::PropertyElement(mitk::pa::PropertyCalculator::ChromophoreType chromophore, int wavelength)
-{
- if (chromophore == mitk::pa::PropertyCalculator::ChromophoreType::ONEENDMEMBER)
- return 1;
- else
- {
- float value = m_PropertyCalculatorEigen->GetAbsorptionForWavelength(chromophore, wavelength);
- if (value == 0)
- mitkThrow() << "WAVELENGTH " << wavelength << "nm NOT SUPPORTED!";
- else
- return value;
- }
-}
-
-float mitk::pa::SpectralUnmixingFilterBase::CalculateRelativeError(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> endmemberMatrix,
- Eigen::VectorXf inputVector, Eigen::VectorXf resultVector)
-{
- float relativeError = (endmemberMatrix*resultVector - inputVector).norm() / inputVector.norm();
- for (int i = 0; i < 2; ++i)
- {
- if (resultVector[i] < m_RelativeErrorSettings[i])
- return 0;
- }
- return relativeError;
-}
diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterLagrange.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterLagrange.cpp
deleted file mode 100644
index bb17f63882..0000000000
--- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterLagrange.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPASpectralUnmixingFilterLagrange.h"
-
-// Includes for AddEnmemberMatrix
-#include "mitkPAPropertyCalculator.h"
-#include <eigen3/Eigen/Dense>
-
-
-mitk::pa::SpectralUnmixingFilterLagrange::SpectralUnmixingFilterLagrange()
-{
-
-}
-
-mitk::pa::SpectralUnmixingFilterLagrange::~SpectralUnmixingFilterLagrange()
-{
-
-}
diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterSimplex.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterSimplex.cpp
deleted file mode 100644
index ed9ef82ce6..0000000000
--- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterSimplex.cpp
+++ /dev/null
@@ -1,172 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkPASpectralUnmixingFilterSimplex.h>
-
-// Includes for AddEnmemberMatrix
-#include <eigen3/Eigen/Dense>
-
-#include <cmath>
-
-mitk::pa::SpectralUnmixingFilterSimplex::SpectralUnmixingFilterSimplex()
-{
-
-}
-
-mitk::pa::SpectralUnmixingFilterSimplex::~SpectralUnmixingFilterSimplex()
-{
-
-}
-
-Eigen::VectorXf mitk::pa::SpectralUnmixingFilterSimplex::SpectralUnmixingAlgorithm(
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> EndmemberMatrix, Eigen::VectorXf inputVector)
-{
- int numberOfChromophores = EndmemberMatrix.cols();
-
- Eigen::VectorXf resultVector(numberOfChromophores);
- Eigen::VectorXf normalizedInputVector(EndmemberMatrix.rows());
- normalizedInputVector = Normalization(EndmemberMatrix, inputVector);
- //normalizedInputVector = inputVector;
-
-
- float VolumeMax = simplexVolume(EndmemberMatrix);
- for (int i = 0; i < numberOfChromophores; ++i)
- {
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> A = GenerateA(EndmemberMatrix, normalizedInputVector, i);
- float Volume = simplexVolume(A);
-
-
- resultVector[i] = Volume / VolumeMax;
-
- myfile << "resultVector["<<i<<"]: " << resultVector[i] << "\n";
- myfile << "Volume: " << Volume << "\n";
- myfile << "VolumeMax: " << VolumeMax << "\n";
-
- }
- //
-
- return resultVector;
- // see code @ linearSUFilter
-}
-
-
-Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> mitk::pa::SpectralUnmixingFilterSimplex::GenerateA
-(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> EndmemberMatrix, Eigen::VectorXf inputVector, int i)
-{
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> A = EndmemberMatrix;
- int numberOfChromophores = EndmemberMatrix.cols();
-
- for (int j = 0; j < numberOfChromophores; ++j)
- {
- A(i, j) = inputVector(j);
- }
-
- return A;
-}
-
-Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> mitk::pa::SpectralUnmixingFilterSimplex::GenerateD2
-(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> A)
-{
- int numberOfChromophores = A.cols();
-
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> D2(numberOfChromophores, numberOfChromophores);
-
- for (int i = 0; i < numberOfChromophores; ++i)
- {
- for (int j = 0; j < numberOfChromophores; ++j)
- {
- Eigen::VectorXf x = A.col(i) - A.col(j);
- //MITK_INFO << "a_col_i: " <<A.col(i);
- //MITK_INFO << "a_col_j: " <<A.col(j);
- //MITK_INFO << "x: " <<x;
- Eigen::VectorXf y = x;
- float foo = x.dot(y);
- //MITK_INFO << "x*y: " << foo;
-
- D2(i, j) = foo;
- }
- }
-
- return D2;
-}
-
-float mitk::pa::SpectralUnmixingFilterSimplex::simplexVolume(Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> Matrix)
-{
- float Volume;
- int numberOfChromophores = Matrix.cols();
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> C(numberOfChromophores + 1, numberOfChromophores + 1);
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> D2 = GenerateD2(Matrix);
-
- for (int i = 0; i < numberOfChromophores; ++i)
- {
- for (int j = 0; j < numberOfChromophores; ++j)
- {
- C(i, j) = D2(i, j);
- }
- C(i, numberOfChromophores) = 1;
- for (int k = 0; k < numberOfChromophores; ++k)
- {
- C(numberOfChromophores, k) = 1;
- }
- C(numberOfChromophores, numberOfChromophores) = 0;
- }
-
- float detC = -C.determinant();// determinate von C
- float denominator = (factorial(numberOfChromophores - 1)) ^ 2 * 2 ^ (numberOfChromophores - 1)*(-1) ^ numberOfChromophores;
- Volume = std::sqrt(detC / denominator);
- //MITK_INFO << "detC: " << detC;
-
- //MITK_INFO << "denominator: " << denominator;
-
- //MITK_INFO << "Volume: " << Volume;
-
- return Volume;
-}
-
-int mitk::pa::SpectralUnmixingFilterSimplex::factorial(int n)
-{
- if (n == 1)
- return 1;
- else
- return n * factorial(n - 1);
-}
-
-Eigen::VectorXf mitk::pa::SpectralUnmixingFilterSimplex::Normalization(
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> EndmemberMatrix, Eigen::VectorXf inputVector)
-{
- int numberOfWavelengths = inputVector.rows();
- Eigen::VectorXf result(numberOfWavelengths);
- float NormalizationFactor = 1;
- float foo;
- float norm = 0;
-
- for (int i = 0; i < numberOfWavelengths; ++i)
- {
- foo = EndmemberMatrix(i, 0) - EndmemberMatrix(i, 1);
- if (std::abs(foo) > norm)
- norm = std::abs(foo);
- }
-
-//ofstream myfile;
-//myfile.open("SimplexNormalisation.txt");
- //NormalizationFactor = inputVector[0] * 2 / norm;
- myfile << "Normalizationfactor " << NormalizationFactor << "\n";
-
- for (int i = 0; i < numberOfWavelengths; ++i)
- {
-
- result[i]=(inputVector[i]/NormalizationFactor);
- }
-//myfile.close();
-
- return result;
-}
diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterVigra.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterVigra.cpp
deleted file mode 100644
index 878e331e06..0000000000
--- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingFilterVigra.cpp
+++ /dev/null
@@ -1,100 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPASpectralUnmixingFilterVigra.h"
-
-// ImageAccessor
-#include <mitkImageReadAccessor.h>
-#include <mitkImageWriteAccessor.h>
-
-//vigra
-#include <vigra/matrix.hxx>
-#include <vigra/regression.hxx>
-#include <vigra/quadprog.hxx>
-
-mitk::pa::SpectralUnmixingFilterVigra::SpectralUnmixingFilterVigra()
-{
-}
-
-mitk::pa::SpectralUnmixingFilterVigra::~SpectralUnmixingFilterVigra()
-{
-}
-
-void mitk::pa::SpectralUnmixingFilterVigra::SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType inputAlgorithmName)
-{
- algorithmName = inputAlgorithmName;
-}
-
-void mitk::pa::SpectralUnmixingFilterVigra::AddWeight(unsigned int weight)
-{
- double value = double(weight) / 100.0;
- weightsvec.push_back(value);
-}
-
-Eigen::VectorXf mitk::pa::SpectralUnmixingFilterVigra::SpectralUnmixingAlgorithm(
- Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic> endmemberMatrix, Eigen::VectorXf inputVector)
-{
- unsigned int numberOfWavelengths = endmemberMatrix.rows();
- unsigned int numberOfChromophores = endmemberMatrix.cols();
-
- // writes endmemberMatrix and inputVector into vigra::Matrix<double>
- std::vector<double> aData;
- std::vector<double> bData;
- for (unsigned int i = 0; i < numberOfWavelengths; ++i)
- {
- bData.push_back((double)inputVector(i));
- for (unsigned int j = 0; j < numberOfChromophores; ++j)
- aData.push_back((double)endmemberMatrix(i, j));
- }
- const double* aDat = aData.data();
- const double* bDat = bData.data();
-
- vigra::Matrix<double> A(vigra::Shape2(numberOfWavelengths, numberOfChromophores), aDat);
- vigra::Matrix<double> b(vigra::Shape2(numberOfWavelengths, 1), bDat);
- vigra::Matrix<double> x(vigra::Shape2(numberOfChromophores, 1));
-
- if (mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS == algorithmName)
- nonnegativeLeastSquares(A, b, x);
-
- else if (mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::GOLDFARB == algorithmName)
- {
- vigra::linalg::Matrix<double> eye(vigra::linalg::identityMatrix<double>(numberOfChromophores)),
- zeros(vigra::Shape2(numberOfChromophores, 1)),
- empty,
- U = vigra::linalg::transpose(A)*A,
- // v= -transpose(A)*b replaced by -v used in "quadraticProgramming"
- v = vigra::linalg::transpose(A)*b;
- x = 0;
- quadraticProgramming(U, -v, empty, empty, eye, zeros, x);
- }
-
- else if (mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED == algorithmName)
- {
- if (weightsvec.size() != numberOfWavelengths)
- mitkThrow() << "Number of weights and wavelengths doesn't match! OR Invalid weight!";
- const double* weightsdat = weightsvec.data();
- vigra::Matrix<double> weigths(vigra::Shape2(numberOfWavelengths, 1), weightsdat);
- vigra::linalg::weightedLeastSquares(A, b, weigths, x);
- }
-
- else if (mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS == algorithmName)
- linearSolve(A, b, x);
-
- else
- mitkThrow() << "404 VIGRA ALGORITHM NOT FOUND";
-
- Eigen::VectorXf resultVector(numberOfChromophores);
- for (unsigned int k = 0; k < numberOfChromophores; ++k)
- resultVector[k] = (float)x(k, 0);
-
- return resultVector;
-}
diff --git a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp b/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp
deleted file mode 100644
index f774b82f0a..0000000000
--- a/Modules/PhotoacousticsLib/src/SUFilter/mitkPASpectralUnmixingSO2.cpp
+++ /dev/null
@@ -1,185 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPASpectralUnmixingSO2.h"
-
-// ImageAccessor
-#include <mitkImageReadAccessor.h>
-#include <mitkImageWriteAccessor.h>
-
-
-mitk::pa::SpectralUnmixingSO2::SpectralUnmixingSO2()
-{
- this->SetNumberOfIndexedInputs(2);
- this->SetNumberOfIndexedOutputs(2);
- this->SetNthOutput(0, mitk::Image::New());
- this->SetNthOutput(1, mitk::Image::New());
-
-}
-
-mitk::pa::SpectralUnmixingSO2::~SpectralUnmixingSO2()
-{
-
-}
-
-void mitk::pa::SpectralUnmixingSO2::Verbose(bool verbose)
-{
- m_Verbose = verbose;
-}
-
-void mitk::pa::SpectralUnmixingSO2::GenerateData()
-{
- MITK_INFO(m_Verbose) << "GENERATING DATA..";
-
- // Get input image
- mitk::Image::Pointer inputHbO2 = GetInput(0);
- mitk::Image::Pointer inputHb = GetInput(1);
-
- CheckPreConditions(inputHbO2, inputHb);
-
- unsigned int xDim = inputHbO2->GetDimensions()[0];
- unsigned int yDim = inputHbO2->GetDimensions()[1];
- unsigned int zDim = inputHbO2->GetDimensions()[2];
-
- InitializeOutputs();
-
- mitk::ImageReadAccessor readAccessHbO2(inputHbO2);
- mitk::ImageReadAccessor readAccessHb(inputHb);
-
- const float* inputDataArrayHbO2 = ((const float*)readAccessHbO2.GetData());
- const float* inputDataArrayHb = ((const float*)readAccessHb.GetData());
-
- auto output = GetOutput(0);
- auto output1 = GetOutput(1);
-
- mitk::ImageWriteAccessor writeOutput(output);
- float* writeBuffer = (float *)writeOutput.GetData();
-
- mitk::ImageWriteAccessor writeOutput1(output1);
- float* writeBuffer1 = (float *)writeOutput1.GetData();
-
- for (unsigned int x = 0; x < xDim; x++)
- {
- for (unsigned int y = 0; y < yDim; y++)
- {
- for (unsigned int z = 0;z < zDim; z++)
- {
- unsigned int pixelNumber = (xDim*yDim * z) + x * yDim + y;
- float pixelHb = inputDataArrayHb[pixelNumber];
- float pixelHbO2 = inputDataArrayHbO2[pixelNumber];
- float resultSO2 = CalculateSO2(pixelHb, pixelHbO2);
- writeBuffer[(xDim*yDim * z) + x * yDim + y] = resultSO2;
- float resultTHb = CalculateTHb(pixelHb, pixelHbO2);
- writeBuffer1[(xDim*yDim * z) + x * yDim + y] = resultTHb;
- }
- }
- }
- MITK_INFO(m_Verbose) << "GENERATING DATA...[DONE]";
-}
-
-void mitk::pa::SpectralUnmixingSO2::CheckPreConditions(mitk::Image::Pointer inputHbO2, mitk::Image::Pointer inputHb)
-{
- unsigned int xDimHb = inputHb->GetDimensions()[0];
- unsigned int yDimHb = inputHb->GetDimensions()[1];
- unsigned int zDimHb = inputHb->GetDimensions()[2];
-
- unsigned int xDimHbO2 = inputHbO2->GetDimensions()[0];
- unsigned int yDimHbO2 = inputHbO2->GetDimensions()[1];
- unsigned int zDimHbO2 = inputHbO2->GetDimensions()[2];
-
- if (xDimHb != xDimHbO2 || yDimHb != yDimHbO2 || zDimHb != zDimHbO2)
- mitkThrow() << "DIMENTIONALITY ERROR!";
-
- if (inputHbO2->GetPixelType() != mitk::MakeScalarPixelType<float>())
- mitkThrow() << "PIXELTYPE ERROR! FLOAT REQUIRED";
-
- if (inputHb->GetPixelType() != mitk::MakeScalarPixelType<float>())
- mitkThrow() << "PIXELTYPE ERROR! FLOAT REQUIRED";
-
- MITK_INFO(m_Verbose) << "CHECK PRECONDITIONS ...[DONE]";
-}
-
-void mitk::pa::SpectralUnmixingSO2::InitializeOutputs()
-{
- // UNUSED unsigned int numberOfInputs = GetNumberOfIndexedInputs();
- unsigned int numberOfOutputs = GetNumberOfIndexedOutputs();
-
- mitk::PixelType pixelType = mitk::MakeScalarPixelType<float>();
- const int NUMBER_OF_SPATIAL_DIMENSIONS = 3;
- auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS];
- for(unsigned int dimIdx=0; dimIdx<NUMBER_OF_SPATIAL_DIMENSIONS; dimIdx++)
- {
- dimensions[dimIdx] = GetInput()->GetDimensions()[dimIdx];
- }
-
- for (unsigned int outputIdx = 0; outputIdx < numberOfOutputs; outputIdx++)
- {
- GetOutput(outputIdx)->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions);
- }
-}
-
-float mitk::pa::SpectralUnmixingSO2::CalculateSO2(float Hb, float HbO2)
-{
- float result = HbO2 / (Hb + HbO2);
-
- if (result != result)
- {
- MITK_WARN(m_Verbose) << "SO2 VALUE NAN! WILL BE SET TO ZERO!";
- return 0;
- }
- else
- {
- if (SO2ValueNotSiginificant(Hb, HbO2, result))
- {
- return 0;
- }
- else return result;
- }
-}
-
-float mitk::pa::SpectralUnmixingSO2::CalculateTHb(float Hb, float HbO2)
-{
- float result = (Hb + HbO2);
-
- if (result != result)
- {
- MITK_WARN(m_Verbose) << "SO2 VALUE NAN! WILL BE SET TO ZERO!";
- return 0;
- }
- else
- {
- return result;
- }
-}
-
-void mitk::pa::SpectralUnmixingSO2::AddSO2Settings(int value)
-{
- m_SO2Settings.push_back(value);
-}
-
-bool mitk::pa::SpectralUnmixingSO2::SO2ValueNotSiginificant(float Hb, float HbO2, float result)
-{
- std::vector<float> significant;
- significant.push_back(HbO2);
- significant.push_back(Hb);
- significant.push_back(HbO2 + Hb);
- significant.push_back(100*(result));
-
- for (unsigned int i = 0; i < m_SO2Settings.size(); ++i)
- {
- if (m_SO2Settings[i] != 0 && m_SO2Settings[i] > significant[i] && (std::abs(m_SO2Settings[i] - significant[i]) > 1e-7))
- {
- return true;
- }
- }
- return false;
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/ProbeDesign/mitkPALightSource.cpp b/Modules/PhotoacousticsLib/src/Utils/ProbeDesign/mitkPALightSource.cpp
deleted file mode 100644
index 5de81de1b1..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/ProbeDesign/mitkPALightSource.cpp
+++ /dev/null
@@ -1,410 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPALightSource.h"
-#include <cmath>
-
-mitk::pa::LightSource::LightSource() :
- m_IsValid(false)
-{
-}
-
-mitk::pa::LightSource::LightSource(TiXmlElement* element, bool verbose) :
- m_IsValid(true),
- m_Verbose(verbose)
-{
- ParseEnergy(element);
- ParsePhotonSpawnArea(element);
- ParsePhotonDirection(element);
-
- if (m_IsValid)
- {
- if (m_Verbose)
- std::cout << "Successfully created LightSource" << std::endl;
- }
- else
- {
- if (m_Verbose)
- std::cout << "Failed creating LightSource." << std::endl;
- }
-}
-
-mitk::pa::LightSource::~LightSource()
-{
-}
-
-mitk::pa::LightSource::TransformResult mitk::pa::LightSource::BoxMuellerTransform(double u1, double u2, double mu, double sigma)
-{
- TransformResult result;
- result.z0 = sqrt(-2.0 * log(u1)) * cos(TWO_PI * u2) * sigma + mu;
- result.z1 = sqrt(-2.0 * log(u1)) * sin(TWO_PI * u2) * sigma + mu;
- return result;
-}
-
-void mitk::pa::LightSource::ParsePhotonDirection(TiXmlElement* element)
-{
- TiXmlElement* direction = element->FirstChildElement(XML_TAG_PHOTON_DIRECTION);
- if (direction)
- {
- ParseAngle(direction, XML_TAG_X_ANGLE);
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_X_ANGLE << "\" field in xml. Setting to default (0, 0, UNIFORM)." << std::endl;
-
- m_AngleXMinimum = 0;
- m_AngleXMaximum = 0;
- m_AngleXMode = DistributionMode::UNIFORM;
- }
-
- direction = element->FirstChildElement(XML_TAG_PHOTON_DIRECTION);
- if (direction)
- {
- ParseAngle(direction, XML_TAG_Y_ANGLE);
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_Y_ANGLE << "\" field in xml. Setting to default (0, 0, UNIFORM)." << std::endl;
-
- m_AngleYMinimum = 0;
- m_AngleYMaximum = 0;
- m_AngleYMode = DistributionMode::UNIFORM;
- }
-}
-
-void mitk::pa::LightSource::ParseAngle(TiXmlElement* direction, std::string angle)
-{
- double minimum;
- double maximum;
- DistributionMode mode = DistributionMode::GAUSSIAN;
-
- if (m_Verbose)
- std::cout << "Parsing " << angle << std::endl;
- TiXmlElement* angleElement = direction->FirstChildElement(angle);
- if (angleElement)
- {
- TiXmlElement* angleMin = angleElement->FirstChildElement(XML_TAG_MINIMUM);
- if (angleMin)
- {
- std::string angleMinText = angleMin->GetText();
- minimum = std::stod(angleMinText);
- if (m_Verbose)
- std::cout << "Setting min=" << minimum << std::endl;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_MINIMUM << "\" tag in xml. Setting min=0" << std::endl;
- minimum = 0;
- }
-
- TiXmlElement* angleMax = angleElement->FirstChildElement(XML_TAG_MAXIMUM);
- if (angleMax)
- {
- std::string angleMaxText = angleMax->GetText();
- maximum = std::stod(angleMaxText);
- if (m_Verbose)
- std::cout << "Setting max=" << maximum << std::endl;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_MAXIMUM << "\" tag in xml. Setting max=0" << std::endl;
- maximum = 0;
- }
-
- TiXmlElement* angleMode = angleElement->FirstChildElement(XML_TAG_MODE);
- if (angleMode)
- {
- std::string angleModeText = angleMode->GetText();
- if (strcmp("UNIFORM", angleModeText.c_str()) == 0)
- {
- mode = DistributionMode::UNIFORM;
- if (m_Verbose)
- std::cout << "Setting mode=UNIFORM" << std::endl;
- }
- else if (strcmp("GAUSSIAN", angleModeText.c_str()) == 0)
- {
- mode = DistributionMode::GAUSSIAN;
- if (m_Verbose)
- std::cout << "Setting mode=GAUSSIAN" << std::endl;
- }
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_MODE << "\" tag in xml. Setting mode=UNIFORM" << std::endl;
- mode = DistributionMode::UNIFORM;
- }
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << angle << "\" field in xml. Setting to default (0, 0, UNIFORM)." << std::endl;
-
- maximum = 0;
- minimum = 0;
- mode = DistributionMode::UNIFORM;
- }
-
- if (strcmp(XML_TAG_X_ANGLE.c_str(), angle.c_str()) == 0)
- {
- m_AngleXMinimum = minimum;
- m_AngleXMaximum = maximum;
- m_AngleXMode = mode;
- }
- else if (strcmp(XML_TAG_Y_ANGLE.c_str(), angle.c_str()) == 0)
- {
- m_AngleYMinimum = minimum;
- m_AngleYMaximum = maximum;
- m_AngleYMode = mode;
- }
-}
-
-void mitk::pa::LightSource::ParseEnergy(TiXmlElement* element)
-{
- TiXmlElement* energy = element->FirstChildElement(XML_TAG_ENERGY);
- if (energy)
- {
- std::string energyText = energy->GetText();
- m_Energy = std::stod(energyText);
- if (m_Verbose)
- std::cout << "Setting energy=" << m_Energy;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_ENERGY << "\" field in xml. Setting Energy=1" << std::endl;
- m_Energy = 1.0;
- }
-}
-
-void mitk::pa::LightSource::ParsePhotonSpawnArea(TiXmlElement* element)
-{
- TiXmlElement* spawnArea = element->FirstChildElement("PhotonSpawnArea");
- if (spawnArea)
- {
- TiXmlElement* spawnType = spawnArea->FirstChildElement(XML_TAG_SPAWN_TYPE);
- if (spawnType)
- {
- std::string spawnTypeText = spawnType->GetText();
- if (strcmp(XML_TAG_SPAWN_TYPE_POINT.c_str(), spawnTypeText.c_str()) == 0)
- {
- m_SpawnType = SpawnType::POINT;
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_SPAWN_TYPE << " = " << XML_TAG_SPAWN_TYPE_POINT << std::endl;
- }
- else if (strcmp(XML_TAG_SPAWN_TYPE_RECTANGLE.c_str(), spawnTypeText.c_str()) == 0)
- {
- m_SpawnType = SpawnType::RECTANGLE;
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_SPAWN_TYPE << " = " << XML_TAG_SPAWN_TYPE_RECTANGLE << std::endl;
- }
- else if (strcmp(XML_TAG_SPAWN_TYPE_CIRCLE.c_str(), spawnTypeText.c_str()) == 0)
- {
- m_SpawnType = SpawnType::CIRCLE;
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_SPAWN_TYPE << " = " << XML_TAG_SPAWN_TYPE_CIRCLE << std::endl;
- }
- else
- {
- std::cerr << "The provided SpawnType (" << spawnTypeText << ") did not match any available spawn type. Light source is not valid." << std::endl;
- m_IsValid = false;
- }
- }
- else
- {
- std::cerr << "The \"" << XML_TAG_SPAWN_TYPE << "\" element was not provided for this light source. Light source is not valid." << std::endl;
- m_IsValid = false;
- }
-
- TiXmlElement* xLocation = spawnArea->FirstChildElement(XML_TAG_X);
- if (xLocation)
- {
- std::string xLocationText = xLocation->GetText();
- m_SpawnLocationX = std::stod(xLocationText);
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_X << "=" << m_SpawnLocationX;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_X << "\" field in xml. Setting " << XML_TAG_X << "=0" << std::endl;
- m_SpawnLocationX = 0;
- }
-
- TiXmlElement* yLocation = spawnArea->FirstChildElement(XML_TAG_Y);
- if (yLocation)
- {
- std::string yLocationText = yLocation->GetText();
- m_SpawnLocationY = std::stod(yLocationText);
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_Y << "=" << m_SpawnLocationY;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_Y << "\" field in xml. Setting " << XML_TAG_Y << "=0" << std::endl;
- m_SpawnLocationY = 0;
- }
-
- TiXmlElement* zLocation = spawnArea->FirstChildElement(XML_TAG_Z);
- if (zLocation)
- {
- std::string zLocationText = zLocation->GetText();
- m_SpawnLocationZ = std::stod(zLocationText);
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_Z << "=" << m_SpawnLocationZ;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_Z << "\" field in xml. Setting " << XML_TAG_Z << "=0.1" << std::endl;
- m_SpawnLocationZ = 0.1;
- }
-
- TiXmlElement* rLocation = spawnArea->FirstChildElement(XML_TAG_R);
- if (rLocation)
- {
- std::string rLocationText = rLocation->GetText();
- m_SpawnLocationRadius = std::stod(rLocationText);
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_R << "=" << m_SpawnLocationRadius;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_R << "\" field in xml. Setting " << XML_TAG_R << "=0" << std::endl;
- m_SpawnLocationRadius = 0;
- }
-
- TiXmlElement* xLength = spawnArea->FirstChildElement(XML_TAG_X_LENGTH);
- if (xLength)
- {
- std::string xLengthText = xLength->GetText();
- m_SpawnLocationXLength = std::stod(xLengthText);
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_X_LENGTH << "=" << m_SpawnLocationXLength << std::endl;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_X_LENGTH << "\" field in xml. Setting " << XML_TAG_X_LENGTH << "=0" << std::endl;
- m_SpawnLocationXLength = 0;
- }
-
- TiXmlElement* yLength = spawnArea->FirstChildElement(XML_TAG_Y_LENGTH);
- if (yLength)
- {
- std::string yLengthText = yLength->GetText();
- m_SpawnLocationYLength = std::stod(yLengthText);
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_Y_LENGTH << "=" << m_SpawnLocationYLength << std::endl;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_Y_LENGTH << "\" field in xml. Setting " << XML_TAG_Y_LENGTH << "=0" << std::endl;
- m_SpawnLocationYLength = 0;
- }
-
- TiXmlElement* zLength = spawnArea->FirstChildElement(XML_TAG_Z_LENGTH);
- if (zLength)
- {
- std::string zLengthText = zLength->GetText();
- m_SpawnLocationZLength = std::stod(zLengthText);
- if (m_Verbose)
- std::cout << "Setting " << XML_TAG_Z_LENGTH << "=" << m_SpawnLocationZLength << std::endl;
- }
- else
- {
- if (m_Verbose)
- std::cerr << "No \"" << XML_TAG_Z_LENGTH << "\" field in xml. Setting " << XML_TAG_Z_LENGTH << "=0" << std::endl;
- m_SpawnLocationZLength = 0;
- }
- }
- else
- m_IsValid = false;
-}
-
-mitk::pa::LightSource::PhotonInformation mitk::pa::LightSource::GetNextPhoton(double rnd1, double rnd2, double rnd3,
- double rnd4, double rnd5, double gau1, double gau2)
-{
- PhotonInformation returnValue;
-
- switch (m_SpawnType)
- {
- case POINT:
- returnValue.xPosition = m_SpawnLocationX;
- returnValue.yPosition = m_SpawnLocationY;
- returnValue.zPosition = m_SpawnLocationZ;
- break;
- case RECTANGLE:
- returnValue.xPosition = m_SpawnLocationX + rnd3 * m_SpawnLocationXLength;
- returnValue.yPosition = m_SpawnLocationY + rnd4 * m_SpawnLocationYLength;
- returnValue.zPosition = m_SpawnLocationZ + rnd5 * m_SpawnLocationZLength;
- break;
- case CIRCLE:
- double radius = rnd3 * m_SpawnLocationRadius;
- double angle = rnd4 * TWO_PI;
-
- returnValue.xPosition = m_SpawnLocationX + radius * cos(angle);
- returnValue.yPosition = m_SpawnLocationY + radius * sin(angle);
- returnValue.zPosition = m_SpawnLocationZ;
- break;
- }
-
- switch (m_AngleXMode)
- {
- case UNIFORM:
- returnValue.xAngle = rnd1 * (m_AngleXMaximum - m_AngleXMinimum) + m_AngleXMinimum;
- break;
- case GAUSSIAN:
- TransformResult trans = BoxMuellerTransform(gau1, gau2, (m_AngleXMaximum - m_AngleXMinimum) / 2 + m_AngleXMinimum, (m_AngleXMaximum - m_AngleXMinimum) / 2.355);
- returnValue.xAngle = trans.z0;
- break;
- }
-
- switch (m_AngleYMode)
- {
- case UNIFORM:
- returnValue.yAngle = rnd2 * (m_AngleYMaximum - m_AngleYMinimum) + m_AngleYMinimum;
- break;
- case GAUSSIAN:
- TransformResult trans = BoxMuellerTransform(gau1, gau2, (m_AngleYMaximum - m_AngleYMinimum) / 2 + m_AngleYMinimum, (m_AngleYMaximum - m_AngleYMinimum) / 2.355);
- returnValue.yAngle = trans.z1;
- break;
- }
-
- if ((returnValue.xAngle*returnValue.xAngle + returnValue.yAngle*returnValue.yAngle) > 1)
- {
- double unify = sqrt(returnValue.xAngle*returnValue.xAngle + returnValue.yAngle*returnValue.yAngle)*1.001;
- returnValue.xAngle = returnValue.xAngle / unify;
- returnValue.yAngle = returnValue.yAngle / unify;
- }
-
- returnValue.zAngle = sqrt(1 - returnValue.xAngle*returnValue.xAngle - returnValue.yAngle*returnValue.yAngle);
-
- if (m_Verbose)
- std::cout << "Created a new photon at (" << returnValue.xPosition << "|" << returnValue.yPosition << "|" <<
- returnValue.zPosition << ") with angle (" << returnValue.xAngle << "|" << returnValue.yAngle << "|" <<
- returnValue.zAngle << ")" << std::endl;
-
- return returnValue;
-}
-
-bool mitk::pa::LightSource::IsValid()
-{
- return m_IsValid;
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/ProbeDesign/mitkPAProbe.cpp b/Modules/PhotoacousticsLib/src/Utils/ProbeDesign/mitkPAProbe.cpp
deleted file mode 100644
index 3293dbdce5..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/ProbeDesign/mitkPAProbe.cpp
+++ /dev/null
@@ -1,129 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAProbe.h"
-
-mitk::pa::Probe::Probe(std::string file, bool verbose) :
- m_TotalEnergy(0),
- m_Verbose(verbose)
-{
- TiXmlDocument xmlDoc(file);
- bool success = xmlDoc.LoadFile(TIXML_ENCODING_UTF8);
- if (m_Verbose)
- {
- std::cout << "reading of document was " << (success ? "" : "not ") << "successful" << std::endl;
- std::cout << "Content of the Xml file:" << std::endl;
- xmlDoc.Print();
- }
- if (success)
- {
- InitProbe(xmlDoc);
- }
- else
- {
- if (m_Verbose)
- {
- std::cerr << "Could not load xml file" << std::endl;
- }
- }
-}
-
-mitk::pa::Probe::Probe(const char* fileStream, bool verbose) :
- m_TotalEnergy(0),
- m_Verbose(verbose)
-{
- TiXmlDocument xmlDoc;
- const char* success = xmlDoc.Parse(fileStream, nullptr, TIXML_ENCODING_UTF8);
- if (m_Verbose)
- {
- std::cout << "reading document was " << (success == nullptr ? "" : "not ") << "successful (" << (success == nullptr ? "NULL" : success) << ")" << std::endl;
- std::cout << "Content of the Xml file:" << std::endl;
- xmlDoc.Print();
- }
- if (success == nullptr || atoi(success) == 0)
- {
- InitProbe(xmlDoc);
- }
- else
- {
- if (m_Verbose)
- {
- std::cerr << "Could not load xml file" << std::endl;
- }
- }
-}
-
-mitk::pa::Probe::~Probe()
-{
-}
-
-mitk::pa::LightSource::PhotonInformation mitk::pa::Probe::GetNextPhoton(double rng1, double rnd2,
- double rnd3, double rnd4, double rnd5,
- double rnd6, double rnd7, double rnd8)
-{
- rng1 = rng1*m_TotalEnergy;
- double currentEnergy = 0;
- for (LightSource::Pointer lightSource : m_LightSources)
- {
- currentEnergy += lightSource->GetEnergy();
- if (currentEnergy >= rng1)
- return lightSource->GetNextPhoton(rnd2, rnd3, rnd4, rnd5, rnd6, rnd7, rnd8);
- }
-
- //Last resort: If something goes wrong, return a position from the first source.
- return m_LightSources[0]->GetNextPhoton(rnd2, rnd3, rnd4, rnd5, rnd6, rnd7, rnd8);
-}
-
-bool mitk::pa::Probe::IsValid()
-{
- return m_IsValid;
-}
-
-void mitk::pa::Probe::InitProbe(TiXmlDocument xmlDoc)
-{
- m_IsValid = true;
-
- TiXmlElement* root = xmlDoc.FirstChildElement(XML_TAG_PROBE);
- if (root)
- {
- for (TiXmlElement* element = root->FirstChildElement(XML_TAG_LIGHT_SOURCE);
- element != nullptr; element = element->NextSiblingElement(XML_TAG_LIGHT_SOURCE))
- {
- LightSource::Pointer lightSource = LightSource::New(element, m_Verbose);
- if (lightSource.IsNotNull() && lightSource->IsValid())
- {
- m_LightSources.push_back(lightSource);
- m_TotalEnergy += lightSource->GetEnergy();
- }
- else
- {
- m_IsValid = false;
- }
- }
- }
- else
- {
- m_IsValid = false;
- }
-
- if (!m_IsValid)
- {
- std::cerr << "Creation of a valid Photoacoustic Probe failed." << std::endl;
- }
- else
- {
- if (m_Verbose)
- {
- std::cout << "Successfully created Photoacoustic Probe." << std::endl;
- }
- }
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/Thread/mitkPAMonteCarloThreadHandler.cpp b/Modules/PhotoacousticsLib/src/Utils/Thread/mitkPAMonteCarloThreadHandler.cpp
deleted file mode 100644
index 1d6ac5a582..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/Thread/mitkPAMonteCarloThreadHandler.cpp
+++ /dev/null
@@ -1,136 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAMonteCarloThreadHandler.h"
-#include "mitkCommon.h"
-
-mitk::pa::MonteCarloThreadHandler::MonteCarloThreadHandler(long timInMillisecondsOrNumberofPhotons, bool simulateOnTimeBasis) :
- MonteCarloThreadHandler(timInMillisecondsOrNumberofPhotons, simulateOnTimeBasis, true){}
-
-mitk::pa::MonteCarloThreadHandler::MonteCarloThreadHandler(long timInMillisecondsOrNumberofPhotons, bool simulateOnTimeBasis, bool verbose)
-{
- m_Verbose = verbose;
- m_SimulateOnTimeBasis = simulateOnTimeBasis;
- m_WorkPackageSize = 10000L;
- m_SimulationTime = 0;
- m_Time = 0;
- m_NumberPhotonsToSimulate = 0;
- m_NumberPhotonsRemaining = 0;
-
- if (m_SimulateOnTimeBasis)
- {
- m_SimulationTime = timInMillisecondsOrNumberofPhotons;
- m_Time = std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::now().time_since_epoch()).count();
- }
- else
- {
- m_NumberPhotonsToSimulate = timInMillisecondsOrNumberofPhotons;
- m_NumberPhotonsRemaining = timInMillisecondsOrNumberofPhotons;
- }
-}
-
-mitk::pa::MonteCarloThreadHandler::~MonteCarloThreadHandler()
-{
-}
-
-long mitk::pa::MonteCarloThreadHandler::GetNextWorkPackage()
-{
- long workPackageSize = 0;
- if (m_SimulateOnTimeBasis)
- {
- long now = std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::now().time_since_epoch()).count();
- if (now - m_Time <= m_SimulationTime)
- {
- workPackageSize = m_WorkPackageSize;
- if (m_Verbose)
- {
- std::cout << "<filter-progress-text progress='" << ((double)(now - m_Time) / m_SimulationTime) << "'></filter-progress-text>" << std::endl;
- }
- }
- }
- else
- {
- m_MutexRemainingPhotonsManipulation.lock();
-
- if (m_NumberPhotonsRemaining < m_WorkPackageSize)
- {
- workPackageSize = m_NumberPhotonsRemaining;
- }
- else
- {
- workPackageSize = m_WorkPackageSize;
- }
-
- m_NumberPhotonsRemaining -= workPackageSize;
- m_MutexRemainingPhotonsManipulation.unlock();
-
- if (m_Verbose)
- {
- std::cout << "<filter-progress-text progress='" << 1.0 - ((double)m_NumberPhotonsRemaining / m_NumberPhotonsToSimulate) << "'></filter-progress-text>" << std::endl;
- }
- }
-
- return workPackageSize;
-}
-
-void mitk::pa::MonteCarloThreadHandler::SetPackageSize(long sizeInMilliseconsOrNumberOfPhotons)
-{
- m_WorkPackageSize = sizeInMilliseconsOrNumberOfPhotons;
-}
-
-bool mitk::pa::Equal(const MonteCarloThreadHandler::Pointer leftHandSide,
- const MonteCarloThreadHandler::Pointer rightHandSide, double /*eps*/, bool verbose)
-{
- if (rightHandSide->GetNumberPhotonsRemaining() != leftHandSide->GetNumberPhotonsRemaining())
- {
- MITK_INFO(verbose) << "Number of Photons remaining wasnt equal: lhs=" <<
- leftHandSide->GetNumberPhotonsRemaining() << " rhs=" << rightHandSide->GetNumberPhotonsRemaining();
- return false;
- }
-
- if (rightHandSide->GetNumberPhotonsToSimulate() != leftHandSide->GetNumberPhotonsToSimulate())
- {
- MITK_INFO(verbose) << "Number of Photons to simulate wasnt equal: lhs=" <<
- leftHandSide->GetNumberPhotonsToSimulate() << " rhs=" << rightHandSide->GetNumberPhotonsToSimulate();
- return false;
- }
-
- if (rightHandSide->GetWorkPackageSize() != leftHandSide->GetWorkPackageSize())
- {
- MITK_INFO(verbose) << "WorkPackageSize wasnt equal: lhs=" <<
- leftHandSide->GetWorkPackageSize() << " rhs=" << rightHandSide->GetWorkPackageSize();
- return false;
- }
-
- if (rightHandSide->GetSimulationTime() != leftHandSide->GetSimulationTime())
- {
- MITK_INFO(verbose) << "Simulationtime wasnt equal: lhs=" <<
- leftHandSide->GetSimulationTime() << " rhs=" << rightHandSide->GetSimulationTime();
- return false;
- }
-
- if (rightHandSide->GetSimulateOnTimeBasis() != leftHandSide->GetSimulateOnTimeBasis())
- {
- MITK_INFO(verbose) << "simulation on time basis wasnt equal: lhs=" <<
- leftHandSide->GetSimulateOnTimeBasis() << " rhs=" << rightHandSide->GetSimulateOnTimeBasis();
- return false;
- }
-
- if (rightHandSide->GetVerbose() != leftHandSide->GetVerbose())
- {
- MITK_INFO(verbose) << "Verbose wasnt equal: lhs=" <<
- leftHandSide->GetVerbose() << " rhs=" << rightHandSide->GetVerbose();
- return false;
- }
-
- return true;
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/mitkPAPropertyCalculator.cpp b/Modules/PhotoacousticsLib/src/Utils/mitkPAPropertyCalculator.cpp
deleted file mode 100644
index 72cdd4f783..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/mitkPAPropertyCalculator.cpp
+++ /dev/null
@@ -1,157 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAPropertyCalculator.h"
-// us
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usGetModuleContext.h>
-#include <usModuleContext.h>
-#include <usModuleResourceStream.h>
-
-mitk::pa::PropertyCalculator::Properties mitk::pa::PropertyCalculator::
-CalculatePropertyForSpecificWavelength(
- TissueType tissueType, int wavelength, double bloodOxygenInFraction)
-{
- Properties returnValue;
-
- if (!m_Valid)
- {
- mitkThrow() << "PhotoacousticPropertyGenerator was not loaded properly.";
- return returnValue;
- }
-
- double bloodOxygenation = bloodOxygenInFraction;
- double bloodVolumeFraction;
- double waterVolumeFraction;
- double fatVolumeFraction;
- double melanosomesVolumeFraction;
- double musp500;
- double fray;
- double bmie;
- double g;
-
- switch (tissueType)
- {
- case AIR:
- returnValue.mua = 1e-4;
- returnValue.mus = 1.0;
- returnValue.g = 1.0;
- return returnValue;
- case BLOOD:
- bloodVolumeFraction = 1.0;
- waterVolumeFraction = 0.95;
- fatVolumeFraction = 0.02;
- melanosomesVolumeFraction = 0;
- musp500 = 10;
- fray = 0;
- bmie = 1;
- g = 0.9;
- break;
- case EPIDERMIS:
- bloodVolumeFraction = 0;
- bloodOxygenation = 0;
- waterVolumeFraction = 0.75;
- fatVolumeFraction = 0.01;
- melanosomesVolumeFraction = 0.02;
- musp500 = 40;
- fray = 0;
- bmie = 1;
- g = 0.9;
- break;
- case FAT:
- bloodVolumeFraction = 0.01;
- bloodOxygenation = 0.75;
- waterVolumeFraction = 0.5;
- fatVolumeFraction = 0.6;
- melanosomesVolumeFraction = 0;
- musp500 = 17.47;
- fray = 0.2;
- bmie = 0.5;
- g = 0.9;
- break;
- case STANDARD_TISSUE:
- default:
- bloodVolumeFraction = 0.02;
- bloodOxygenation = 0.75;
- waterVolumeFraction = 0.8;
- fatVolumeFraction = 0.05;
- melanosomesVolumeFraction = 0;
- musp500 = 25;
- fray = 0.25;
- bmie = 1;
- g = 0.9;
- break;
- }
-
- // We want the reduced scattering coefficient directly.
- double musp = musp500 * (fray * pow(wavelength / 500.0, -4.0) + ((1 - fray) * pow(wavelength / 500.0, -bmie)));
- returnValue.mus = musp;
- returnValue.mus = 15;//musp;
-
- double mua = bloodVolumeFraction*bloodOxygenation*m_SpectralLibMap[ChromophoreType::OXYGENATED][wavelength] +
- bloodVolumeFraction*(1 - bloodOxygenation)*m_SpectralLibMap[ChromophoreType::DEOXYGENATED][wavelength] +
- waterVolumeFraction*m_SpectralLibMap[ChromophoreType::WATER][wavelength] +
- fatVolumeFraction*m_SpectralLibMap[ChromophoreType::FATTY][wavelength] +
- melanosomesVolumeFraction*m_SpectralLibMap[ChromophoreType::MELANIN][wavelength];
-
- returnValue.mua = mua;
-
- returnValue.g = g;
-
- return returnValue;
-}
-
-mitk::pa::PropertyCalculator::PropertyCalculator()
-{
- us::ModuleResource resource = us::GetModuleContext()->GetModule()->GetResource("spectralLIB.dat");
-
- if (resource.IsValid())
- {
- us::ModuleResourceStream resourceStream(resource);
- std::string line;
- int wavelength = 300;
- int counter = 0;
- while (std::getline(resourceStream, line, '\t'))
- {
- int currentLineIdx = counter % 6;
- if (currentLineIdx == 0)
- wavelength = std::stoi(line);
- else
- {
- std::istringstream lineStream(line);
- double tempDouble;
- lineStream >> tempDouble;
- m_SpectralLibMap[currentLineIdx][wavelength] = tempDouble;
- }
- ++counter;
- }
- }
- else
- {
- m_Valid = false;
- }
-
- m_Valid = true;
-}
-
-mitk::pa::PropertyCalculator::~PropertyCalculator()
-{
- m_SpectralLibMap.clear();
- m_Valid = false;
-}
-
-double mitk::pa::PropertyCalculator::GetAbsorptionForWavelength(
- ChromophoreType ChromophoreType, int wavelength)
-{
- return m_SpectralLibMap[ChromophoreType][wavelength];
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/mitkPATissueGeneratorParameters.cpp b/Modules/PhotoacousticsLib/src/Utils/mitkPATissueGeneratorParameters.cpp
deleted file mode 100644
index af644788e2..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/mitkPATissueGeneratorParameters.cpp
+++ /dev/null
@@ -1,76 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPATissueGeneratorParameters.h"
-
-mitk::pa::TissueGeneratorParameters::TissueGeneratorParameters()
-{
- m_XDim = 50;
- m_YDim = 50;
- m_ZDim = 50;
- m_VoxelSpacingInCentimeters = 1;
- m_DoPartialVolume = false;
- m_UseRngSeed = false;
- m_RngSeed = 1337L;
- m_RandomizePhysicalProperties = false;
- m_RandomizePhysicalPropertiesPercentage = 0;
- m_ForceVesselsMoveAlongYDirection = false;
-
- m_MinBackgroundAbsorption = 0.1;
- m_MaxBackgroundAbsorption = 0.1;
- m_BackgroundScattering = 15;
- m_BackgroundAnisotropy = 0.9;
- m_AirAbsorption = 0.0001;
- m_AirScattering = 1;
- m_AirAnisotropy = 1;
- m_AirThicknessInMillimeters = 0;
- m_SkinAbsorption = 0.1;
- m_SkinScattering = 15;
- m_SkinAnisotropy = 0.9;
- m_SkinThicknessInMillimeters = 0;
-
- m_CalculateNewVesselPositionCallback = &VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector;
- m_MinNumberOfVessels = 0;
- m_MaxNumberOfVessels = 0;
- m_MinVesselBending = 0;
- m_MaxVesselBending = 0.1;
- m_MinVesselAbsorption = 1;
- m_MaxVesselAbsorption = 8;
- m_MinVesselRadiusInMillimeters = 1;
- m_MaxVesselRadiusInMillimeters = 3;
- m_VesselBifurcationFrequency = 25;
- m_MinVesselScattering = 15;
- m_MaxVesselScattering = 15;
- m_MinVesselAnisotropy = 0.9;
- m_MaxVesselAnisotropy = 0.9;
- m_MinVesselZOrigin = 10;
- m_MaxVesselZOrigin = 40;
-
- m_MCflag = 1;
- m_MCLaunchflag = 0;
- m_MCBoundaryflag = 2;
- m_MCLaunchPointX = 25;
- m_MCLaunchPointY = 25;
- m_MCLaunchPointZ = 2;
- m_MCFocusPointX = 25;
- m_MCFocusPointY = 25;
- m_MCFocusPointZ = 25;
- m_MCTrajectoryVectorX = 0;
- m_MCTrajectoryVectorY = 0;
- m_MCTrajectoryVectorZ = 1;
- m_MCRadius = 2;
- m_MCWaist = 4;
-}
-
-mitk::pa::TissueGeneratorParameters::~TissueGeneratorParameters()
-{
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/mitkPAVector.cpp b/Modules/PhotoacousticsLib/src/Utils/mitkPAVector.cpp
deleted file mode 100644
index fd82072890..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/mitkPAVector.cpp
+++ /dev/null
@@ -1,178 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVector.h"
-#include "chrono"
-#include <cmath>
-mitk::pa::Vector::Vector()
-{
- m_Vector.Fill(0);
-}
-
-mitk::pa::Vector::~Vector()
-{
- m_Vector.Fill(0);
-}
-
-double mitk::pa::Vector::GetNorm()
-{
- return m_Vector.GetNorm();
-}
-
-double mitk::pa::Vector::GetElement(unsigned short index)
-{
- return m_Vector.GetElement(index);
-}
-
-void mitk::pa::Vector::SetElement(unsigned short index, double value)
-{
- m_Vector.SetElement(index, value);
-}
-
-void mitk::pa::Vector::Normalize()
-{
- double norm = m_Vector.GetNorm();
- m_Vector.SetElement(0, m_Vector.GetElement(0) / norm);
- m_Vector.SetElement(1, m_Vector.GetElement(1) / norm);
- m_Vector.SetElement(2, m_Vector.GetElement(2) / norm);
-}
-
-void mitk::pa::Vector::SetValue(mitk::pa::Vector::Pointer value)
-{
- m_Vector.SetElement(0, value->GetElement(0));
- m_Vector.SetElement(1, value->GetElement(1));
- m_Vector.SetElement(2, value->GetElement(2));
-}
-
-void mitk::pa::Vector::RandomizeByPercentage(double percentage, double bendingFactor, std::mt19937* rng)
-{
- std::uniform_real_distribution<> range(-percentage, percentage);
- m_Vector.SetElement(0, m_Vector.GetElement(0) + (bendingFactor * range(*rng)));
- m_Vector.SetElement(1, m_Vector.GetElement(1) + (bendingFactor * range(*rng)));
- m_Vector.SetElement(2, m_Vector.GetElement(2) + (bendingFactor * range(*rng)));
-}
-
-void mitk::pa::Vector::Randomize(double xLowerLimit, double xUpperLimit, double yLowerLimit, double yUpperLimit, double zLowerLimit, double zUpperLimit, std::mt19937* rng)
-{
- std::uniform_real_distribution<> rangeX(xLowerLimit, xUpperLimit);
- std::uniform_real_distribution<> rangeY(yLowerLimit, yUpperLimit);
- std::uniform_real_distribution<> rangeZ(zLowerLimit, zUpperLimit);
- m_Vector.SetElement(0, rangeX(*rng));
- m_Vector.SetElement(1, rangeY(*rng));
- m_Vector.SetElement(2, rangeZ(*rng));
-}
-
-void mitk::pa::Vector::Randomize(double xLimit, double yLimit, double zLimit, std::mt19937* rng)
-{
- Randomize(0, xLimit, 0, yLimit, 0, zLimit, rng);
-}
-
-void mitk::pa::Vector::Randomize(std::mt19937* rng)
-{
- Randomize(-1, 1, -1, 1, -1, 1, rng);
-}
-
-void mitk::pa::Vector::PrintSelf(std::ostream& os, itk::Indent /*indent*/) const
-{
- os << "X: " << m_Vector.GetElement(0) << std::endl;
- os << "Y: " << m_Vector.GetElement(1) << std::endl;
- os << "Z: " << m_Vector.GetElement(2) << std::endl;
- os << "Length: " << m_Vector.GetNorm() << std::endl;
-}
-
-void mitk::pa::Vector::Rotate(double thetaChange, double phiChange)
-{
- MITK_DEBUG << "Vector before rotation: (" << GetElement(0) << "|" << GetElement(1) << "|" << GetElement(2) << ")";
- if (thetaChange == 0 && phiChange == 0)
- return;
-
- double x = GetElement(0);
- double y = GetElement(1);
- double z = GetElement(2);
-
- double r = sqrt(x*x + y*y + z*z);
- if (r == 0)
- return;
-
- double theta = acos(z / r);
- double phi = atan2(y, x);
-
- theta += thetaChange;
- phi += phiChange;
-
- SetElement(0, r * sin(theta) * cos(phi));
- SetElement(1, r * sin(theta) * sin(phi));
- SetElement(2, r * cos(theta));
-
- MITK_DEBUG << "Vector after rotation: (" << GetElement(0) << "|" << GetElement(1) << "|" << GetElement(2) << ")";
-}
-
-void mitk::pa::Vector::Scale(double factor)
-{
- m_Vector.SetElement(0, m_Vector.GetElement(0)*factor);
- m_Vector.SetElement(1, m_Vector.GetElement(1)*factor);
- m_Vector.SetElement(2, m_Vector.GetElement(2)*factor);
-}
-
-mitk::pa::Vector::Pointer mitk::pa::Vector::Clone()
-{
- auto returnVector = Vector::New();
- returnVector->SetElement(0, this->GetElement(0));
- returnVector->SetElement(1, this->GetElement(1));
- returnVector->SetElement(2, this->GetElement(2));
- return returnVector;
-}
-
-void mitk::pa::Vector::Subtract(Vector::Pointer other)
-{
- m_Vector.SetElement(0, m_Vector.GetElement(0) - other->GetElement(0));
- m_Vector.SetElement(1, m_Vector.GetElement(1) - other->GetElement(1));
- m_Vector.SetElement(2, m_Vector.GetElement(2) - other->GetElement(2));
-}
-
-void mitk::pa::Vector::Add(Vector::Pointer other)
-{
- m_Vector.SetElement(0, m_Vector.GetElement(0) + other->GetElement(0));
- m_Vector.SetElement(1, m_Vector.GetElement(1) + other->GetElement(1));
- m_Vector.SetElement(2, m_Vector.GetElement(2) + other->GetElement(2));
-}
-
-bool mitk::pa::Equal(const Vector::Pointer leftHandSide, const Vector::Pointer rightHandSide, double eps, bool verbose)
-{
- MITK_INFO(verbose) << "=== mitk::pa::Vector Equal ===";
-
- if (rightHandSide.IsNull() || leftHandSide.IsNull())
- {
- MITK_INFO(verbose) << "Cannot compare nullpointers";
- return false;
- }
-
- if (leftHandSide->GetElement(0) - rightHandSide->GetElement(0) > eps)
- {
- MITK_INFO(verbose) << "Element[0] not equal";
- return false;
- }
-
- if (leftHandSide->GetElement(1) - rightHandSide->GetElement(1) > eps)
- {
- MITK_INFO(verbose) << "Element[1] not equal";
- return false;
- }
-
- if (leftHandSide->GetElement(2) - rightHandSide->GetElement(2) > eps)
- {
- MITK_INFO(verbose) << "Element[2] not equal";
- return false;
- }
-
- return true;
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/mitkPAVesselDrawer.cpp b/Modules/PhotoacousticsLib/src/Utils/mitkPAVesselDrawer.cpp
deleted file mode 100644
index 30c46f0432..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/mitkPAVesselDrawer.cpp
+++ /dev/null
@@ -1,77 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVesselDrawer.h"
-#include "mitkPAVesselProperties.h"
-
-mitk::pa::VesselDrawer::VesselDrawer()
-{
-}
-
-mitk::pa::VesselDrawer::~VesselDrawer()
-{
-}
-
-void mitk::pa::VesselDrawer::ExpandAndDrawVesselInVolume(
- VesselProperties::Pointer properties,
- InSilicoTissueVolume::Pointer volume)
-{
- Vector::Pointer stepDirection = properties->GetDirectionVector();
- Vector::Pointer fromPosition = properties->GetPositionVector()->Clone();
-
- Vector::Pointer totalWalkingDistance = stepDirection->Clone();
- totalWalkingDistance->Scale(1.0 / volume->GetSpacing());
-
- while (totalWalkingDistance->GetNorm() >= 1)
- {
- double xPos = fromPosition->GetElement(0);
- double yPos = fromPosition->GetElement(1);
- double zPos = fromPosition->GetElement(2);
-
- if (!volume->IsInsideVolume(xPos, yPos, zPos))
- {
- properties->SetRadiusInVoxel(0);
- return;
- }
-
- double radius = properties->GetRadiusInVoxel();
- double ceiledRadius = ceil(radius);
-
- for (int x = xPos - ceiledRadius; x <= xPos + ceiledRadius; x += 1)
- for (int y = yPos - ceiledRadius; y <= yPos + ceiledRadius; y += 1)
- for (int z = zPos - ceiledRadius; z <= zPos + ceiledRadius; z += 1)
- {
- if (!volume->IsInsideVolume(x, y, z))
- {
- continue;
- }
- double xDiff = x - xPos;
- double yDiff = y - yPos;
- double zDiff = z - zPos;
- double vectorLengthDiff = radius - sqrt(xDiff*xDiff + yDiff*yDiff + zDiff*zDiff);
-
- if (vectorLengthDiff > 0)
- {
- volume->SetVolumeValues(x, y, z,
- properties->GetAbsorptionCoefficient(),
- properties->GetScatteringCoefficient(),
- properties->GetAnisotopyCoefficient(),
- mitk::pa::InSilicoTissueVolume::SegmentationType::VESSEL);
- }
- }
-
- totalWalkingDistance->Subtract(stepDirection);
- fromPosition->Add(stepDirection);
- }
-
- properties->SetPositionVector(fromPosition);
-}
diff --git a/Modules/PhotoacousticsLib/src/Utils/mitkPAVolumeManipulator.cpp b/Modules/PhotoacousticsLib/src/Utils/mitkPAVolumeManipulator.cpp
deleted file mode 100644
index 89c609158b..0000000000
--- a/Modules/PhotoacousticsLib/src/Utils/mitkPAVolumeManipulator.cpp
+++ /dev/null
@@ -1,232 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkPAVolumeManipulator.h"
-#include "mitkPAExceptions.h"
-#include "mitkPAInSilicoTissueVolume.h"
-#include "itkResampleImageFilter.h"
-#include "itkGaussianInterpolateImageFunction.h"
-
-// Includes for image casting between ITK and MITK
-#include <mitkImageCast.h>
-#include <mitkITKImageImport.h>
-
-#include <mitkIOUtil.h>
-
-mitk::pa::VolumeManipulator::VolumeManipulator() {}
-
-mitk::pa::VolumeManipulator::~VolumeManipulator() {}
-
-void mitk::pa::VolumeManipulator::ThresholdImage(Volume::Pointer image, double threshold)
-{
- for (unsigned int z = 0; z < image->GetZDim(); z++)
- for (unsigned int y = 0; y < image->GetYDim(); y++)
- for (unsigned int x = 0; x < image->GetXDim(); x++)
- if (image->GetData(x, y, z) > threshold)
- image->SetData(1, x, y, z);
- else
- image->SetData(0, x, y, z);
-}
-
-void mitk::pa::VolumeManipulator::MultiplyImage(Volume::Pointer image, double factor)
-{
- for (unsigned int z = 0; z < image->GetZDim(); z++)
- for (unsigned int y = 0; y < image->GetYDim(); y++)
- for (unsigned int x = 0; x < image->GetXDim(); x++)
- image->SetData(image->GetData(x, y, z)*factor, x, y, z);
-}
-
-void mitk::pa::VolumeManipulator::Log10Image(Volume::Pointer image)
-{
- for (unsigned int z = 0; z < image->GetZDim(); z++)
- for (unsigned int y = 0; y < image->GetYDim(); y++)
- for (unsigned int x = 0; x < image->GetXDim(); x++)
- {
- if (image->GetData(x, y, z) < 0)
- {
- MITK_ERROR << "Signal was smaller than 0. There is an error in the input image file.";
- throw InvalidValueException("Signal was smaller than 0. There is an error in the input image file.");
- }
- image->SetData(log10(image->GetData(x, y, z)), x, y, z);
- }
-}
-
-void mitk::pa::VolumeManipulator::RescaleImage(InSilicoTissueVolume::Pointer image, double ratio)
-{
- MITK_INFO << "Rescaling images..";
- double sigma = image->GetSpacing() / (ratio * 2);
- image->SetAbsorptionVolume(RescaleImage(image->GetAbsorptionVolume(), ratio, sigma));
- image->SetScatteringVolume(RescaleImage(image->GetScatteringVolume(), ratio, sigma));
- image->SetAnisotropyVolume(RescaleImage(image->GetAnisotropyVolume(), ratio, sigma));
- image->SetSegmentationVolume(RescaleImage(image->GetSegmentationVolume(), ratio, 0));
- MITK_INFO << "Rescaling images..[Done]";
-}
-
-mitk::pa::Volume::Pointer mitk::pa::VolumeManipulator::RescaleImage(Volume::Pointer image, double ratio, double sigma)
-{
- MITK_INFO << "Rescaling image..";
- typedef itk::Image<double, 3> ImageType;
- typedef itk::ResampleImageFilter<ImageType, ImageType> FilterType;
- typedef itk::GaussianInterpolateImageFunction<ImageType, double> InterpolatorType;
-
- auto input = image->AsMitkImage();
- ImageType::Pointer itkInput = ImageType::New();
- mitk::CastToItkImage(input, itkInput);
-
- ImageType::SizeType outputSize;
- outputSize[0] = input->GetDimensions()[0] * ratio;
- outputSize[1] = input->GetDimensions()[1] * ratio;
- outputSize[2] = input->GetDimensions()[2] * ratio;
-
- FilterType::Pointer resampleImageFilter = FilterType::New();
- resampleImageFilter->SetInput(itkInput);
- resampleImageFilter->SetSize(outputSize);
- if (sigma > mitk::eps)
- {
- auto interpolator = InterpolatorType::New();
- interpolator->SetSigma(sigma);
- resampleImageFilter->SetInterpolator(interpolator);
- }
- resampleImageFilter->SetOutputSpacing(input->GetGeometry()->GetSpacing()[0] / ratio);
-
- MITK_INFO << "Update..";
- resampleImageFilter->UpdateLargestPossibleRegion();
- MITK_INFO << "Update..[Done]";
-
- ImageType::Pointer output = resampleImageFilter->GetOutput();
- mitk::Image::Pointer mitkOutput = mitk::Image::New();
-
- GrabItkImageMemory(output, mitkOutput);
- MITK_INFO << "Rescaling image..[Done]";
- return Volume::New(mitkOutput);
-}
-
-/**
-* @brief Fast 3D Gaussian convolution IIR approximation
-* @param paVolume
-* @param sigma
-* @author Pascal Getreuer <getreuer@gmail.com>
-*
-* Copyright (c) 2011, Pascal Getreuer
-* All rights reserved.
-*
-* This program is free software: you can redistribute it and/or modify it
-* under the terms of the simplified BSD license.
-*
-* You should have received a copy of these licenses along with this program.
-* If not, see <http://www.opensource.org/licenses/bsd-license.html>.
-*/
-void mitk::pa::VolumeManipulator::GaussianBlur3D(mitk::pa::Volume::Pointer paVolume, double sigma)
-{
- double* volume = paVolume->GetData();
- long width = paVolume->GetYDim();
- long height = paVolume->GetXDim();
- long depth = paVolume->GetZDim();
- const long plane = width*height;
- const long numel = plane*depth;
- double lambda, dnu;
- double nu, boundaryscale, postscale;
- double *ptr;
- long i, x, y, z;
- int step;
-
- if (sigma <= 0)
- return;
-
- lambda = (sigma*sigma) / (8.0);
- dnu = (1.0 + 2.0*lambda - sqrt(1.0 + 4.0*lambda)) / (2.0*lambda);
- nu = dnu;
- boundaryscale = 1.0 / (1.0 - dnu);
- postscale = pow(dnu / lambda, 12);
-
- /* Filter horizontally along each row */
- for (z = 0; z < depth; z++)
- {
- for (y = 0; y < height; y++)
- {
- for (step = 0; step < 4; step++)
- {
- ptr = volume + width*(y + height*z);
- ptr[0] *= boundaryscale;
-
- /* Filter rightwards */
- for (x = 1; x < width; x++)
- {
- ptr[x] += nu*ptr[x - 1];
- }
-
- ptr[x = width - 1] *= boundaryscale;
- /* Filter leftwards */
- for (; x > 0; x--)
- {
- ptr[x - 1] += nu*ptr[x];
- }
- }
- }
- }
- /* Filter vertically along each column */
- for (z = 0; z < depth; z++)
- {
- for (x = 0; x < width; x++)
- {
- for (step = 0; step < 4; step++)
- {
- ptr = volume + x + plane*z;
- ptr[0] *= boundaryscale;
-
- /* Filter downwards */
- for (i = width; i < plane; i += width)
- {
- ptr[i] += nu*ptr[i - width];
- }
-
- ptr[i = plane - width] *= boundaryscale;
-
- /* Filter upwards */
- for (; i > 0; i -= width)
- {
- ptr[i - width] += nu*ptr[i];
- }
- }
- }
- }
-
- /* Filter along z-dimension */
- for (y = 0; y < height; y++)
- {
- for (x = 0; x < width; x++)
- {
- for (step = 0; step < 4; step++)
- {
- ptr = volume + x + width*y;
- ptr[0] *= boundaryscale;
-
- for (i = plane; i < numel; i += plane)
- {
- ptr[i] += nu*ptr[i - plane];
- }
-
- ptr[i = numel - plane] *= boundaryscale;
-
- for (; i > 0; i -= plane)
- {
- ptr[i - plane] += nu*ptr[i];
- }
- }
- }
- }
-
- for (i = 0; i < numel; i++)
- {
- volume[i] *= postscale;
- }
-}
diff --git a/Modules/PhotoacousticsLib/test/CMakeLists.txt b/Modules/PhotoacousticsLib/test/CMakeLists.txt
deleted file mode 100644
index 153cd81e2e..0000000000
--- a/Modules/PhotoacousticsLib/test/CMakeLists.txt
+++ /dev/null
@@ -1 +0,0 @@
-MITK_CREATE_MODULE_TESTS()
diff --git a/Modules/PhotoacousticsLib/test/Resources/allsources.xml b/Modules/PhotoacousticsLib/test/Resources/allsources.xml
deleted file mode 100644
index 36a213c5f9..0000000000
--- a/Modules/PhotoacousticsLib/test/Resources/allsources.xml
+++ /dev/null
@@ -1,70 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<Probe>
- <LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>POINT</SpawnType>
- <x>0.3</x>
- <y>0.2</y>
- <z>0.1</z>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.1</min>
- <max>0.1</max>
- <mode>UNIFORM</mode>
- </xAngle>
- <yAngle>
- <min>-0.2</min>
- <max>0.2</max>
- <mode>UNIFORM</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
- <LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>RECTANGLE</SpawnType>
- <x>0.4</x>
- <y>0.5</y>
- <z>0.6</z>
- <xLength>0.7</xLength>
- <yLength>0.8</yLength>
- <zLength>0.9</zLength>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.3</min>
- <max>0.3</max>
- <mode>GAUSSIAN</mode>
- </xAngle>
- <yAngle>
- <min>-0.4</min>
- <max>0.4</max>
- <mode>GAUSSIAN</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
- <LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>CIRCLE</SpawnType>
- <x>0.4</x>
- <y>0.5</y>
- <z>0.6</z>
- <r>0.5</r>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.3</min>
- <max>0.3</max>
- <mode>GAUSSIAN</mode>
- </xAngle>
- <yAngle>
- <min>-0.4</min>
- <max>0.4</max>
- <mode>GAUSSIAN</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
-</Probe>
diff --git a/Modules/PhotoacousticsLib/test/Resources/circlesource.xml b/Modules/PhotoacousticsLib/test/Resources/circlesource.xml
deleted file mode 100644
index 14ef65dd58..0000000000
--- a/Modules/PhotoacousticsLib/test/Resources/circlesource.xml
+++ /dev/null
@@ -1,25 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<Probe>
- <LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>CIRCLE</SpawnType>
- <x>0.3</x>
- <y>0.2</y>
- <z>0.1</z>
- <r>2</r>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.1</min>
- <max>0.1</max>
- <mode>GAUSSIAN</mode>
- </xAngle>
- <yAngle>
- <min>-0.2</min>
- <max>0.2</max>
- <mode>UNIFORM</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
-</Probe>
diff --git a/Modules/PhotoacousticsLib/test/Resources/pointsource.xml b/Modules/PhotoacousticsLib/test/Resources/pointsource.xml
deleted file mode 100644
index 0ab73fdb8d..0000000000
--- a/Modules/PhotoacousticsLib/test/Resources/pointsource.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<Probe>
- <LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>POINT</SpawnType>
- <x>0.3</x>
- <y>0.2</y>
- <z>0.1</z>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.1</min>
- <max>0.1</max>
- <mode>UNIFORM</mode>
- </xAngle>
- <yAngle>
- <min>-0.2</min>
- <max>0.2</max>
- <mode>UNIFORM</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
-</Probe>
diff --git a/Modules/PhotoacousticsLib/test/Resources/rectanglesource.xml b/Modules/PhotoacousticsLib/test/Resources/rectanglesource.xml
deleted file mode 100644
index 7c9a4f2f9e..0000000000
--- a/Modules/PhotoacousticsLib/test/Resources/rectanglesource.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<Probe>
- <LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>RECTANGLE</SpawnType>
- <x>0.3</x>
- <y>0.2</y>
- <z>0.1</z>
- <xLength>1</xLength>
- <yLength>2</yLength>
- <zLength>3</zLength>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.1</min>
- <max>0.1</max>
- <mode>UNIFORM</mode>
- </xAngle>
- <yAngle>
- <min>-0.2</min>
- <max>0.2</max>
- <mode>UNIFORM</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
-</Probe>
diff --git a/Modules/PhotoacousticsLib/test/Resources/twopointsources.xml b/Modules/PhotoacousticsLib/test/Resources/twopointsources.xml
deleted file mode 100644
index 5054ee51c8..0000000000
--- a/Modules/PhotoacousticsLib/test/Resources/twopointsources.xml
+++ /dev/null
@@ -1,45 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<Probe>
- <LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>POINT</SpawnType>
- <x>0.3</x>
- <y>0.2</y>
- <z>0.1</z>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.1</min>
- <max>0.1</max>
- <mode>UNIFORM</mode>
- </xAngle>
- <yAngle>
- <min>-0.2</min>
- <max>0.2</max>
- <mode>UNIFORM</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
-<LightSource>
- <Energy>1</Energy>
- <PhotonSpawnArea>
- <SpawnType>POINT</SpawnType>
- <x>0.4</x>
- <y>0.5</y>
- <z>0.6</z>
- </PhotonSpawnArea>
- <PhotonDirection>
- <xAngle>
- <min>-0.3</min>
- <max>0.3</max>
- <mode>GAUSSIAN</mode>
- </xAngle>
- <yAngle>
- <min>-0.4</min>
- <max>0.4</max>
- <mode>GAUSSIAN</mode>
- </yAngle>
- </PhotonDirection>
- </LightSource>
-</Probe>
diff --git a/Modules/PhotoacousticsLib/test/files.cmake b/Modules/PhotoacousticsLib/test/files.cmake
deleted file mode 100644
index 4026e7fcf2..0000000000
--- a/Modules/PhotoacousticsLib/test/files.cmake
+++ /dev/null
@@ -1,40 +0,0 @@
-set(MODULE_TESTS
- # IMPORTANT: If you plan to deactivate / comment out a test please write a bug number to the commented out line of code.
- #
- # Example: #mitkMyTest #this test is commented out because of bug 12345
- #
- # It is important that the bug is open and that the test will be activated again before the bug is closed. This assures that
- # no test is forgotten after it was commented out. If there is no bug for your current problem, please add a new one and
- # mark it as critical.
-
- ################## ON THE FENCE TESTS #################################################
- # none
-
- ################## DISABLED TESTS #####################################################
- # mitkMCThreadHandlerTest.cpp #Timing issue on VMs
- # mitkPhotoacousticIOTest.cpp #Not suitable for large scale testing as it performs IO actions.
- ################# RUNNING TESTS #######################################################
-
- mitkSlicedVolumeGeneratorTest.cpp
- mitkPhotoacousticTissueGeneratorTest.cpp
- mitkPhotoacousticVectorTest.cpp
- mitkPhotoacoustic3dVolumeTest.cpp
- # mitkPhotoacousticVolumeTest.cpp (See T27024)
- mitkPhotoacousticVesselTreeTest.cpp
- mitkMcxyzXmlTest.cpp
- mitkPhotoacousticComposedVolumeTest.cpp
- mitkPhotoacousticNoiseGeneratorTest.cpp
- mitkSimulationBatchGeneratorTest.cpp
- mitkPropertyCalculatorTest.cpp
- # mitkSpectralUnmixingTest.cpp (See T27024)
- mitkPhotoacousticVesselMeanderStrategyTest.cpp
- mitkPhotoacousticVesselTest.cpp
-)
-
-set(RESOURCE_FILES
- pointsource.xml
- circlesource.xml
- rectanglesource.xml
- twopointsources.xml
- allsources.xml
-)
diff --git a/Modules/PhotoacousticsLib/test/mitkMCThreadHandlerTest.cpp b/Modules/PhotoacousticsLib/test/mitkMCThreadHandlerTest.cpp
deleted file mode 100644
index 65247b86a2..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkMCThreadHandlerTest.cpp
+++ /dev/null
@@ -1,101 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPAMonteCarloThreadHandler.h>
-
-// us
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usGetModuleContext.h>
-#include <usModuleContext.h>
-#include <usModuleResourceStream.h>
-
-#include <random>
-#include <chrono>
-
-class mitkMCThreadHandlerTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkMCThreadHandlerTestSuite);
- MITK_TEST(testConstructorBehavior);
- MITK_TEST(testCorrectNumberOfPhotons);
- MITK_TEST(testCorrectNumberOfPhotonsWithUnevenPackageSize);
- MITK_TEST(testCorrectNumberOfPhotonsWithTooLargePackageSize);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::pa::MonteCarloThreadHandler::Pointer m_MonteCarloThreadHandler;
- long m_NumberOrTime = 500;
-
-public:
-
- void setUp() override
- {
- }
-
- void testConstructorBehavior()
- {
- auto threadHandler1 = mitk::pa::MonteCarloThreadHandler::New(m_NumberOrTime, true, true);
- auto threadHandler2 = mitk::pa::MonteCarloThreadHandler::New(m_NumberOrTime, true);
-
- CPPUNIT_ASSERT(mitk::pa::Equal(threadHandler1, threadHandler2, 1e-6, true));
- }
-
- void testCorrectNumberOfPhotons()
- {
- m_MonteCarloThreadHandler = mitk::pa::MonteCarloThreadHandler::New(m_NumberOrTime, false, false);
- m_MonteCarloThreadHandler->SetPackageSize(100);
- long numberOfPhotonsSimulated = 0;
- long nextWorkPackage = 0;
- while ((nextWorkPackage = m_MonteCarloThreadHandler->GetNextWorkPackage()) > 0)
- {
- numberOfPhotonsSimulated += nextWorkPackage;
- }
- CPPUNIT_ASSERT(numberOfPhotonsSimulated == m_NumberOrTime);
- }
-
- void testCorrectNumberOfPhotonsWithUnevenPackageSize()
- {
- m_MonteCarloThreadHandler = mitk::pa::MonteCarloThreadHandler::New(m_NumberOrTime, false, false);
- m_MonteCarloThreadHandler->SetPackageSize(77);
- long numberOfPhotonsSimulated = 0;
- long nextWorkPackage = 0;
- while ((nextWorkPackage = m_MonteCarloThreadHandler->GetNextWorkPackage()) > 0)
- {
- numberOfPhotonsSimulated += nextWorkPackage;
- }
- CPPUNIT_ASSERT(numberOfPhotonsSimulated == m_NumberOrTime);
- }
-
- void testCorrectNumberOfPhotonsWithTooLargePackageSize()
- {
- m_MonteCarloThreadHandler = mitk::pa::MonteCarloThreadHandler::New(m_NumberOrTime, false, false);
- m_MonteCarloThreadHandler->SetPackageSize(10000);
- long numberOfPhotonsSimulated = 0;
- long nextWorkPackage = 0;
- while ((nextWorkPackage = m_MonteCarloThreadHandler->GetNextWorkPackage()) > 0)
- {
- numberOfPhotonsSimulated += nextWorkPackage;
- }
- CPPUNIT_ASSERT(numberOfPhotonsSimulated == m_NumberOrTime);
- }
-
- void tearDown() override
- {
- m_MonteCarloThreadHandler = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkMCThreadHandler)
diff --git a/Modules/PhotoacousticsLib/test/mitkMcxyzXmlTest.cpp b/Modules/PhotoacousticsLib/test/mitkMcxyzXmlTest.cpp
deleted file mode 100644
index ac773e6309..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkMcxyzXmlTest.cpp
+++ /dev/null
@@ -1,238 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPAProbe.h>
-
-// us
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usGetModuleContext.h>
-#include <usModuleContext.h>
-#include <usModuleResourceStream.h>
-#include <mitkLocaleSwitch.h>
-#include <random>
-#include <chrono>
-
-class mitkMcxyzXmlTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkMcxyzXmlTestSuite);
- MITK_TEST(TestCreatePointSourceProbe);
- MITK_TEST(TestCreateCircleSourceProbe);
- MITK_TEST(TestCreateRectangleSourceProbe);
- MITK_TEST(TestCreateTwoPointSourcesProbe);
- MITK_TEST(TestCreateAllSourcesProbe);
- MITK_TEST(TestValuesAreInBoundsUniformRectangle);
- MITK_TEST(TestValuesAreInBoundsGaussianRectangle);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::pa::LightSource::Pointer m_LightSource;
- mitk::pa::Probe::Pointer m_Probe;
- std::string m_XmlProbePointSource;
- std::string m_XmlProbeCircleSource;
- std::string m_XmlProbeRectangleSource;
- std::string m_XmlProbeTwoPointSources;
- std::string m_XmlProbeAllSources;
-
-public:
-
- void setUp() override
- {
- m_LightSource = mitk::pa::LightSource::New();
- LoadXmlFile("pointsource.xml", &m_XmlProbePointSource);
- LoadXmlFile("circlesource.xml", &m_XmlProbeCircleSource);
- LoadXmlFile("rectanglesource.xml", &m_XmlProbeRectangleSource);
- LoadXmlFile("twopointsources.xml", &m_XmlProbeTwoPointSources);
- LoadXmlFile("allsources.xml", &m_XmlProbeAllSources);
- }
-
- void LoadXmlFile(std::string filename, std::string* lines)
- {
- us::ModuleResource pointSourceXml = us::GetModuleContext()->GetModule()->GetResource(filename);
- std::string line;
- if (pointSourceXml.IsValid() && pointSourceXml.IsFile())
- {
- us::ModuleResourceStream stream(pointSourceXml);
- stream.std::istream::imbue(std::locale("C"));
- while (std::getline(stream, line))
- {
- *lines = *lines + line + " ";
- }
- }
- else
- {
- MITK_ERROR << "Xml file was not valid";
- }
- }
-
- void TestCreatePointSourceProbe()
- {
- m_Probe = mitk::pa::Probe::New(m_XmlProbePointSource.c_str(), true);
- CPPUNIT_ASSERT(true == m_Probe->IsValid());
- }
-
- void TestCreateCircleSourceProbe()
- {
- m_Probe = mitk::pa::Probe::New(m_XmlProbeCircleSource.c_str(), true);
- CPPUNIT_ASSERT(true == m_Probe->IsValid());
- }
-
- void TestCreateRectangleSourceProbe()
- {
- m_Probe = mitk::pa::Probe::New(m_XmlProbeRectangleSource.c_str(), true);
- CPPUNIT_ASSERT(true == m_Probe->IsValid());
- }
-
- void TestCreateTwoPointSourcesProbe()
- {
- m_Probe = mitk::pa::Probe::New(m_XmlProbeTwoPointSources.c_str(), true);
- CPPUNIT_ASSERT(true == m_Probe->IsValid());
- }
-
- void TestCreateAllSourcesProbe()
- {
- m_Probe = mitk::pa::Probe::New(m_XmlProbeAllSources.c_str(), true);
- CPPUNIT_ASSERT(true == m_Probe->IsValid());
- }
-
- void TestValuesAreInBoundsUniformRectangle()
- {
- int MAXIMUM = 2;
- int MINIMUM = -2;
-
- int ANGLE_MAXIMUM = 1;
- int ANGLE_MINIMUM = -1;
-
- m_LightSource->SetAngleXMode(mitk::pa::LightSource::DistributionMode::UNIFORM);
- m_LightSource->SetAngleYMode(mitk::pa::LightSource::DistributionMode::UNIFORM);
-
- m_LightSource->SetAngleXMaximum(ANGLE_MAXIMUM);
- m_LightSource->SetAngleXMinimum(ANGLE_MINIMUM);
-
- m_LightSource->SetAngleYMaximum(ANGLE_MAXIMUM);
- m_LightSource->SetAngleYMinimum(ANGLE_MINIMUM);
-
- m_LightSource->SetSpawnLocationX(MINIMUM);
- m_LightSource->SetSpawnLocationXLength(2 * MAXIMUM);
-
- m_LightSource->SetSpawnLocationY(MINIMUM);
- m_LightSource->SetSpawnLocationYLength(2 * MAXIMUM);
-
- m_LightSource->SetSpawnLocationZ(MINIMUM);
- m_LightSource->SetSpawnLocationZLength(2 * MAXIMUM);
-
- m_LightSource->SetSpawnLocationRadius(MAXIMUM);
-
- m_LightSource->SetVerbose(false);
-
- m_LightSource->SetSpawnType(mitk::pa::LightSource::SpawnType::RECTANGLE);
-
- std::mt19937 rng;
- rng.seed(std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::
- now().time_since_epoch()).count());
- std::uniform_real_distribution<> realDist(0, 1);
-
- for (int i = 0, length = 10000; i < length; i++)
- {
- auto result =
- m_LightSource->GetNextPhoton(realDist(rng), realDist(rng), realDist(rng), realDist(rng),
- realDist(rng), realDist(rng), realDist(rng));
-
- CPPUNIT_ASSERT(result.xAngle >= ANGLE_MINIMUM);
- CPPUNIT_ASSERT(result.xAngle <= ANGLE_MAXIMUM);
- CPPUNIT_ASSERT(result.yAngle >= ANGLE_MINIMUM);
- CPPUNIT_ASSERT(result.yAngle <= ANGLE_MAXIMUM);
- CPPUNIT_ASSERT(result.zAngle >= 0);
- CPPUNIT_ASSERT(result.zAngle <= ANGLE_MAXIMUM);
- CPPUNIT_ASSERT(result.xPosition >= MINIMUM);
- CPPUNIT_ASSERT(result.xPosition <= MAXIMUM);
- CPPUNIT_ASSERT(result.yPosition >= MINIMUM);
- CPPUNIT_ASSERT(result.yPosition <= MAXIMUM);
- CPPUNIT_ASSERT(result.zPosition >= MINIMUM);
- CPPUNIT_ASSERT(result.zPosition <= MAXIMUM);
- }
- }
-
- void TestValuesAreInBoundsGaussianRectangle()
- {
- int MAXIMUM = 2;
- int MINIMUM = -2;
-
- int ANGLE_MAXIMUM = 1;
- int ANGLE_MINIMUM = -1;
-
- m_LightSource->SetAngleXMode(mitk::pa::LightSource::DistributionMode::GAUSSIAN);
- m_LightSource->SetAngleYMode(mitk::pa::LightSource::DistributionMode::GAUSSIAN);
-
- m_LightSource->SetAngleXMaximum(ANGLE_MAXIMUM);
- m_LightSource->SetAngleXMinimum(ANGLE_MINIMUM);
-
- m_LightSource->SetAngleYMaximum(ANGLE_MAXIMUM);
- m_LightSource->SetAngleYMinimum(ANGLE_MINIMUM);
-
- m_LightSource->SetSpawnLocationX(MINIMUM);
- m_LightSource->SetSpawnLocationXLength(2 * MAXIMUM);
-
- m_LightSource->SetSpawnLocationY(MINIMUM);
- m_LightSource->SetSpawnLocationYLength(2 * MAXIMUM);
-
- m_LightSource->SetSpawnLocationZ(MINIMUM);
- m_LightSource->SetSpawnLocationZLength(2 * MAXIMUM);
-
- m_LightSource->SetSpawnLocationRadius(MAXIMUM);
-
- m_LightSource->SetVerbose(false);
-
- m_LightSource->SetSpawnType(mitk::pa::LightSource::SpawnType::RECTANGLE);
-
- std::mt19937 rng;
- rng.seed(std::chrono::duration_cast<std::chrono::milliseconds>(std::chrono::high_resolution_clock::
- now().time_since_epoch()).count());
- std::uniform_real_distribution<> realDist(0, 1);
-
- for (int i = 0, length = 10000; i < length; i++)
- {
- auto result =
- m_LightSource->GetNextPhoton(realDist(rng), realDist(rng), realDist(rng), realDist(rng),
- realDist(rng), realDist(rng), realDist(rng));
-
- CPPUNIT_ASSERT(result.xAngle >= ANGLE_MINIMUM);
- CPPUNIT_ASSERT(result.xAngle <= ANGLE_MAXIMUM);
- CPPUNIT_ASSERT(result.yAngle >= ANGLE_MINIMUM);
- CPPUNIT_ASSERT(result.yAngle <= ANGLE_MAXIMUM);
- CPPUNIT_ASSERT(result.zAngle >= 0);
- CPPUNIT_ASSERT(result.zAngle <= ANGLE_MAXIMUM);
- CPPUNIT_ASSERT(result.xPosition >= MINIMUM);
- CPPUNIT_ASSERT(result.xPosition <= MAXIMUM);
- CPPUNIT_ASSERT(result.yPosition >= MINIMUM);
- CPPUNIT_ASSERT(result.yPosition <= MAXIMUM);
- CPPUNIT_ASSERT(result.zPosition >= MINIMUM);
- CPPUNIT_ASSERT(result.zPosition <= MAXIMUM);
- }
- }
-
- void tearDown() override
- {
- m_XmlProbePointSource = "";
- m_XmlProbeCircleSource = "";
- m_XmlProbeRectangleSource = "";
- m_XmlProbeTwoPointSources = "";
- m_XmlProbeAllSources = "";
- m_Probe = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkMcxyzXml)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacoustic3dVolumeTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacoustic3dVolumeTest.cpp
deleted file mode 100644
index 8452bdc5b7..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacoustic3dVolumeTest.cpp
+++ /dev/null
@@ -1,220 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include "mitkPAVolume.h"
-#include <mitkImage.h>
-#include <mitkImageReadAccessor.h>
-
-class mitkPhotoacoustic3dVolumeTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacoustic3dVolumeTestSuite);
- MITK_TEST(TestCorrectGetDataAndSetDataBehavior);
- MITK_TEST(TestCallingConstructorWithNullParameter);
- MITK_TEST(TestCallingConstructorWithCorrectParameters);
- MITK_TEST(TestModifyImage);
- MITK_TEST(TestModifyComplexImage);
- MITK_TEST(TestConvertToMitkImage);
- MITK_TEST(TestDeepCopy);
- MITK_TEST(TestCatchException);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::pa::Volume::Pointer m_Photoacoustic3dVolume;
-
-public:
-
- void setUp() override
- {
- }
-
- void TestCallingConstructorWithNullParameter()
- {
- bool exceptionEncountered = false;
- try
- {
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(nullptr, 3, 3, 3, 1);
- }
- catch (...)
- {
- exceptionEncountered = true;
- }
- CPPUNIT_ASSERT(exceptionEncountered);
- }
-
- void TestCallingConstructorWithCorrectParameters()
- {
- auto* data = new double[1];
- data[0] = 3;
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(data, 1, 1, 1, 1);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 0) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetXDim() == 1);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetYDim() == 1);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetZDim() == 1);
- }
-
- void TestModifyImage()
- {
- auto* data = new double[1];
- data[0] = 3;
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(data, 1, 1, 1, 1);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_Photoacoustic3dVolume->GetData(0, 0, 0)), m_Photoacoustic3dVolume->GetData(0, 0, 0) == 3);
- m_Photoacoustic3dVolume->SetData(17, 0, 0, 0);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 0) == 17);
- }
-
- void TestModifyComplexImage()
- {
- unsigned int xDim = 4;
- unsigned int yDim = 7;
- unsigned int zDim = 12;
- unsigned int length = xDim * yDim * zDim;
- auto* data = new double[length];
- for (unsigned int i = 0; i < length; i++)
- data[i] = 5;
-
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(data, xDim, yDim, zDim, 1);
-
- for (unsigned int z = 0; z < zDim; z++)
- for (unsigned int y = 0; y < yDim; y++)
- for (unsigned int x = 0; x < xDim; x++)
- {
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(x, y, z) == 5);
- m_Photoacoustic3dVolume->SetData((x + y)*(z + 1), x, y, z);
- CPPUNIT_ASSERT(std::abs(m_Photoacoustic3dVolume->GetData(x, y, z) - (x + y)*(z + 1)) < mitk::eps);
- }
- }
-
- void TestCorrectGetDataAndSetDataBehavior()
- {
- unsigned int xDim = 40;
- unsigned int yDim = 7;
- unsigned int zDim = 12;
- unsigned int length = xDim * yDim * zDim;
- auto* data = new double[length];
- for (unsigned int i = 0; i < length; i++)
- data[i] = 0;
-
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(data, xDim, yDim, zDim, 1);
-
- for (unsigned int z = 0; z < zDim; z++)
- for (unsigned int y = 0; y < yDim; y++)
- for (unsigned int x = 0; x < xDim; x++)
- {
- int index = z*xDim*yDim + x*yDim + y;
- m_Photoacoustic3dVolume->SetData(index, x, y, z);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(index), m_Photoacoustic3dVolume->GetData(x, y, z) == index);
- }
- }
-
- void TestConvertToMitkImage()
- {
- auto* data = new double[6];
- data[0] = 3;
- data[1] = 3;
- data[2] = 3;
- data[3] = 3;
- data[4] = 3;
- data[5] = 3;
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(data, 1, 2, 3, 1);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 0) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 1) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 2) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 1, 0) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 1, 1) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 1, 2) == 3);
-
- m_Photoacoustic3dVolume->SetData(17, 0, 0, 0);
- m_Photoacoustic3dVolume->SetData(17, 0, 1, 0);
- m_Photoacoustic3dVolume->SetData(17, 0, 1, 2);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 0) == 17);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 1) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 2) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 1, 0) == 17);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 1, 1) == 3);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 1, 2) == 17);
-
- mitk::Image::Pointer mitkImage = m_Photoacoustic3dVolume->AsMitkImage();
- CPPUNIT_ASSERT(mitkImage->GetDimensions()[0] == 2);
- CPPUNIT_ASSERT(mitkImage->GetDimensions()[1] == 1);
- CPPUNIT_ASSERT(mitkImage->GetDimensions()[2] == 3);
-
- mitk::ImageReadAccessor readAccess(mitkImage, mitkImage->GetVolumeData());
- auto* copyData = (double*)readAccess.GetData();
- CPPUNIT_ASSERT_MESSAGE(std::to_string(copyData[0]), copyData[0] == 17);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(copyData[1]), copyData[1] == 17);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(copyData[2]), copyData[2] == 3);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(copyData[3]), copyData[3] == 3);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(copyData[4]), copyData[4] == 3);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(copyData[5]), copyData[5] == 17);
- }
-
- void TestDeepCopy()
- {
- auto* data = new double[1];
- data[0] = 3;
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(data, 1, 1, 1, 1);
- mitk::pa::Volume::Pointer copiedVolume = m_Photoacoustic3dVolume->DeepCopy();
-
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetXDim() == copiedVolume->GetXDim());
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetYDim() == copiedVolume->GetYDim());
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetZDim() == copiedVolume->GetZDim());
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 0) == 3);
- CPPUNIT_ASSERT(copiedVolume->GetData(0, 0, 0) == 3);
- m_Photoacoustic3dVolume->SetData(17, 0, 0, 0);
- CPPUNIT_ASSERT(m_Photoacoustic3dVolume->GetData(0, 0, 0) == 17);
- CPPUNIT_ASSERT(copiedVolume->GetData(0, 0, 0) == 3);
- }
-
- void AssertIndexException(unsigned int x, unsigned int y, unsigned int z)
- {
- bool exceptionCaught = false;
- try
- {
- double thisIsIrrelevant = m_Photoacoustic3dVolume->GetData(x, y, z);
- thisIsIrrelevant += 1;
- }
- catch (...)
- {
- exceptionCaught = true;
- if (exceptionCaught)
- exceptionCaught = true;
- }
-#ifdef _DEBUG
-
- CPPUNIT_ASSERT(exceptionCaught);
-
-#endif
- }
-
- void TestCatchException()
- {
- auto* data = new double[1];
- data[0] = 3;
- m_Photoacoustic3dVolume = mitk::pa::Volume::New(data, 1, 1, 1, 1);
-
- AssertIndexException(1, 0, 0);
- AssertIndexException(0, 1, 0);
- AssertIndexException(0, 0, 1);
- AssertIndexException(18, 1, 222);
- }
-
- void tearDown() override
- {
- m_Photoacoustic3dVolume = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacoustic3dVolume)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticComposedVolumeTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticComposedVolumeTest.cpp
deleted file mode 100644
index 5d5b05a955..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticComposedVolumeTest.cpp
+++ /dev/null
@@ -1,145 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include "mitkPAComposedVolume.h"
-#include "mitkIOUtil.h"
-#include "mitkImageReadAccessor.h"
-#include <string>
-
-class mitkPhotoacousticComposedVolumeTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticComposedVolumeTestSuite);
- MITK_TEST(TestCreateAndDestructComposedVolume);
- MITK_TEST(TestAccessInvalidFluenceComponent);
- MITK_TEST(TestAccessInvalidFluenceComponentIndex);
- MITK_TEST(TestAddMultiplePairs);
- MITK_TEST(TestSortFunctionality);
- MITK_TEST(TestAccessInvalidFluenceComponentForYOffset);
- CPPUNIT_TEST_SUITE_END();
-
-private:
- mitk::pa::ComposedVolume::Pointer m_ComposedVolume;
- mitk::pa::TissueGeneratorParameters::Pointer m_DefaultParameters;
- mitk::pa::InSilicoTissueVolume::Pointer m_InSilicoTissueVolume;
-
-public:
-
- void setUp() override
- {
- m_DefaultParameters = mitk::pa::TissueGeneratorParameters::New();
- m_DefaultParameters->SetXDim(5);
- m_DefaultParameters->SetYDim(5);
- m_DefaultParameters->SetZDim(5);
- auto rng = std::mt19937();
- m_InSilicoTissueVolume = mitk::pa::InSilicoTissueVolume::New(m_DefaultParameters, &rng);
- m_ComposedVolume = mitk::pa::ComposedVolume::New(m_InSilicoTissueVolume);
- }
-
- mitk::pa::FluenceYOffsetPair::Pointer createFluenceYOffsetPair(double value, double yOffset)
- {
- auto* data = new double[125];
- for (int i = 0; i < 125; ++i)
- data[i] = value;
- mitk::pa::Volume::Pointer volume = mitk::pa::Volume::New(data, 5, 5, 5, 1);
- return mitk::pa::FluenceYOffsetPair::New(volume, yOffset);
- }
-
- void TestCreateAndDestructComposedVolume()
- {
- CPPUNIT_ASSERT(m_ComposedVolume->GetNumberOfFluenceComponents() == 0);
- }
-
- void TestAccessInvalidFluenceComponent()
- {
- bool caughtException = false;
- try
- {
- m_ComposedVolume->GetFluenceValue(0, 0, 0, 0);
- }
- catch (const mitk::Exception &)
- {
- caughtException = true;
- }
- CPPUNIT_ASSERT(caughtException);
- }
-
- void TestAddMultiplePairs()
- {
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(0, 0));
- CPPUNIT_ASSERT(m_ComposedVolume->GetNumberOfFluenceComponents() == 1);
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(1, 1));
- CPPUNIT_ASSERT(m_ComposedVolume->GetNumberOfFluenceComponents() == 2);
- }
-
- void TestSortFunctionality()
- {
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(2, 2));
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(-1, -1));
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(1, 1));
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(0, 0));
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(-2, -2));
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(0, 0, 2, 0) == 2);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(1, 0, 2, 0) == -1);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(2, 0, 2, 0) == 1);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(3, 0, 2, 0) == 0);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(4, 0, 2, 0) == -2);
-
- m_ComposedVolume->Sort();
-
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(0, 0, 2, 0) == -2);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(1, 0, 2, 0) == -1);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(2, 0, 2, 0) == 0);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(3, 0, 2, 0) == 1);
- CPPUNIT_ASSERT(m_ComposedVolume->GetFluenceValue(4, 0, 2, 0) == 2);
- }
-
- void TestAccessInvalidFluenceComponentIndex()
- {
-#ifdef _DEBUG
- m_ComposedVolume->AddSlice(createFluenceYOffsetPair(0, 0));
- bool caughtException = false;
- try
- {
- double unusedValue = m_ComposedVolume->GetFluenceValue(0, 1, 2, 300);
- unusedValue = 0;
- }
- catch (const mitk::Exception e)
- {
- caughtException = true;
- }
- CPPUNIT_ASSERT(caughtException);
-#endif
- }
-
- void TestAccessInvalidFluenceComponentForYOffset()
- {
- bool caughtException = false;
- try
- {
- m_ComposedVolume->GetYOffsetForFluenceComponentInPixels(0);
- }
- catch (const mitk::Exception &)
- {
- caughtException = true;
- }
- CPPUNIT_ASSERT(caughtException);
- }
-
- void tearDown() override
- {
- m_ComposedVolume = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticComposedVolume)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticIOTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticIOTest.cpp
deleted file mode 100644
index c242b55f46..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticIOTest.cpp
+++ /dev/null
@@ -1,185 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPAVesselTree.h>
-#include <mitkPAIOUtil.h>
-#include <mitkIOUtil.h>
-#include <mitkCoreServices.h>
-#include <mitkPropertyPersistence.h>
-#include <mitkPropertyPersistenceInfo.h>
-#include <itkFileTools.h>
-
-class mitkPhotoacousticIOTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticIOTestSuite);
- MITK_TEST(testLoadInSilicoTissueNrrdFile);
- MITK_TEST(testLoad3DVolumeNrrdFile);
- MITK_TEST(testLoad3DVolumeNrrdFileWithBlur);
- MITK_TEST(testGetNumberOfNrrdFilesInTestDir);
- MITK_TEST(testGetChildFoldersFromFolder);
- MITK_TEST(testLoadFCMs);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- const std::string TEST_FOLDER_PATH = "testFiles/";
- const std::string TEST_IN_SILICO_VOLUME_PATH = "testInSilicoVolume";
- const std::string TEST_3D_Volume_PATH = "test3DVolume";
- const std::string TEST_FILE_ENDING = ".nrrd";
- const std::string TEST_QUALIFIED_FOLDER_PATH = TEST_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + "/";
- const std::string FOLDER_FOLDER = "folder/";
- const std::string FCM_PATH = TEST_FOLDER_PATH + "fcms/";
- const int NUMBER_OF_NRRD_FILES_IN_TEST_DIR = 2;
- mitk::pa::TissueGeneratorParameters::Pointer m_VolumeProperties;
- mitk::pa::InSilicoTissueVolume::Pointer m_TestInSilicoVolume;
- mitk::pa::Volume::Pointer m_Test3DVolume;
-
-public:
-
- void setUp() override
- {
- m_VolumeProperties = createTestVolumeParameters();
- auto rng = std::mt19937();
- m_TestInSilicoVolume = mitk::pa::InSilicoTissueVolume::New(m_VolumeProperties, &rng);
- m_Test3DVolume = createTest3DVolume(5);
- itk::FileTools::CreateDirectory(TEST_FOLDER_PATH);
- itk::FileTools::CreateDirectory(TEST_QUALIFIED_FOLDER_PATH);
- itk::FileTools::CreateDirectory(TEST_FOLDER_PATH + FOLDER_FOLDER + FOLDER_FOLDER);
- itk::FileTools::CreateDirectory(FCM_PATH);
- CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(TEST_FOLDER_PATH));
- CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(TEST_QUALIFIED_FOLDER_PATH));
- CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(TEST_FOLDER_PATH + FOLDER_FOLDER + FOLDER_FOLDER));
- CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(FCM_PATH));
-
- mitk::IOUtil::Save(m_TestInSilicoVolume->ConvertToMitkImage(),
- TEST_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + TEST_FILE_ENDING);
- mitk::IOUtil::Save(m_Test3DVolume->AsMitkImage(),
- TEST_FOLDER_PATH + TEST_3D_Volume_PATH + TEST_FILE_ENDING);
- auto yo0 = createTest3DVolume(1)->AsMitkImage();
- auto yo1 = createTest3DVolume(2)->AsMitkImage();
-
- yo0->GetPropertyList()->SetStringProperty("y-offset", "0");
- yo1->GetPropertyList()->SetStringProperty("y-offset", "1");
- mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New("y-offset"));
-
- mitk::IOUtil::Save(yo0, TEST_QUALIFIED_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + "_yo0" + TEST_FILE_ENDING);
- mitk::IOUtil::Save(yo1, TEST_QUALIFIED_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + "_yo1" + TEST_FILE_ENDING);
- }
-
- mitk::pa::Volume::Pointer createTest3DVolume(double value)
- {
- unsigned int xDim = 10;
- unsigned int yDim = 10;
- unsigned int zDim = 10;
- unsigned int length = xDim * yDim * zDim;
- auto* data = new double[length];
- for (unsigned int i = 0; i < length; i++)
- data[i] = value;
-
- return mitk::pa::Volume::New(data, xDim, yDim, zDim, 1);
- }
-
- mitk::pa::TissueGeneratorParameters::Pointer createTestVolumeParameters()
- {
- auto returnParameters = mitk::pa::TissueGeneratorParameters::New();
- returnParameters->SetXDim(10);
- returnParameters->SetYDim(10);
- returnParameters->SetZDim(10);
- returnParameters->SetMinBackgroundAbsorption(0);
- returnParameters->SetMaxBackgroundAbsorption(0);
- returnParameters->SetBackgroundScattering(0);
- returnParameters->SetBackgroundAnisotropy(0);
- return returnParameters;
- }
-
- void assertEqual(mitk::pa::Volume::Pointer first, mitk::pa::Volume::Pointer second)
- {
- CPPUNIT_ASSERT(first->GetXDim() == second->GetXDim());
- CPPUNIT_ASSERT(first->GetYDim() == second->GetYDim());
- CPPUNIT_ASSERT(first->GetZDim() == second->GetZDim());
- for (unsigned int x = 0; x < first->GetXDim(); ++x)
- for (unsigned int y = 0; y < first->GetYDim(); ++y)
- for (unsigned int z = 0; z < first->GetZDim(); ++z)
- {
- std::string message = "Expected " + std::to_string(first->GetData(x, y, z)) + " but was " + std::to_string(second->GetData(x, y, z));
- CPPUNIT_ASSERT_MESSAGE(message, std::abs(first->GetData(x, y, z) - second->GetData(x, y, z)) < 1e-6);
- }
- }
-
- void testLoadInSilicoTissueNrrdFile()
- {
- auto loadedVolume = mitk::pa::IOUtil::LoadInSilicoTissueVolumeFromNrrdFile(TEST_FOLDER_PATH + TEST_IN_SILICO_VOLUME_PATH + TEST_FILE_ENDING);
- CPPUNIT_ASSERT(loadedVolume->GetTDim() == m_TestInSilicoVolume->GetTDim());
- assertEqual(m_TestInSilicoVolume->GetAbsorptionVolume(), loadedVolume->GetAbsorptionVolume());
- assertEqual(m_TestInSilicoVolume->GetScatteringVolume(), loadedVolume->GetScatteringVolume());
- assertEqual(m_TestInSilicoVolume->GetAnisotropyVolume(), loadedVolume->GetAnisotropyVolume());
- }
-
- void testLoad3DVolumeNrrdFile()
- {
- auto loadedVolume = mitk::pa::IOUtil::LoadNrrd(TEST_FOLDER_PATH + TEST_3D_Volume_PATH + TEST_FILE_ENDING);
- assertEqual(loadedVolume, m_Test3DVolume);
- }
-
- void testLoad3DVolumeNrrdFileWithBlur()
- {
- auto loadedVolume = mitk::pa::IOUtil::LoadNrrd(TEST_FOLDER_PATH + TEST_3D_Volume_PATH + TEST_FILE_ENDING, 1);
- assertEqual(loadedVolume, m_Test3DVolume);
- }
-
- void testGetNumberOfNrrdFilesInTestDir()
- {
- int numberOfFiles = mitk::pa::IOUtil::GetNumberOfNrrdFilesInDirectory(TEST_FOLDER_PATH);
- CPPUNIT_ASSERT(numberOfFiles == NUMBER_OF_NRRD_FILES_IN_TEST_DIR);
- }
-
- void testGetChildFoldersFromFolder()
- {
- std::vector<std::string> childFolders = mitk::pa::IOUtil::GetAllChildfoldersFromFolder(TEST_FOLDER_PATH);
- CPPUNIT_ASSERT(childFolders.size() == 1);
- CPPUNIT_ASSERT(childFolders[0] == TEST_FOLDER_PATH);
- childFolders = mitk::pa::IOUtil::GetAllChildfoldersFromFolder(TEST_FOLDER_PATH + FOLDER_FOLDER);
- MITK_INFO << "ChildFolders: " << childFolders.size();
- CPPUNIT_ASSERT(childFolders.size() == 1);
- CPPUNIT_ASSERT(childFolders[0] == TEST_FOLDER_PATH + FOLDER_FOLDER + "/folder");
- }
-
- void testLoadFCMs()
- {
- auto fcm1 = createTest3DVolume(1);
- auto fcm2 = createTest3DVolume(2);
- auto fcm3 = createTest3DVolume(3);
- auto fcm4 = createTest3DVolume(4);
- mitk::IOUtil::Save(fcm1->AsMitkImage(), FCM_PATH + "fcm1_p0,0,0FluenceContributionMap.nrrd");
- mitk::IOUtil::Save(fcm2->AsMitkImage(), FCM_PATH + "fcm1_p0,0,1FluenceContributionMap.nrrd");
- mitk::IOUtil::Save(fcm3->AsMitkImage(), FCM_PATH + "fcm1_p1,0,0FluenceContributionMap.nrrd");
- mitk::IOUtil::Save(fcm4->AsMitkImage(), FCM_PATH + "fcm1_p1,0,1FluenceContributionMap.nrrd");
-
- int prog = 0;
- auto map = mitk::pa::IOUtil::LoadFluenceContributionMaps(FCM_PATH, 0, &prog);
-
- assertEqual(fcm1, map[mitk::pa::IOUtil::Position{ 0,0 }]);
- assertEqual(fcm2, map[mitk::pa::IOUtil::Position{ 0,1 }]);
- assertEqual(fcm3, map[mitk::pa::IOUtil::Position{ 1,0 }]);
- assertEqual(fcm4, map[mitk::pa::IOUtil::Position{ 1,1 }]);
- }
-
- void tearDown() override
- {
- //CPPUNIT_ASSERT_MESSAGE("Resource leak of test files onto hard drive..", itksys::SystemTools::RemoveADirectory(TEST_FOLDER_PATH) == true);
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticIO)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticNoiseGeneratorTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticNoiseGeneratorTest.cpp
deleted file mode 100644
index 38a5b5f3ce..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticNoiseGeneratorTest.cpp
+++ /dev/null
@@ -1,67 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkImageReadAccessor.h>
-
-#include "mitkPAVolume.h"
-#include "mitkPANoiseGenerator.h"
-
-class mitkPhotoacousticNoiseGeneratorTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticNoiseGeneratorTestSuite);
- MITK_TEST(testNoiseGenerator);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
-public:
-
- mitk::pa::Volume::Pointer m_Volume;
-
- void setUp() override
- {
- }
-
- void testNoiseGenerator()
- {
- int size = 1000 * 100 * 100;
- auto* volume = new double[size];
- for (int i = 0; i < size; i++)
- {
- volume[i] = 1;
- }
- m_Volume = mitk::pa::Volume::New(volume, 1000, 100, 100, 1);
- mitk::pa::NoiseGenerator::ApplyNoiseModel(m_Volume, 0.75, 0.1);
-
- int negativecounter = 0;
-
- for (int i = 0; i < size; i++)
- {
- if (m_Volume->GetData()[i] <= 0)
- {
- negativecounter++;
- }
- }
- CPPUNIT_ASSERT_EQUAL_MESSAGE("More than one negative: " +
- std::to_string(negativecounter) + " (" +
- std::to_string((((double)negativecounter) / size) * 100) + "%)", negativecounter, 0);
- }
-
- void tearDown() override
- {
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticNoiseGenerator)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticTissueGeneratorTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticTissueGeneratorTest.cpp
deleted file mode 100644
index 7168f292fa..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticTissueGeneratorTest.cpp
+++ /dev/null
@@ -1,81 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include "mitkPATissueGenerator.h"
-
-class mitkPhotoacousticTissueGeneratorTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticTissueGeneratorTestSuite);
- MITK_TEST(testCallWithEmptyParameters);
- MITK_TEST(testCallWithWorkingParameters);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
-public:
-
- void setUp() override
- {
- }
-
- mitk::pa::TissueGeneratorParameters::Pointer createRandomTestVolumeParameters()
- {
- auto returnParameters = mitk::pa::TissueGeneratorParameters::New();
-
- returnParameters->SetXDim(rand() % 50 + 1);
- returnParameters->SetYDim(rand() % 50 + 1);
- returnParameters->SetZDim(rand() % 50 + 1);
- double absorb = rand() % 100 / 10.0;
- returnParameters->SetMinBackgroundAbsorption(absorb);
- returnParameters->SetMaxBackgroundAbsorption(absorb);
- returnParameters->SetBackgroundScattering(rand() % 100 / 10.0);
- returnParameters->SetBackgroundAnisotropy(rand() % 100 / 10.0);
- int min = rand() % 10;
- returnParameters->SetMinNumberOfVessels(min);
- returnParameters->SetMaxNumberOfVessels(min + (rand() % 10));
- returnParameters->SetCalculateNewVesselPositionCallback(
- &mitk::pa::VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
- returnParameters->SetMinVesselZOrigin(rand() % 3 + 1);
- returnParameters->SetMaxVesselZOrigin(rand() % 3 + 1);
- int minRad = rand() % 100;
- returnParameters->SetMinVesselRadiusInMillimeters(minRad);
- returnParameters->SetMaxVesselRadiusInMillimeters(minRad + (rand() % 100));
- returnParameters->SetVoxelSpacingInCentimeters(1);
- return returnParameters;
- }
-
- void testCallWithEmptyParameters()
- {
- auto parameters = mitk::pa::TissueGeneratorParameters::New();
- auto volume = mitk::pa::InSilicoTissueGenerator::GenerateInSilicoData(parameters);
- CPPUNIT_ASSERT(volume.IsNotNull());
- }
-
- void testCallWithWorkingParameters()
- {
- for (int i = 0; i < 20; i++)
- {
- auto parameters = createRandomTestVolumeParameters();
- auto volume = mitk::pa::InSilicoTissueGenerator::GenerateInSilicoData(parameters);
- CPPUNIT_ASSERT(volume.IsNotNull());
- }
- }
-
- void tearDown() override
- {
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticTissueGenerator)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVectorTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticVectorTest.cpp
deleted file mode 100644
index ac579e29b6..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVectorTest.cpp
+++ /dev/null
@@ -1,254 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include "mitkPAVector.h"
-
-class mitkPhotoacousticVectorTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticVectorTestSuite);
-
- MITK_TEST(TestNormalizeVector);
- MITK_TEST(TestRotateVectorZeroDegrees);
- MITK_TEST(TestRotatedVectorPositiveDegrees);
- MITK_TEST(TestRotateVectorZeroDegrees);
- MITK_TEST(TestScaleVector);
- MITK_TEST(TestCloneVector);
-
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::pa::Vector::Pointer m_TestVector;
- mitk::pa::Vector::Pointer m_TestReturnVector;
-
- const double DIF_VAL = 0.001;
- const double TWO_PI = 6.283185;
-
-public:
-
- void setUp() override
- {
- m_TestVector = mitk::pa::Vector::New();
- m_TestReturnVector = mitk::pa::Vector::New();
- }
-
- void TestNormalizeVector()
- {
- std::stringstream output;
- int a = 2;
- int b = 3;
- int c = 4;
-
- m_TestVector->SetElement(0, a);
- m_TestVector->SetElement(1, b);
- m_TestVector->SetElement(2, c);
-
- output << "The vectorlength should be";
- output << sqrt(a*a + b*b + c*c);
- CPPUNIT_ASSERT_EQUAL_MESSAGE(output.str(), sqrt(a*a + b*b + c*c), m_TestVector->GetNorm());
- output.flush();
-
- m_TestVector->Normalize();
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vectorlength should be 1.", true, m_TestVector->GetNorm() - 1 < DIF_VAL);
- }
-
- void TestRotateVectorZeroDegrees()
- {
- int a = 1;
- int b = 2;
- int c = 3;
-
- double length;
-
- m_TestVector->SetElement(0, a);
- m_TestVector->SetElement(1, b);
- m_TestVector->SetElement(2, c);
-
- length = m_TestVector->GetNorm();
-
- m_TestVector->Rotate(0, 0);
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector length should be equal", length, m_TestVector->GetNorm());
-
- CPPUNIT_ASSERT_MESSAGE("The vector value at index0 should be 1.0", m_TestVector->GetElement(0) - 1 < DIF_VAL);
- CPPUNIT_ASSERT_MESSAGE("The vector value at index1 should be 2.0", m_TestVector->GetElement(1) - 2 < DIF_VAL);
- CPPUNIT_ASSERT_MESSAGE("The vector value at index2 should be 3.0", m_TestVector->GetElement(2) - 3 < DIF_VAL);
- }
-
- void TestRotatedVectorPositiveDegrees()
- {
- MITK_INFO << atan2(0, 0);
-
- for (int r = 0; r < 10; r++)
- {
- for (double phi = 0.1; phi < 3; phi += 0.1)
- {
- for (double theta = 0.1; theta < 3; theta += 0.1)
- {
- double rotateTheta = 0.1;
- double rotatePhi = 0.1;
-
- m_TestVector->SetElement(0, r * sin(theta) * cos(phi));
- m_TestVector->SetElement(1, r * sin(theta) * sin(phi));
- m_TestVector->SetElement(2, r * cos(theta));
-
- m_TestVector->Rotate(rotateTheta, rotatePhi);
-
- double newTheta = fmod(theta + rotateTheta, TWO_PI);
- double newPhi = fmod(phi + rotatePhi, TWO_PI);
-
- double expectedX = r * sin(newTheta) * cos(newPhi);
- double expectedY = r * sin(newTheta) * sin(newPhi);
- double expectedZ = r * cos(newTheta);
-
- CPPUNIT_ASSERT_MESSAGE("The vector value at index0 should be " + std::to_string(expectedX) + " but was " + std::to_string(m_TestVector->GetElement(0))
- + " at r=" + std::to_string(r) + " phi=" + std::to_string(phi) + " theta=" + std::to_string(theta),
- m_TestVector->GetElement(0) - expectedX < DIF_VAL);
- CPPUNIT_ASSERT_MESSAGE("The vector value at index1 should be " + std::to_string(expectedY) + " but was " + std::to_string(m_TestVector->GetElement(0))
- + " at r=" + std::to_string(r) + " phi=" + std::to_string(phi) + " theta=" + std::to_string(theta),
- m_TestVector->GetElement(1) - expectedY < DIF_VAL);
- CPPUNIT_ASSERT_MESSAGE("The vector value at index2 should be " + std::to_string(expectedZ) + " but was " + std::to_string(m_TestVector->GetElement(0))
- + " at r=" + std::to_string(r) + " phi=" + std::to_string(phi) + " theta=" + std::to_string(theta),
- m_TestVector->GetElement(2) - expectedZ < DIF_VAL);
- }
- }
- }
- }
-
- void TestRotatedVectorNegativeDegrees()
- {
- for (int r = 0; r < 10; r++)
- {
- for (double phi = -0.1; phi > -3; phi -= 0.1)
- {
- for (double theta = -0.1; theta > -3; theta -= 0.1)
- {
- double rotateTheta = -0.1;
- double rotatePhi = -0.1;
-
- m_TestVector->SetElement(0, r * sin(theta) * cos(phi));
- m_TestVector->SetElement(1, r * sin(theta) * sin(phi));
- m_TestVector->SetElement(2, r * cos(theta));
-
- m_TestVector->Rotate(rotateTheta, rotatePhi);
-
- double newTheta = fmod(theta + rotateTheta, TWO_PI);
- double newPhi = fmod(phi + rotatePhi, TWO_PI);
-
- double expectedX = r * sin(newTheta) * cos(newPhi);
- double expectedY = r * sin(newTheta) * sin(newPhi);
- double expectedZ = r * cos(newTheta);
-
- CPPUNIT_ASSERT_MESSAGE("The vector value at index0 should be " + std::to_string(expectedX) + " but was " + std::to_string(m_TestVector->GetElement(0))
- + " at r=" + std::to_string(r) + " phi=" + std::to_string(phi) + " theta=" + std::to_string(theta),
- m_TestVector->GetElement(0) - expectedX < DIF_VAL);
- CPPUNIT_ASSERT_MESSAGE("The vector value at index1 should be " + std::to_string(expectedY) + " but was " + std::to_string(m_TestVector->GetElement(0))
- + " at r=" + std::to_string(r) + " phi=" + std::to_string(phi) + " theta=" + std::to_string(theta),
- m_TestVector->GetElement(1) - expectedY < DIF_VAL);
- CPPUNIT_ASSERT_MESSAGE("The vector value at index2 should be " + std::to_string(expectedZ) + " but was " + std::to_string(m_TestVector->GetElement(0))
- + " at r=" + std::to_string(r) + " phi=" + std::to_string(phi) + " theta=" + std::to_string(theta),
- m_TestVector->GetElement(2) - expectedZ < DIF_VAL);
- }
- }
- }
- }
-
- void TestScaleVector()
- {
- double a = 1.0;
- double b = 2.0;
- double c = 3.0;
-
- for (double testFactor = -2.0; testFactor <= 2.0; testFactor += 0.3)
- {
- double potElement0Fctr;
- double potElement1Fctr;
- double potElement2Fctr;
-
- std::stringstream output;
-
- m_TestVector->SetElement(0, a);
- m_TestVector->SetElement(1, b);
- m_TestVector->SetElement(2, c);
-
- potElement0Fctr = (m_TestVector->GetElement(0)*testFactor)*(m_TestVector->GetElement(0)*testFactor);
- potElement1Fctr = (m_TestVector->GetElement(1)*testFactor)*(m_TestVector->GetElement(1)*testFactor);
- potElement2Fctr = (m_TestVector->GetElement(2)*testFactor)*(m_TestVector->GetElement(2)*testFactor);
-
- m_TestVector->Scale(testFactor);
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector length should not be equal",
- sqrt(potElement0Fctr + potElement1Fctr + potElement2Fctr), m_TestVector->GetNorm());
-
- output << "The vector value at index0 should be";
- output << a*testFactor;
- CPPUNIT_ASSERT_EQUAL_MESSAGE(output.str(), a*testFactor, m_TestVector->GetElement(0));
- output.flush();
-
- output << "The vector value at index1 should be";
- output << b*testFactor;
- CPPUNIT_ASSERT_EQUAL_MESSAGE(output.str(), b*testFactor, m_TestVector->GetElement(1));
- output.flush();
-
- output << "The vector value at index2 should be";
- output << c*testFactor;
- CPPUNIT_ASSERT_EQUAL_MESSAGE(output.str(), c*testFactor, m_TestVector->GetElement(2));
- output.flush();
- }
- }
-
- void TestCloneVector()
- {
- int a = 1;
- int b = 2;
- int c = 3;
-
- m_TestVector->SetElement(0, a);
- m_TestVector->SetElement(1, b);
- m_TestVector->SetElement(2, c);
-
- m_TestReturnVector = m_TestVector->Clone();
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector length should be equal", (m_TestVector->GetNorm()), m_TestReturnVector->GetNorm());
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index0 should be equal", m_TestVector->GetElement(0), m_TestReturnVector->GetElement(0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index1 should be equal", m_TestVector->GetElement(1), m_TestReturnVector->GetElement(1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index2 should be equal", m_TestVector->GetElement(2), m_TestReturnVector->GetElement(2));
-
- m_TestReturnVector->Rotate(itk::Math::pi / 4, itk::Math::pi / 4);
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index0 should be not equal", true, m_TestVector->GetElement(0) != m_TestReturnVector->GetElement(0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index0 should be not equal", true, m_TestVector->GetElement(1) != m_TestReturnVector->GetElement(1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index0 should be not equal", true, m_TestVector->GetElement(2) != m_TestReturnVector->GetElement(2));
-
- for (double testFactor = -2.0; testFactor <= 2.0; testFactor += 0.3)
- {
- m_TestReturnVector->Scale(testFactor);
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index0 should be not equal", true, m_TestVector->GetElement(0) != m_TestReturnVector->GetElement(0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index0 should be not equal", true, m_TestVector->GetElement(1) != m_TestReturnVector->GetElement(1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("The vector value at index0 should be not equal", true, m_TestVector->GetElement(2) != m_TestReturnVector->GetElement(2));
- }
- }
-
- void tearDown() override
- {
- m_TestVector = nullptr;
- m_TestReturnVector = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticVector)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselMeanderStrategyTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselMeanderStrategyTest.cpp
deleted file mode 100644
index 717c60ede0..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselMeanderStrategyTest.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkImageReadAccessor.h>
-
-#include "mitkPAInSilicoTissueVolume.h"
-#include "mitkPATissueGenerator.h"
-#include "mitkPAVesselMeanderStrategy.h"
-
-class mitkPhotoacousticVesselMeanderStrategyTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticVesselMeanderStrategyTestSuite);
- MITK_TEST(TestCalculateNewPositionInStraightLine);
-
- CPPUNIT_TEST_SUITE_END();
-
-private:
- mitk::pa::VesselMeanderStrategy::Pointer m_TestStrategy;
- mitk::pa::Vector::Pointer m_TestDirection;
-
-public:
-
- void setUp() override
- {
- m_TestStrategy = mitk::pa::VesselMeanderStrategy::New();
- m_TestDirection = mitk::pa::Vector::New();
- }
-
- void TestCalculateNewPositionInStraightLine()
- {
- int d = 3;
- int e = 4;
- int f = 5;
-
- for (int i = -2; i <= 2; i++)
- {
- if (i == 0)
- {
- i++;
- }
-
- for (int j = -2; j <= 2; j++)
- {
- if (j == 0)
- {
- j++;
- }
-
- m_TestDirection->SetElement(0, d*j);
- m_TestDirection->SetElement(1, e*j);
- m_TestDirection->SetElement(2, f*j);
-
- mitk::pa::Vector::Pointer directionBefore = m_TestDirection->Clone();
- m_TestStrategy->CalculateNewDirectionVectorInStraightLine(m_TestDirection, 0, nullptr);
- CPPUNIT_ASSERT(mitk::pa::Equal(directionBefore, m_TestDirection, 1e-6, false));
- }
- }
- }
-
- void tearDown() override
- {
- m_TestStrategy = nullptr;
- m_TestDirection = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticVesselMeanderStrategy)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselTest.cpp
deleted file mode 100644
index ac144f5b57..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselTest.cpp
+++ /dev/null
@@ -1,180 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkImageReadAccessor.h>
-
-#include "mitkPAInSilicoTissueVolume.h"
-#include "mitkPAVector.h"
-#include "mitkPAVessel.h"
-
-class mitkPhotoacousticVesselTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticVesselTestSuite);
- MITK_TEST(testEmptyInitializationProperties);
- MITK_TEST(testWalkInStraightLine);
- MITK_TEST(testBifurcate);
- CPPUNIT_TEST_SUITE_END();
-
-private:
- mitk::pa::Vessel::Pointer m_TestVessel;
- mitk::pa::Vessel::CalculateNewVesselPositionCallback m_StraightLine;
- mitk::pa::Vessel::CalculateNewVesselPositionCallback m_Diverging;
- mitk::pa::InSilicoTissueVolume::Pointer m_TestInSilicoVolume;
- mitk::pa::TissueGeneratorParameters::Pointer m_TestVolumeParameters;
-
-public:
-
- void setUp() override
- {
- auto params = mitk::pa::VesselProperties::New();
- m_TestVessel = mitk::pa::Vessel::New(params);
- m_StraightLine = &mitk::pa::VesselMeanderStrategy::CalculateNewDirectionVectorInStraightLine;
- m_Diverging = &mitk::pa::VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector;
- m_TestVolumeParameters = createTestVolumeParameters();
- auto rng = std::mt19937();
- m_TestInSilicoVolume = mitk::pa::InSilicoTissueVolume::New(m_TestVolumeParameters, &rng);
- }
-
- mitk::pa::TissueGeneratorParameters::Pointer createTestVolumeParameters()
- {
- auto returnParameters =
- mitk::pa::TissueGeneratorParameters::New();
-
- returnParameters->SetXDim(10);
- returnParameters->SetYDim(10);
- returnParameters->SetZDim(10);
- returnParameters->SetMinBackgroundAbsorption(0);
- returnParameters->SetMaxBackgroundAbsorption(0);
- returnParameters->SetBackgroundScattering(0);
- returnParameters->SetBackgroundAnisotropy(0);
- return returnParameters;
- }
-
- void testEmptyInitializationProperties()
- {
- CPPUNIT_ASSERT(m_TestVessel->CanBifurcate() == false);
- CPPUNIT_ASSERT(m_TestVessel->IsFinished() == true);
- }
-
- void testWalkInStraightLine()
- {
- auto testPosition = mitk::pa::Vector::New();
- testPosition->SetElement(0, 0);
- testPosition->SetElement(1, 4);
- testPosition->SetElement(2, 4);
- auto testDirection = mitk::pa::Vector::New();
- testDirection->SetElement(0, 1);
- testDirection->SetElement(1, 0);
- testDirection->SetElement(2, 0);
- auto params = mitk::pa::VesselProperties::New();
- params->SetDoPartialVolume(false);
- params->SetRadiusInVoxel(1);
- params->SetBifurcationFrequency(100);
- params->SetAbsorptionCoefficient(10);
- params->SetScatteringCoefficient(10);
- params->SetAnisotopyCoefficient(10);
- params->SetPositionVector(testPosition);
- params->SetDirectionVector(testDirection);
- m_TestVessel = mitk::pa::Vessel::New(params);
-
- CPPUNIT_ASSERT(m_TestVessel->CanBifurcate() == false);
- CPPUNIT_ASSERT(m_TestVessel->IsFinished() == false);
-
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 4)) <= mitk::eps);
-
- m_TestVessel->ExpandVessel(m_TestInSilicoVolume, m_StraightLine, 0, nullptr);
-
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 4) - 10) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 5, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 5, 4)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 6, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 6, 4)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 5)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 5)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 6)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 6)) <= mitk::eps);
-
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 4)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(2, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(2, 4, 4)) <= mitk::eps);
-
- m_TestVessel->ExpandVessel(m_TestInSilicoVolume, m_StraightLine, 0, nullptr);
-
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 4) - 10) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 5, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 5, 4)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 6, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 6, 4)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 5)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 5)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 6)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 6)) <= mitk::eps);
-
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 4) - 10) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(1, 4, 4) - 10) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(2, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(2, 4, 4)) <= mitk::eps);
- CPPUNIT_ASSERT_MESSAGE(std::to_string(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(3, 4, 4)),
- std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(3, 4, 4)) <= mitk::eps);
- }
-
- void testBifurcate()
- {
- auto testPosition = mitk::pa::Vector::New();
- testPosition->SetElement(0, 0);
- testPosition->SetElement(1, 4);
- testPosition->SetElement(2, 4);
- auto testDirection = mitk::pa::Vector::New();
- testDirection->SetElement(0, 1);
- testDirection->SetElement(1, 0);
- testDirection->SetElement(2, 0);
- auto params = mitk::pa::VesselProperties::New();
- params->SetRadiusInVoxel(1);
- params->SetBifurcationFrequency(1);
- params->SetAbsorptionCoefficient(10);
- params->SetScatteringCoefficient(10);
- params->SetAnisotopyCoefficient(10);
- params->SetPositionVector(testPosition);
- params->SetDirectionVector(testDirection);
- m_TestVessel = mitk::pa::Vessel::New(params);
-
- CPPUNIT_ASSERT(m_TestVessel->CanBifurcate() == false);
- CPPUNIT_ASSERT(m_TestVessel->IsFinished() == false);
-
- CPPUNIT_ASSERT(std::abs(m_TestInSilicoVolume->GetAbsorptionVolume()->GetData(0, 4, 4)) <= mitk::eps);
-
- m_TestVessel->ExpandVessel(m_TestInSilicoVolume, m_StraightLine, 0, nullptr);
- m_TestVessel->ExpandVessel(m_TestInSilicoVolume, m_StraightLine, 0, nullptr);
-
- CPPUNIT_ASSERT(m_TestVessel->CanBifurcate() == true);
- std::mt19937 rng;
- auto bifurcationVessel = m_TestVessel->Bifurcate(&rng);
-
- CPPUNIT_ASSERT(m_TestVessel->CanBifurcate() == false);
- CPPUNIT_ASSERT(bifurcationVessel->CanBifurcate() == false);
- }
-
- void tearDown() override
- {
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticVessel)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselTreeTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselTreeTest.cpp
deleted file mode 100644
index 058f6d1d05..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVesselTreeTest.cpp
+++ /dev/null
@@ -1,104 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkImageReadAccessor.h>
-
-#include "mitkPAVesselTree.h"
-#include "mitkPAInSilicoTissueVolume.h"
-
-using namespace mitk::pa;
-
-class mitkPhotoacousticVesselTreeTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticVesselTreeTestSuite);
- MITK_TEST(testVesselTreeInitialBehavior);
- MITK_TEST(testCallStepMethod);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
-public:
-
- VesselTree::Pointer m_Tree;
- VesselProperties::Pointer m_VesselProperties;
- Vessel::CalculateNewVesselPositionCallback m_StraightLine;
- InSilicoTissueVolume::Pointer m_TestInSilicoVolume;
-
- void setUp() override
- {
- m_VesselProperties = VesselProperties::New();
- m_Tree = VesselTree::New(m_VesselProperties);
- m_StraightLine = &VesselMeanderStrategy::CalculateNewDirectionVectorInStraightLine;
- auto rng = std::mt19937();
- m_TestInSilicoVolume = InSilicoTissueVolume::New(createTestVolumeParameters(), &rng);
- }
-
- TissueGeneratorParameters::Pointer createTestVolumeParameters()
- {
- auto returnParameters =
- TissueGeneratorParameters::New();
-
- returnParameters->SetXDim(10);
- returnParameters->SetYDim(10);
- returnParameters->SetZDim(10);
- returnParameters->SetMinBackgroundAbsorption(0);
- returnParameters->SetMaxBackgroundAbsorption(0);
- returnParameters->SetBackgroundScattering(0);
- returnParameters->SetBackgroundAnisotropy(0);
- return returnParameters;
- }
-
- void testVesselTreeInitialBehavior()
- {
- CPPUNIT_ASSERT(m_Tree->IsFinished() == true);
- }
-
- void testCallStepMethod()
- {
- //really bad test atm.. The only thing that is tested is that the method can be called without a crash.
- //But hey - it is something :P
- m_VesselProperties->SetRadiusInVoxel(2);
- std::mt19937 rng;
- rng.seed(1);
- m_Tree = VesselTree::New(m_VesselProperties);
- m_Tree->Step(m_TestInSilicoVolume, m_StraightLine, 0, &rng);
-
- rng.seed(1);
- auto secondTree = VesselTree::New(m_VesselProperties);
- secondTree->Step(m_TestInSilicoVolume, m_StraightLine, 0, &rng);
-
- CPPUNIT_ASSERT(Equal(m_Tree, secondTree, 1e-6, true));
-
- secondTree->Step(m_TestInSilicoVolume, m_StraightLine, 0, &rng);
-
- CPPUNIT_ASSERT(!Equal(m_Tree, secondTree, 1e-6, true));
-
- int i = 0;
- for (; i < 1000; i++)
- {
- secondTree->Step(m_TestInSilicoVolume, m_StraightLine, 0, &rng);
- if (secondTree->IsFinished())
- break;
- }
-
- CPPUNIT_ASSERT(i < 999);
- }
-
- void tearDown() override
- {
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticVesselTree)
diff --git a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVolumeTest.cpp b/Modules/PhotoacousticsLib/test/mitkPhotoacousticVolumeTest.cpp
deleted file mode 100644
index e92fdfc1f3..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPhotoacousticVolumeTest.cpp
+++ /dev/null
@@ -1,382 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkImageReadAccessor.h>
-
-#include "mitkPAInSilicoTissueVolume.h"
-#include "mitkPATissueGeneratorParameters.h"
-
-class mitkPhotoacousticVolumeTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPhotoacousticVolumeTestSuite);
- MITK_TEST(TestUniformDistributionIsUniform);
- MITK_TEST(TestInitializedTissueContainsOnlyZeros);
- MITK_TEST(TestConvertedMitkImageContainsOnlyZerosOrAir);
- MITK_TEST(TestTissueVolumeContainsCorrectAbsorptionNumber);
- MITK_TEST(TestTissueVolumeContainsCorrectScatteringNumber);
- MITK_TEST(TestTissueVolumeContainsCorrectAnisotropyNumber);
- MITK_TEST(testSecondConstructor);
- MITK_TEST(testCompleteAirVoxelInclusion);
- MITK_TEST(testHalfAirVoxelInclusion);
- MITK_TEST(testCompleteAirAndSkinVoxelInclusion);
- MITK_TEST(testRandomizeCoefficients);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::pa::InSilicoTissueVolume::Pointer m_PhotoacousticVolume;
- mitk::pa::TissueGeneratorParameters::Pointer m_TissueGeneratorParameters;
-
-public:
-
- void setUp() override
- {
- m_TissueGeneratorParameters = mitk::pa::TissueGeneratorParameters::New();
- auto rng = std::mt19937();
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(m_TissueGeneratorParameters, &rng);
- }
-
- void TestUniformDistributionIsUniform()
- {
-
- int dims = 30;
- m_TissueGeneratorParameters->SetXDim(dims);
- m_TissueGeneratorParameters->SetYDim(dims);
- m_TissueGeneratorParameters->SetZDim(dims);
- m_TissueGeneratorParameters->SetAirThicknessInMillimeters(0);
-
- m_TissueGeneratorParameters->SetMinBackgroundAbsorption(0.001);
- m_TissueGeneratorParameters->SetMaxBackgroundAbsorption(0.2);
-
- auto rng = std::mt19937();
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(m_TissueGeneratorParameters, &rng);
-
- for (int x = 0; x < dims; x++)
- {
- for (int y = 0; y < dims; y++)
- {
- for (int z = 0; z < dims; z++)
- {
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Every absorption should be in bounds.",
- m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(x, y, z) >= 0.001 &&
- m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(x, y, z) <= 0.2, true);
- }
- }
- }
-
- }
-
- void TestInitializedTissueContainsOnlyZeros()
- {
- int dims = 30;
- m_TissueGeneratorParameters->SetXDim(dims);
- m_TissueGeneratorParameters->SetYDim(dims);
- m_TissueGeneratorParameters->SetZDim(dims);
- m_TissueGeneratorParameters->SetAirThicknessInMillimeters(0);
- m_TissueGeneratorParameters->SetMinBackgroundAbsorption(0);
- m_TissueGeneratorParameters->SetMaxBackgroundAbsorption(0);
- auto rng = std::mt19937();
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(m_TissueGeneratorParameters, &rng);
-
- for (int x = 0; x < dims; x++)
- {
- for (int y = 0; y < dims; y++)
- {
- for (int z = 0; z < dims; z++)
- {
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Every field should be initialized with 0.", std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(x, y, z)) < mitk::eps, true);
- }
- }
- }
- }
-
- void TestConvertedMitkImageContainsOnlyZerosOrAir()
- {
- int dims = 30;
- m_TissueGeneratorParameters->SetXDim(dims);
- m_TissueGeneratorParameters->SetYDim(dims);
- m_TissueGeneratorParameters->SetZDim(dims);
- auto rng = std::mt19937();
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(m_TissueGeneratorParameters, &rng);
-
- mitk::Image::Pointer testImage = m_PhotoacousticVolume->ConvertToMitkImage();
-
- mitk::ImageReadAccessor imgMemAcc(testImage);
- auto* imagePointer = (double*)imgMemAcc.GetData();
-
- for (int index = 0; index < dims*dims*dims; index++, imagePointer++)
- {
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Every voxel in image should be 0.1 or 0.0001.", true, std::abs(*imagePointer - 0.1) <= mitk::eps || std::abs(*imagePointer - 0.0001) <= mitk::eps);
- }
- }
-
- void TestTissueVolumeContainsCorrectAbsorptionNumber()
- {
- int dims = 2;
- m_TissueGeneratorParameters->SetXDim(dims);
- m_TissueGeneratorParameters->SetYDim(dims);
- m_TissueGeneratorParameters->SetZDim(dims);
- auto rng = std::mt19937();
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(m_TissueGeneratorParameters, &rng);
-
- m_PhotoacousticVolume->SetVolumeValues(0, 0, 0, 0, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(0, 0, 1, 1, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(0, 1, 0, 2, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(0, 1, 1, 3, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 0, 0, 4, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 0, 1, 5, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 1, 0, 6, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 1, 1, 7, 0, 0);
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 0.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 0, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 1.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 0, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 2.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 1, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 3.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 1, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 4.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 0, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 5.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 0, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 6.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 7.0, m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 1));
- }
-
- void TestTissueVolumeContainsCorrectScatteringNumber()
- {
- int dims = 2;
- m_TissueGeneratorParameters->SetXDim(dims);
- m_TissueGeneratorParameters->SetYDim(dims);
- m_TissueGeneratorParameters->SetZDim(dims);
- auto rng = std::mt19937();
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(m_TissueGeneratorParameters, &rng);
-
- m_PhotoacousticVolume->SetVolumeValues(0, 0, 0, 0, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(0, 0, 1, 0, 1, 0);
- m_PhotoacousticVolume->SetVolumeValues(0, 1, 0, 0, 2, 0);
- m_PhotoacousticVolume->SetVolumeValues(0, 1, 1, 0, 3, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 0, 0, 0, 4, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 0, 1, 0, 5, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 1, 0, 0, 6, 0);
- m_PhotoacousticVolume->SetVolumeValues(1, 1, 1, 0, 7, 0);
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 0.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 0, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 1.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 0, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 2.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 1, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 3.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 1, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 4.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 0, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 5.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 0, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 6.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 7.0, m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 1));
- }
-
- void TestTissueVolumeContainsCorrectAnisotropyNumber()
- {
- int dims = 2;
- m_TissueGeneratorParameters->SetXDim(dims);
- m_TissueGeneratorParameters->SetYDim(dims);
- m_TissueGeneratorParameters->SetZDim(dims);
- auto rng = std::mt19937();
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(m_TissueGeneratorParameters, &rng);
-
- m_PhotoacousticVolume->SetVolumeValues(0, 0, 0, 0, 0, 0);
- m_PhotoacousticVolume->SetVolumeValues(0, 0, 1, 0, 0, 1);
- m_PhotoacousticVolume->SetVolumeValues(0, 1, 0, 0, 0, 2);
- m_PhotoacousticVolume->SetVolumeValues(0, 1, 1, 0, 0, 3);
- m_PhotoacousticVolume->SetVolumeValues(1, 0, 0, 0, 0, 4);
- m_PhotoacousticVolume->SetVolumeValues(1, 0, 1, 0, 0, 5);
- m_PhotoacousticVolume->SetVolumeValues(1, 1, 0, 0, 0, 6);
- m_PhotoacousticVolume->SetVolumeValues(1, 1, 1, 0, 0, 7);
-
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 0.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 0, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 1.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 0, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 2.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 1, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 3.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 1, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 4.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 0, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 5.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 0, 1));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 6.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 0));
- CPPUNIT_ASSERT_EQUAL_MESSAGE("Should be correct value", 7.0, m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 1));
- }
-
- mitk::pa::Volume::Pointer createTestVolume(double value)
- {
- auto* data = new double[27];
- for (int i = 0; i < 27; ++i)
- data[i] = value;
- return mitk::pa::Volume::New(data, 3, 3, 3, 1);
- }
-
- void assertEqual(mitk::pa::Volume::Pointer first, mitk::pa::Volume::Pointer second)
- {
- CPPUNIT_ASSERT(first->GetXDim() == second->GetXDim());
- CPPUNIT_ASSERT(first->GetYDim() == second->GetYDim());
- CPPUNIT_ASSERT(first->GetZDim() == second->GetZDim());
- for (unsigned int x = 0; x < first->GetXDim(); ++x)
- for (unsigned int y = 0; y < first->GetYDim(); ++y)
- for (unsigned int z = 0; z < first->GetZDim(); ++z)
- CPPUNIT_ASSERT(std::abs(first->GetData(x, y, z) - second->GetData(x, y, z)) < mitk::eps);
- }
-
- void testSecondConstructor()
- {
- mitk::pa::Volume::Pointer absorption = createTestVolume(1);
- mitk::pa::Volume::Pointer scattering = createTestVolume(2);
- mitk::pa::Volume::Pointer anisotropy = createTestVolume(3);
- mitk::pa::Volume::Pointer segmentation = createTestVolume(4);
- mitk::PropertyList::Pointer properties = mitk::PropertyList::New();
-
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(absorption,
- scattering, anisotropy, segmentation, m_TissueGeneratorParameters, properties);
-
- assertEqual(m_PhotoacousticVolume->GetAbsorptionVolume(), absorption);
- assertEqual(m_PhotoacousticVolume->GetScatteringVolume(), scattering);
- assertEqual(m_PhotoacousticVolume->GetAnisotropyVolume(), anisotropy);
- assertEqual(m_PhotoacousticVolume->GetSegmentationVolume(), segmentation);
- }
-
- void testCompleteAirVoxelInclusion()
- {
- mitk::pa::Volume::Pointer absorption = createTestVolume(1);
- mitk::pa::Volume::Pointer scattering = createTestVolume(2);
- mitk::pa::Volume::Pointer anisotropy = createTestVolume(3);
- mitk::pa::Volume::Pointer segmentation = createTestVolume(4);
- mitk::PropertyList::Pointer properties = mitk::PropertyList::New();
- m_TissueGeneratorParameters->SetXDim(3);
- m_TissueGeneratorParameters->SetYDim(3);
- m_TissueGeneratorParameters->SetZDim(3);
- m_TissueGeneratorParameters->SetAirThicknessInMillimeters(10);
- m_TissueGeneratorParameters->SetSkinThicknessInMillimeters(0);
- m_TissueGeneratorParameters->SetAirAbsorption(2);
- m_TissueGeneratorParameters->SetAirScattering(4);
- m_TissueGeneratorParameters->SetAirAnisotropy(6);
-
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(absorption,
- scattering, anisotropy, segmentation, m_TissueGeneratorParameters, properties);
-
- m_PhotoacousticVolume->FinalizeVolume();
-
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 0, 0) - 2) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 1) - 1) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 2) - 1) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 0, 0) - 4) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 1) - 2) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 2) - 2) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 0, 0) - 6) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 1) - 3) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 2) - 3) < mitk::eps);
- }
-
- void testRandomizeCoefficients()
- {
- mitk::pa::Volume::Pointer absorption = createTestVolume(1);
- mitk::pa::Volume::Pointer scattering = createTestVolume(1);
- mitk::pa::Volume::Pointer anisotropy = createTestVolume(1);
- mitk::pa::Volume::Pointer segmentation = createTestVolume(4);
- mitk::PropertyList::Pointer properties = mitk::PropertyList::New();
- m_TissueGeneratorParameters->SetXDim(3);
- m_TissueGeneratorParameters->SetYDim(3);
- m_TissueGeneratorParameters->SetZDim(3);
- m_TissueGeneratorParameters->SetRandomizePhysicalProperties(true);
- m_TissueGeneratorParameters->SetRandomizePhysicalPropertiesPercentage(1);
- m_TissueGeneratorParameters->SetRngSeed(17);
- m_TissueGeneratorParameters->SetUseRngSeed(true);
-
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(absorption,
- scattering, anisotropy, segmentation, m_TissueGeneratorParameters, properties);
-
- m_PhotoacousticVolume->FinalizeVolume();
-
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 0, 0) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 1) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 2) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 0, 0) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 1) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 2) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 0, 0) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 1) - 1) < 0.1);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 2) - 1) < 0.1);
- }
-
- void testCompleteAirAndSkinVoxelInclusion()
- {
- mitk::pa::Volume::Pointer absorption = createTestVolume(1);
- mitk::pa::Volume::Pointer scattering = createTestVolume(2);
- mitk::pa::Volume::Pointer anisotropy = createTestVolume(3);
- mitk::pa::Volume::Pointer segmentation = createTestVolume(4);
- mitk::PropertyList::Pointer properties = mitk::PropertyList::New();
- m_TissueGeneratorParameters->SetXDim(3);
- m_TissueGeneratorParameters->SetYDim(3);
- m_TissueGeneratorParameters->SetZDim(3);
- m_TissueGeneratorParameters->SetAirThicknessInMillimeters(10);
- m_TissueGeneratorParameters->SetSkinThicknessInMillimeters(10);
- m_TissueGeneratorParameters->SetAirAbsorption(2);
- m_TissueGeneratorParameters->SetAirScattering(4);
- m_TissueGeneratorParameters->SetAirAnisotropy(6);
- m_TissueGeneratorParameters->SetSkinAbsorption(4);
- m_TissueGeneratorParameters->SetSkinScattering(8);
- m_TissueGeneratorParameters->SetSkinAnisotropy(12);
-
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(absorption,
- scattering, anisotropy, segmentation, m_TissueGeneratorParameters, properties);
-
- m_PhotoacousticVolume->FinalizeVolume();
-
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 0, 0) - 2) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 1) - 4) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 2) - 1) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 0, 0) - 4) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 1) - 8) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 2) - 2) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 0, 0) - 6) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 1) - 12) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 2) - 3) < mitk::eps);
- }
-
- void testHalfAirVoxelInclusion()
- {
- mitk::pa::Volume::Pointer absorption = createTestVolume(1);
- mitk::pa::Volume::Pointer scattering = createTestVolume(2);
- mitk::pa::Volume::Pointer anisotropy = createTestVolume(3);
- mitk::pa::Volume::Pointer segmentation = createTestVolume(4);
- mitk::PropertyList::Pointer properties = mitk::PropertyList::New();
- m_TissueGeneratorParameters->SetXDim(3);
- m_TissueGeneratorParameters->SetYDim(3);
- m_TissueGeneratorParameters->SetZDim(3);
- m_TissueGeneratorParameters->SetAirThicknessInMillimeters(15);
- m_TissueGeneratorParameters->SetSkinThicknessInMillimeters(0);
- m_TissueGeneratorParameters->SetAirAbsorption(2);
- m_TissueGeneratorParameters->SetAirScattering(4);
- m_TissueGeneratorParameters->SetAirAnisotropy(6);
-
- m_PhotoacousticVolume = mitk::pa::InSilicoTissueVolume::New(absorption,
- scattering, anisotropy, segmentation, m_TissueGeneratorParameters, properties);
-
- m_PhotoacousticVolume->FinalizeVolume();
-
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(0, 0, 0) - 2) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 1) - 1.5) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAbsorptionVolume()->GetData(1, 1, 2) - 1) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(0, 0, 0) - 4) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 1) - 3) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetScatteringVolume()->GetData(1, 1, 2) - 2) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(0, 0, 0) - 6) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 1) - 4.5) < mitk::eps);
- CPPUNIT_ASSERT(std::abs(m_PhotoacousticVolume->GetAnisotropyVolume()->GetData(1, 1, 2) - 3) < mitk::eps);
- }
-
- void tearDown() override
- {
- m_TissueGeneratorParameters = nullptr;
- m_PhotoacousticVolume = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPhotoacousticVolume)
diff --git a/Modules/PhotoacousticsLib/test/mitkPropertyCalculatorTest.cpp b/Modules/PhotoacousticsLib/test/mitkPropertyCalculatorTest.cpp
deleted file mode 100644
index 1b780a7fa6..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkPropertyCalculatorTest.cpp
+++ /dev/null
@@ -1,75 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPAPropertyCalculator.h>
-
-class mitkPropertyCalculatorTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkPropertyCalculatorTestSuite);
- MITK_TEST(testOutputIsNotEmpty);
- CPPUNIT_TEST_SUITE_END();
-
-private:
- mitk::pa::PropertyCalculator::Pointer m_PropertyCalculator;
-
-public:
-
- void setUp() override
- {
- m_PropertyCalculator = mitk::pa::PropertyCalculator::New();
- }
-
- void assertProperties(mitk::pa::PropertyCalculator::Properties properties,
- std::string type, int wavelength, int oxygenation)
- {
- CPPUNIT_ASSERT_MESSAGE("anisotropy " + std::to_string(properties.g) + " not bigger than 0 at type "
- + type + " wv: " + std::to_string(wavelength) + " ox: " + std::to_string(oxygenation), properties.g > 0);
- CPPUNIT_ASSERT_MESSAGE("absorption " + std::to_string(properties.mua) + " not bigger than 0 at type "
- + type + " wv: " + std::to_string(wavelength) + " ox: " + std::to_string(oxygenation), properties.mua > 0);
- CPPUNIT_ASSERT_MESSAGE("scattering " + std::to_string(properties.mus) + " not bigger than 0 at type "
- + type + " wv: " + std::to_string(wavelength) + " ox: " + std::to_string(oxygenation), properties.mus > 0);
- }
-
- void testOutputIsNotEmpty()
- {
- for (double oxygenation = 0; oxygenation <= 1; oxygenation += 0.05)
- {
- for (int wavelength = 700; wavelength <= 900; wavelength += 5)
- {
- auto properties = m_PropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::AIR, wavelength, oxygenation);
- assertProperties(properties, "AIR", wavelength, oxygenation);
- properties = m_PropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::BLOOD, wavelength, oxygenation);
- assertProperties(properties, "BLOOD", wavelength, oxygenation);
- properties = m_PropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::EPIDERMIS, wavelength, oxygenation);
- assertProperties(properties, "EPIDERMIS", wavelength, oxygenation);
- properties = m_PropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::FAT, wavelength, oxygenation);
- assertProperties(properties, "FAT", wavelength, oxygenation);
- properties = m_PropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::STANDARD_TISSUE, wavelength, oxygenation);
- assertProperties(properties, "STANDARD_TISSUE", wavelength, oxygenation);
- }
- }
- }
-
- void tearDown() override
- {
- m_PropertyCalculator = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkPropertyCalculator)
diff --git a/Modules/PhotoacousticsLib/test/mitkSimulationBatchGeneratorTest.cpp b/Modules/PhotoacousticsLib/test/mitkSimulationBatchGeneratorTest.cpp
deleted file mode 100644
index 7c8f44b1de..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkSimulationBatchGeneratorTest.cpp
+++ /dev/null
@@ -1,86 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPASimulationBatchGenerator.h>
-#include <mitkPAVolume.h>
-#include <itkFileTools.h>
-
-class mitkSimulationBatchGeneratorTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkSimulationBatchGeneratorTestSuite);
- MITK_TEST(testGenerateBatchFileString);
- MITK_TEST(testGenerateBatchFileAndSaveFile);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- const std::string TEST_FOLDER_PATH = "testFiles/";
- mitk::pa::SimulationBatchGeneratorParameters::Pointer m_Parameters;
- mitk::pa::Volume::Pointer m_Test3DVolume;
-
-public:
-
- void setUp() override
- {
- m_Parameters = mitk::pa::SimulationBatchGeneratorParameters::New();
- m_Parameters->SetBinaryPath("binary");
- m_Parameters->SetNrrdFilePath(TEST_FOLDER_PATH);
- m_Parameters->SetNumberOfPhotons(100);
- m_Parameters->SetTissueName("tissueName");
- m_Parameters->SetVolumeIndex(0);
- m_Parameters->SetYOffsetLowerThresholdInCentimeters(-1);
- m_Parameters->SetYOffsetUpperThresholdInCentimeters(1);
- m_Parameters->SetYOffsetStepInCentimeters(0.5);
-
- m_Test3DVolume = createTest3DVolume(5);
- itk::FileTools::CreateDirectory(TEST_FOLDER_PATH);
- CPPUNIT_ASSERT(itksys::SystemTools::FileIsDirectory(TEST_FOLDER_PATH));
- }
-
- mitk::pa::Volume::Pointer createTest3DVolume(double value)
- {
- unsigned int xDim = 10;
- unsigned int yDim = 10;
- unsigned int zDim = 10;
- unsigned int length = xDim * yDim * zDim;
- auto* data = new double[length];
- for (unsigned int i = 0; i < length; i++)
- data[i] = value;
-
- return mitk::pa::Volume::New(data, xDim, yDim, zDim, 1);
- }
-
- void testGenerateBatchFileString()
- {
- std::string batchGenerationString = mitk::pa::SimulationBatchGenerator::CreateBatchSimulationString(m_Parameters);
- CPPUNIT_ASSERT(!batchGenerationString.empty());
- }
-
- void testGenerateBatchFileAndSaveFile()
- {
- mitk::pa::SimulationBatchGenerator::WriteBatchFileAndSaveTissueVolume(m_Parameters, m_Test3DVolume->AsMitkImage());
- CPPUNIT_ASSERT(itksys::SystemTools::FileExists(TEST_FOLDER_PATH + m_Parameters->GetTissueName() + "000.nrrd"));
- CPPUNIT_ASSERT(itksys::SystemTools::FileExists(TEST_FOLDER_PATH + "simulate_all.sh") || itksys::SystemTools::FileExists(TEST_FOLDER_PATH + "simulate_all.bat"));
- CPPUNIT_ASSERT(itksys::SystemTools::FileExists(TEST_FOLDER_PATH + m_Parameters->GetTissueName() + "000")
- && itksys::SystemTools::FileIsDirectory(TEST_FOLDER_PATH + m_Parameters->GetTissueName() + "000"));
- }
-
- void tearDown() override
- {
- m_Parameters = nullptr;
- CPPUNIT_ASSERT_MESSAGE("Resource leak of test files onto hard drive..", itksys::SystemTools::RemoveADirectory(TEST_FOLDER_PATH) == true);
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkSimulationBatchGenerator)
diff --git a/Modules/PhotoacousticsLib/test/mitkSlicedVolumeGeneratorTest.cpp b/Modules/PhotoacousticsLib/test/mitkSlicedVolumeGeneratorTest.cpp
deleted file mode 100644
index 85f28da73f..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkSlicedVolumeGeneratorTest.cpp
+++ /dev/null
@@ -1,184 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPASlicedVolumeGenerator.h>
-
-class mitkSlicedVolumeGeneratorTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkSlicedVolumeGeneratorTestSuite);
- MITK_TEST(testConstructorDestructor);
- MITK_TEST(testGetSlicedFluenceVolume);
- MITK_TEST(testGetSlicedFluenceVolumeInverse);
- MITK_TEST(testGetSlicedFluenceVolumeWithPrecorrection);
- MITK_TEST(testGetSlicedFluenceVolumeWithPrecorrectionInverse);
- MITK_TEST(testGetSlicedSignalVolume);
- MITK_TEST(testGetSlicedAbsorptionVolume);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::pa::ComposedVolume::Pointer m_ComposedVolume;
- mitk::pa::TissueGeneratorParameters::Pointer m_DefaultParameters;
- mitk::pa::InSilicoTissueVolume::Pointer m_InSilicoTissueVolume;
- mitk::pa::SlicedVolumeGenerator::Pointer m_SlicedVolumeGenerator;
- mitk::pa::Volume::Pointer m_PrecorrectionVolume;
-
-public:
-
- void setUp() override
- {
- m_SlicedVolumeGenerator = nullptr;
- m_DefaultParameters = mitk::pa::TissueGeneratorParameters::New();
- m_DefaultParameters->SetXDim(3);
- m_DefaultParameters->SetYDim(3);
- m_DefaultParameters->SetZDim(3);
- auto rng = std::mt19937();
- m_InSilicoTissueVolume = mitk::pa::InSilicoTissueVolume::New(m_DefaultParameters, &rng);
- m_ComposedVolume = mitk::pa::ComposedVolume::New(m_InSilicoTissueVolume);
- m_ComposedVolume->AddSlice(CreateValidationPair(-1, 1));
- m_ComposedVolume->AddSlice(CreateValidationPair(0, 3));
- m_ComposedVolume->AddSlice(CreateValidationPair(1, 6));
- m_PrecorrectionVolume = CreatePrecorrectionVolume();
- }
-
- mitk::pa::Volume::Pointer CreatePrecorrectionVolume()
- {
- auto* data = new double[27];
- for (int i = 0; i < 27; ++i)
- data[i] = 0.5;
- return mitk::pa::Volume::New(data, 3, 3, 3, 1);
- }
-
- void FillYSliceWith(mitk::pa::Volume::Pointer fluenceVolume, double ySlice, double value)
- {
- for (unsigned int x = 0; x < fluenceVolume->GetXDim(); ++x)
- for (unsigned int z = 0; z < fluenceVolume->GetZDim(); ++z)
- {
- fluenceVolume->SetData(value, x, ySlice, z);
- }
- }
-
- mitk::pa::FluenceYOffsetPair::Pointer CreateValidationPair(double yOffset, int start)
- {
- auto* data = new double[27];
- mitk::pa::Volume::Pointer fluenceVolume = mitk::pa::Volume::New(data, 3, 3, 3, 1);
-
- FillYSliceWith(fluenceVolume, 0, start + 0);
- FillYSliceWith(fluenceVolume, 1, start + 1);
- FillYSliceWith(fluenceVolume, 2, start + 2);
-
- return mitk::pa::FluenceYOffsetPair::New(fluenceVolume, yOffset);
- }
-
- void AssertYSliceValue(mitk::pa::Volume::Pointer fluenceVolume, double ySlice, double value)
- {
- for (unsigned int x = 0; x < fluenceVolume->GetXDim(); ++x)
- for (unsigned int z = 0; z < fluenceVolume->GetZDim(); ++z)
- {
- std::string msg = "Expected: " + std::to_string(value) + " actual: " + std::to_string(fluenceVolume->GetData(x, ySlice, z));
- CPPUNIT_ASSERT_MESSAGE(msg, std::abs(fluenceVolume->GetData(x, ySlice, z) - value) < mitk::eps);
- }
- }
-
- void testConstructorDestructor()
- {
- m_SlicedVolumeGenerator = mitk::pa::SlicedVolumeGenerator::New(0, false, nullptr, false);
- CPPUNIT_ASSERT(m_SlicedVolumeGenerator.IsNotNull());
- }
-
- void testGetSlicedFluenceVolume()
- {
- m_SlicedVolumeGenerator = mitk::pa::SlicedVolumeGenerator::New(1, false, nullptr, false);
- mitk::pa::Volume::Pointer slicedFluence =
- m_SlicedVolumeGenerator->GetSlicedFluenceImageFromComposedVolume(m_ComposedVolume);
- CPPUNIT_ASSERT(slicedFluence->GetXDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetYDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetZDim() == 3);
- AssertYSliceValue(slicedFluence, 0, 1);
- AssertYSliceValue(slicedFluence, 1, 4);
- AssertYSliceValue(slicedFluence, 2, 8);
- }
-
- void testGetSlicedFluenceVolumeInverse()
- {
- m_SlicedVolumeGenerator = mitk::pa::SlicedVolumeGenerator::New(1, false, nullptr, true);
- mitk::pa::Volume::Pointer slicedFluence =
- m_SlicedVolumeGenerator->GetSlicedFluenceImageFromComposedVolume(m_ComposedVolume);
- CPPUNIT_ASSERT(slicedFluence->GetXDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetYDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetZDim() == 3);
- AssertYSliceValue(slicedFluence, 0, 1);
- AssertYSliceValue(slicedFluence, 1, 1.0 / 4.0);
- AssertYSliceValue(slicedFluence, 2, 1.0 / 8.0);
- }
-
- void testGetSlicedFluenceVolumeWithPrecorrection()
- {
- m_SlicedVolumeGenerator = mitk::pa::SlicedVolumeGenerator::New(1, true, m_PrecorrectionVolume, false);
- mitk::pa::Volume::Pointer slicedFluence =
- m_SlicedVolumeGenerator->GetSlicedFluenceImageFromComposedVolume(m_ComposedVolume);
- CPPUNIT_ASSERT(slicedFluence->GetXDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetYDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetZDim() == 3);
- AssertYSliceValue(slicedFluence, 0, 2);
- AssertYSliceValue(slicedFluence, 1, 8);
- AssertYSliceValue(slicedFluence, 2, 16);
- }
-
- void testGetSlicedFluenceVolumeWithPrecorrectionInverse()
- {
- m_SlicedVolumeGenerator = mitk::pa::SlicedVolumeGenerator::New(1, true, m_PrecorrectionVolume, true);
- mitk::pa::Volume::Pointer slicedFluence =
- m_SlicedVolumeGenerator->GetSlicedFluenceImageFromComposedVolume(m_ComposedVolume);
- CPPUNIT_ASSERT(slicedFluence->GetXDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetYDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetZDim() == 3);
- AssertYSliceValue(slicedFluence, 0, 1.0 / 2);
- AssertYSliceValue(slicedFluence, 1, 1.0 / 8);
- AssertYSliceValue(slicedFluence, 2, 1.0 / 16);
- }
-
- void testGetSlicedSignalVolume()
- {
- m_SlicedVolumeGenerator = mitk::pa::SlicedVolumeGenerator::New(1, false, nullptr, false);
- mitk::pa::Volume::Pointer slicedFluence =
- m_SlicedVolumeGenerator->GetSlicedSignalImageFromComposedVolume(m_ComposedVolume);
- CPPUNIT_ASSERT(slicedFluence->GetXDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetYDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetZDim() == 3);
- AssertYSliceValue(slicedFluence, 0, 1 * m_DefaultParameters->GetMinBackgroundAbsorption());
- AssertYSliceValue(slicedFluence, 1, 4 * m_DefaultParameters->GetMinBackgroundAbsorption());
- AssertYSliceValue(slicedFluence, 2, 8 * m_DefaultParameters->GetMinBackgroundAbsorption());
- }
-
- void testGetSlicedAbsorptionVolume()
- {
- m_SlicedVolumeGenerator = mitk::pa::SlicedVolumeGenerator::New(1, false, nullptr, false);
- mitk::pa::Volume::Pointer slicedFluence =
- m_SlicedVolumeGenerator->GetSlicedGroundTruthImageFromComposedVolume(m_ComposedVolume);
- CPPUNIT_ASSERT(slicedFluence->GetXDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetYDim() == 3);
- CPPUNIT_ASSERT(slicedFluence->GetZDim() == 3);
- AssertYSliceValue(slicedFluence, 0, m_DefaultParameters->GetMinBackgroundAbsorption());
- AssertYSliceValue(slicedFluence, 1, m_DefaultParameters->GetMinBackgroundAbsorption());
- AssertYSliceValue(slicedFluence, 2, m_DefaultParameters->GetMinBackgroundAbsorption());
- }
-
- void tearDown() override
- {
- m_SlicedVolumeGenerator = nullptr;
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkSlicedVolumeGenerator)
diff --git a/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp b/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp
deleted file mode 100644
index fc449d4b35..0000000000
--- a/Modules/PhotoacousticsLib/test/mitkSpectralUnmixingTest.cpp
+++ /dev/null
@@ -1,680 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-
-#include <mitkPASpectralUnmixingFilterBase.h>
-#include <mitkPALinearSpectralUnmixingFilter.h>
-#include <mitkPASpectralUnmixingFilterVigra.h>
-#include <mitkPASpectralUnmixingFilterSimplex.h>
-#include <mitkPASpectralUnmixingSO2.h>
-#include <mitkImageReadAccessor.h>
-
-class mitkSpectralUnmixingTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkSpectralUnmixingTestSuite);
- MITK_TEST(testEigenSUAlgorithm);
- MITK_TEST(testVigraSUAlgorithm);
- //MITK_TEST(testSimplexSUAlgorithm);
- MITK_TEST(testSO2);
- MITK_TEST(testExceptionSO2);
- MITK_TEST(testWavelengthExceptions);
- MITK_TEST(testNoChromophoresSelected);
- MITK_TEST(testInputImage);
- MITK_TEST(testAddOutput);
- MITK_TEST(testWeightsError);
- MITK_TEST(testOutputs);
- CPPUNIT_TEST_SUITE_END();
-
-private:
- mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter;
- mitk::Image::Pointer inputImage;
- std::vector<int> m_inputWavelengths;
- std::vector<double> m_inputWeights;
- std::vector<float> m_CorrectResult;
- float threshold;
-
-public:
-
- void setUp() override
- {
- //Set empty input image:
- inputImage = mitk::Image::New();
- mitk::PixelType pixelType = mitk::MakeScalarPixelType<float>();
- const int NUMBER_OF_SPATIAL_DIMENSIONS = 3;
- auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS];
-
- dimensions[0] = 1;
- dimensions[1] = 1;
- dimensions[2] = 5;
-
- inputImage->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions);
-
- //Set wavelengths for unmixing:
- m_inputWavelengths.push_back(750);
- m_inputWavelengths.push_back(800);
-
- m_inputWeights.push_back(50);
- m_inputWeights.push_back(100);
-
- //Set fraction of Hb and HbO2 to unmix:
- float fracHb = 100;
- float fracHbO2 = 300;
- m_CorrectResult.push_back(fracHbO2);
- m_CorrectResult.push_back(fracHb);
- m_CorrectResult.push_back(fracHbO2 + 10);
- m_CorrectResult.push_back(fracHb - 10);
- threshold = 0.01;
-
- //Multiply values of wavelengths (750,800,850 nm) with fractions to get pixel values:
- float px1 = fracHb * 7.52 + fracHbO2 * 2.77;
- float px2 = fracHb * 4.08 + fracHbO2 * 4.37;
- float px3 = (fracHb - 10) * 7.52 + (fracHbO2 + 10) * 2.77;
- float px4 = (fracHb - 10) * 4.08 + (fracHbO2 + 10) * 4.37;
-
- float* data = new float[6];
- data[0] = px1;
- data[1] = px2;
- data[2] = px3;
- data[3] = px4;
- data[5] = 0;
-
- inputImage->SetImportVolume(data, mitk::Image::ImportMemoryManagementType::CopyMemory);
- delete[] data;
- }
-
- // Tests implemented EIGEN algortihms with correct inputs
- void testEigenSUAlgorithm()
- {
- MITK_INFO << "START FILTER TEST ... ";
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- //Set Chromophores to filter
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- ofstream myfile;
- myfile.open("EigenTestResult.txt");
-
- std::vector<mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType> m_Eigen = {
- mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR, /* mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LDLT,
- mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LLT,*/ mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::COLPIVHOUSEHOLDERQR,
- mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD, mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU,
- mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVHOUSEHOLDERQR};
-
- for (unsigned int Algorithmidx = 0; Algorithmidx < m_Eigen.size();++Algorithmidx)
- {
- m_SpectralUnmixingFilter->SetAlgorithm(m_Eigen[Algorithmidx]);
-
- m_SpectralUnmixingFilter->Update();
-
-
- /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/
-
- for (int i = 0; i < 2; ++i)
- {
- mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i);
- mitk::ImageReadAccessor readAccess(output);
- const float* inputDataArray = ((const float*)readAccess.GetData());
- auto pixel = inputDataArray[0];
- auto pixel2 = inputDataArray[1];
-
- myfile << "Algorithmidx: " << Algorithmidx << "\n Output " << i << ": " << "\n" << inputDataArray[0] << "\n" << inputDataArray[1] << "\n";
- myfile << "Correct Result: " << "\n" << m_CorrectResult[i] << "\n" << m_CorrectResult[i + 2] << "\n";
-
- CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i]) < threshold);
- CPPUNIT_ASSERT(std::abs(pixel2 - m_CorrectResult[i + 2]) < threshold);
- }
- }
- myfile.close();
- MITK_INFO << "EIGEN FILTER TEST SUCCESFULL :)";
- }
-
- // Tests implemented VIGRA algortihms with correct inputs
- void testVigraSUAlgorithm()
- {
- MITK_INFO << "START FILTER TEST ... ";
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
-
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- double Weight = m_inputWeights[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- m_SpectralUnmixingFilter->AddWeight(Weight);
- }
-
- //Set Chromophores to filter
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
-
- std::vector<mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType> Vigra = {
- mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS, mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::GOLDFARB,
- mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED, mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS/*,
- mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::vigratest*/};
-
- ofstream myfile;
- myfile.open("VigraTestResult.txt");
-
- for (unsigned int Algorithmidx = 0; Algorithmidx < Vigra.size();++Algorithmidx)
- {
- m_SpectralUnmixingFilter->SetAlgorithm(Vigra[0]);
-
- m_SpectralUnmixingFilter->Update();
-
-
- /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/
-
- for (int i = 0; i < 2; ++i)
- {
- mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i);
- mitk::ImageReadAccessor readAccess(output);
- const float* inputDataArray = ((const float*)readAccess.GetData());
- auto pixel = inputDataArray[0];
- auto pixel2 = inputDataArray[1];
-
- myfile << "Algorithmidx: " << Algorithmidx << "\n Output " << i << ": " << "\n" << inputDataArray[0] << "\n" << inputDataArray[1] << "\n";
- myfile << "Correct Result: " << "\n" << m_CorrectResult[i] << "\n" << m_CorrectResult[i + 2] << "\n";
-
- CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i]) < threshold);
- CPPUNIT_ASSERT(std::abs(pixel2 - m_CorrectResult[i + 2]) < threshold);
- }
- }
- myfile.close();
- MITK_INFO << "VIGRA FILTER TEST SUCCESFULL :)";
- }
-
- void testSimplexSUAlgorithm()
- {
- MITK_INFO << "START FILTER TEST ... ";
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterSimplex::New();
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
- m_SpectralUnmixingFilter->Verbose(true);
- m_SpectralUnmixingFilter->RelativeError(false);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- //Set Chromophores to filter
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- m_SpectralUnmixingFilter->Update();
-
-
- /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/
- ofstream myfile;
- myfile.open("SimplexTestResult.txt");
- for (int i = 0; i < 2; ++i)
- {
- mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i);
- mitk::ImageReadAccessor readAccess(output);
- const float* inputDataArray = ((const float*)readAccess.GetData());
- auto pixel = inputDataArray[0];
- auto pixel2 = inputDataArray[1];
-
- myfile << "Output " << i << ": " << "\n" << inputDataArray[0] << "\n" << inputDataArray[1] << "\n";
- myfile << "Correct Result: " << "\n" << m_CorrectResult[i] << "\n" << m_CorrectResult[i + 2] << "\n";
-
- CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i])<threshold);
- CPPUNIT_ASSERT(std::abs(pixel2 - m_CorrectResult[i + 2])<threshold);
- }
- myfile.close();
- MITK_INFO << "SIMPLEX FILTER TEST SUCCESFULL :)";
- }
-
- // Tests SO2 Filter with unequal inputs
- void testExceptionSO2()
- {
- MITK_INFO << "START EXCEPTION SO2 TEST ... ";
-
- auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New();
- m_sO2->SetInput(0, inputImage);
-
- inputImage = nullptr;
- inputImage = mitk::Image::New();
- mitk::PixelType pixelType = mitk::MakeScalarPixelType<float>();
- const int NUMBER_OF_SPATIAL_DIMENSIONS = 3;
- auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS];
-
- dimensions[0] = 1;
- dimensions[1] = 1;
- dimensions[2] = 4;
-
- inputImage->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions);
-
- float* data = new float[4];
- data[0] = 1;
- data[1] = 2;
- data[2] = 3;
- data[3] = 4;
-
- inputImage->SetImportVolume(data, mitk::Image::ImportMemoryManagementType::CopyMemory);
- delete[] data;
-
- m_sO2->SetInput(1, inputImage);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_sO2->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
- }
-
- // Tests SO2 Filter with correct inputs
- void testSO2()
- {
- MITK_INFO << "START SO2 TEST ... ";
- std::vector<float> CorrectSO2Result1 = { 0, 0, 0, 0, 0 };
- std::vector<float> Test1 = { 0,0,0,51 };
- std::vector<float> CorrectSO2Result2 = { 0, 0.5, 0, 0.5, 0 };
- std::vector<float> Test2 = { 1584, 0, 0, 0 };
- std::vector<float> CorrectSO2Result3 = { 0.5, 0.5, 0, 0.5, 0 };
- std::vector<float> Test3 = { 0, 1536, 0, 0 };
- std::vector<float> CorrectSO2Result4 = { 0.5, 0.5, 0, 0.5, 0 };
- std::vector<float> Test4 = { 0, 0, 3072, 49 };
- std::vector<float> CorrectSO2Result5 = { 0.5, 0.5, 0.5, 0.5, 0 };
- std::vector<float> Test5 = { 1, 1, 1, 49 };
-
- std::vector<std::vector<float>> TestList;
- std::vector<std::vector<float>> ResultList;
-
- TestList.push_back(Test1);
- TestList.push_back(Test2);
- TestList.push_back(Test3);
- TestList.push_back(Test4);
- TestList.push_back(Test5);
-
- ResultList.push_back(CorrectSO2Result1);
- ResultList.push_back(CorrectSO2Result2);
- ResultList.push_back(CorrectSO2Result3);
- ResultList.push_back(CorrectSO2Result4);
- ResultList.push_back(CorrectSO2Result5);
-
- /*For printed pixel values and results look at: [...]\mitk-superbuild\MITK-build\Modules\PhotoacousticsLib\test\*/
- ofstream myfile;
- myfile.open("SO2TestResult.txt");
-
- for (int k = 0; k < 5; ++k)
- {
- std::vector<float> SO2Settings = TestList[k];
- std::vector<float> m_CorrectSO2Result = ResultList[k];
- auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New();
- m_sO2->SetInput(0, inputImage);
- m_sO2->SetInput(1, inputImage);
- for (unsigned int i = 0; i < SO2Settings.size(); ++i)
- m_sO2->AddSO2Settings(SO2Settings[i]);
- m_sO2->Update();
-
- mitk::Image::Pointer output = m_sO2->GetOutput(0);
- mitk::ImageReadAccessor readAccess(output);
- const float* inputDataArray = ((const float*)readAccess.GetData());
-
- for (unsigned int Pixel = 0; Pixel < inputImage->GetDimensions()[2]; ++Pixel)
- {
- auto Value = inputDataArray[Pixel];
-
- myfile << "Output(Test " << k << ") " << Pixel << ": " << "\n" << Value << "\n";
- myfile << "Correct Result: " << "\n" << m_CorrectSO2Result[Pixel] << "\n";
-
- CPPUNIT_ASSERT(std::abs(Value - m_CorrectSO2Result[Pixel]) < threshold);
- }
- }
- myfile.close();
- MITK_INFO << "SO2 TEST SUCCESFULL :)";
- }
-
- // Test exceptions for wrong wavelength inputs
- void testWavelengthExceptions()
- {
- MITK_INFO << "START WavelengthExceptions TEST ... ";
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
-
- m_SpectralUnmixingFilter->AddWavelength(300);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
-
- m_SpectralUnmixingFilter->AddWavelength(299);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
- MITK_INFO << "DONE";
- }
-
- // Test exceptions for wrong chromophore inputs
- void testNoChromophoresSelected()
- {
- MITK_INFO << "testNoChromophoresSelected";
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
- }
-
- // Test exceptions for wrong input image
- void testInputImage()
- {
- MITK_INFO << "INPUT IMAGE TEST";
- inputImage = nullptr;
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- //m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
-
- inputImage = mitk::Image::New();
- mitk::PixelType pixelType = mitk::MakeScalarPixelType<double>();
- const int NUMBER_OF_SPATIAL_DIMENSIONS = 3;
- auto* dimensions = new unsigned int[NUMBER_OF_SPATIAL_DIMENSIONS];
-
- dimensions[0] = 1;
- dimensions[1] = 1;
- dimensions[2] = 5;
-
- inputImage->Initialize(pixelType, NUMBER_OF_SPATIAL_DIMENSIONS, dimensions);
-
- double* data = new double[6];
- data[0] = 1;
- data[1] = 2;
- data[2] = 3;
- data[3] = 4;
- data[5] = 0;
-
- inputImage->SetImportVolume(data, mitk::Image::ImportMemoryManagementType::CopyMemory);
- delete[] data;
-
- m_SpectralUnmixingFilter->SetInput(inputImage);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
- }
-
- // Test exceptions for addOutputs method
- void testAddOutput()
- {
- MITK_INFO << "addOutputs TEST";
-
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->SetInput(inputImage);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
-
- for (int i = 0; i < 4; ++i)
- {
- MITK_INFO << "i: " << i;
- if (i != 2)
- {
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->AddOutputs(i);
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
- }
- else
- {
- m_SpectralUnmixingFilter->AddOutputs(2);
- m_SpectralUnmixingFilter->Update();
- for (int i = 0; i < 2; ++i)
- {
- mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i);
- mitk::ImageReadAccessor readAccess(output);
- const float* inputDataArray = ((const float*)readAccess.GetData());
- auto pixel = inputDataArray[0];
- auto pixel2 = inputDataArray[1];
-
- CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i]) < threshold);
- CPPUNIT_ASSERT(std::abs(pixel2 - m_CorrectResult[i + 2]) < threshold);
- }
- }
- }
- }
-
- // Test exceptions for weights error
- void testWeightsError()
- {
- MITK_INFO << "testWeightsError";
-
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED);
-
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
-
- m_SpectralUnmixingFilter->AddWeight(50);
- MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
-
- m_SpectralUnmixingFilter->AddWeight(50);
- m_SpectralUnmixingFilter->Update();
-
- for (int i = 0; i < 2; ++i)
- {
- mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i);
- mitk::ImageReadAccessor readAccess(output);
- const float* inputDataArray = ((const float*)readAccess.GetData());
- auto pixel = inputDataArray[0];
- auto pixel2 = inputDataArray[1];
-
- CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i]) < threshold);
- CPPUNIT_ASSERT(std::abs(pixel2 - m_CorrectResult[i + 2]) < threshold);
- }
- }
-
- // Test correct outputs
- void testOutputs()
- {
- MITK_INFO << "TEST";
-
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
-
- m_SpectralUnmixingFilter->Update();
-
- for (int i = 0; i < 2; ++i)
- {
- mitk::Image::Pointer output = m_SpectralUnmixingFilter->GetOutput(i);
- mitk::ImageReadAccessor readAccess(output);
- const float* inputDataArray = ((const float*)readAccess.GetData());
- auto pixel = inputDataArray[0];
- auto pixel2 = inputDataArray[1];
-
- CPPUNIT_ASSERT(std::abs(pixel - m_CorrectResult[i]) < threshold);
- CPPUNIT_ASSERT(std::abs(pixel2 - m_CorrectResult[i + 2]) < threshold);
-
- // test correct output dimensions and pixel type
- CPPUNIT_ASSERT(inputImage->GetDimensions()[0] == output->GetDimensions()[0]);
- CPPUNIT_ASSERT(inputImage->GetDimensions()[0] == output->GetDimensions()[1]);
- CPPUNIT_ASSERT(2 == output->GetDimensions()[2]);
- CPPUNIT_ASSERT(output->GetPixelType() == mitk::MakeScalarPixelType<float>());
- }
- }
-
- // TEST TEMPLATE:
- /*
- // Test exceptions for
- void test()
- {
- MITK_INFO << "TEST";
-
- // Set input image
- auto m_SpectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- m_SpectralUnmixingFilter->Verbose(false);
- m_SpectralUnmixingFilter->RelativeError(false);
- m_SpectralUnmixingFilter->SetInput(inputImage);
- m_SpectralUnmixingFilter->AddOutputs(2);
-
- //Set wavelengths to filter
- for (unsigned int imageIndex = 0; imageIndex < m_inputWavelengths.size(); imageIndex++)
- {
- unsigned int wavelength = m_inputWavelengths[imageIndex];
- m_SpectralUnmixingFilter->AddWavelength(wavelength);
- }
-
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED);
- m_SpectralUnmixingFilter->AddChromophore(
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED);
-
- m_SpectralUnmixingFilter->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
-
- //MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject)
- m_SpectralUnmixingFilter->Update();
- //MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject)
-
- }*/
-
- void tearDown() override
- {
- m_SpectralUnmixingFilter = nullptr;
- inputImage = nullptr;
- m_inputWavelengths.clear();
- m_CorrectResult.clear();
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkSpectralUnmixing)
diff --git a/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.cpp b/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.cpp
index 246a8c2843..8407bb074e 100644
--- a/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.cpp
+++ b/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.cpp
@@ -1,560 +1,562 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <mitkPlanarFigureIO.h>
#include "mitkCustomMimeType.h"
#include "mitkIOMimeTypes.h"
#include "mitkExceptionMacro.h"
#include "mitkPlanarAngle.h"
#include "mitkPlanarArrow.h"
#include "mitkPlanarBezierCurve.h"
#include "mitkPlanarCircle.h"
#include "mitkPlanarCross.h"
#include "mitkPlanarDoubleEllipse.h"
#include "mitkPlanarEllipse.h"
#include "mitkPlanarFourPointAngle.h"
#include "mitkPlanarLine.h"
#include "mitkPlanarPolygon.h"
#include "mitkPlanarRectangle.h"
#include "mitkPlanarSubdivisionPolygon.h"
#include "mitkPlaneGeometry.h"
#include "mitkBasePropertySerializer.h"
#include <mitkLocaleSwitch.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
namespace mitk
{
PlanarFigureIO::PlanarFigureIO()
: AbstractFileIO(PlanarFigure::GetStaticNameOfClass())
{
std::string category = "MITK PlanarFigure File";
CustomMimeType customMimeType;
customMimeType.SetCategory(category);
customMimeType.AddExtension("pf");
this->AbstractFileIOWriter::SetMimeType(customMimeType);
this->AbstractFileIOWriter::SetDescription(category);
customMimeType.AddExtension("pf");
customMimeType.AddExtension("PF");
this->AbstractFileIOReader::SetMimeType(customMimeType);
this->AbstractFileIOReader::SetDescription(category);
AbstractFileWriter::SetRanking(10);
AbstractFileReader::SetRanking(10);
this->RegisterService();
}
IFileIO::ConfidenceLevel PlanarFigureIO::GetWriterConfidenceLevel() const
{
if (AbstractFileIO::GetWriterConfidenceLevel() == Unsupported)
return Unsupported;
const auto *input = static_cast<const PlanarFigure *>(this->GetInput());
if (input != nullptr)
return Supported;
else
return Unsupported;
}
void PlanarFigureIO::Write()
{
this->ValidateOutputLocation();
mitk::LocaleSwitch localeSwitch("C");
- TiXmlDocument document;
- auto decl = new TiXmlDeclaration("1.0", "", ""); // TODO what to write here? encoding? etc....
- document.LinkEndChild(decl);
+ tinyxml2::XMLDocument document;
+ document.InsertEndChild(document.NewDeclaration());
- auto version = new TiXmlElement("Version");
+ auto *version = document.NewElement("Version");
version->SetAttribute("Writer", __FILE__);
version->SetAttribute("CVSRevision", "$Revision: 17055 $");
version->SetAttribute("FileVersion", 1);
- document.LinkEndChild(version);
+ document.InsertEndChild(version);
auto pf = dynamic_cast<const PlanarFigure*>(this->GetInput());
if (pf == nullptr)
{
mitkThrow() << "Try to safe a BaseData instance as PlanarFigure. That is not a planar figure. This should not happen and is a violated precondition. Please check the program logic.";
}
- auto pfElement = new TiXmlElement("PlanarFigure");
+ auto *pfElement = document.NewElement("PlanarFigure");
pfElement->SetAttribute("type", pf->GetNameOfClass());
- document.LinkEndChild(pfElement);
+ document.InsertEndChild(pfElement);
// Serialize property list of PlanarFigure
mitk::PropertyList::Pointer propertyList = pf->GetPropertyList();
mitk::PropertyList::PropertyMap::const_iterator it;
for (it = propertyList->GetMap()->begin(); it != propertyList->GetMap()->end(); ++it)
{
// Create seralizer for this property
const mitk::BaseProperty* prop = it->second;
std::string serializerName = std::string(prop->GetNameOfClass()) + "Serializer";
std::list<itk::LightObject::Pointer> allSerializers =
itk::ObjectFactoryBase::CreateAllInstance(serializerName.c_str());
if (allSerializers.size() != 1)
{
// No or too many serializer(s) found, skip this property
continue;
}
auto* serializer =
dynamic_cast<mitk::BasePropertySerializer*>(allSerializers.begin()->GetPointer());
if (serializer == nullptr)
{
// Serializer not valid; skip this property
}
- auto keyElement = new TiXmlElement("property");
- keyElement->SetAttribute("key", it->first);
+ auto *keyElement = document.NewElement("property");
+ keyElement->SetAttribute("key", it->first.c_str());
keyElement->SetAttribute("type", prop->GetNameOfClass());
serializer->SetProperty(prop);
- TiXmlElement* valueElement = nullptr;
+ tinyxml2::XMLElement* valueElement = nullptr;
try
{
- valueElement = serializer->Serialize();
+ valueElement = serializer->Serialize(document);
}
catch (...)
{
}
if (valueElement == nullptr)
{
// Serialization failed; skip this property
continue;
}
// Add value to property element
- keyElement->LinkEndChild(valueElement);
+ keyElement->InsertEndChild(valueElement);
// Append serialized property to property list
- pfElement->LinkEndChild(keyElement);
+ pfElement->InsertEndChild(keyElement);
}
// Serialize control points of PlanarFigure
- auto controlPointsElement = new TiXmlElement("ControlPoints");
- pfElement->LinkEndChild(controlPointsElement);
+ auto *controlPointsElement = document.NewElement("ControlPoints");
+ pfElement->InsertEndChild(controlPointsElement);
for (unsigned int i = 0; i < pf->GetNumberOfControlPoints(); i++)
{
- auto vElement = new TiXmlElement("Vertex");
+ auto *vElement = document.NewElement("Vertex");
vElement->SetAttribute("id", i);
- vElement->SetDoubleAttribute("x", pf->GetControlPoint(i)[0]);
- vElement->SetDoubleAttribute("y", pf->GetControlPoint(i)[1]);
- controlPointsElement->LinkEndChild(vElement);
+ vElement->SetAttribute("x", pf->GetControlPoint(i)[0]);
+ vElement->SetAttribute("y", pf->GetControlPoint(i)[1]);
+ controlPointsElement->InsertEndChild(vElement);
}
- auto geoElement = new TiXmlElement("Geometry");
+ auto *geoElement = document.NewElement("Geometry");
const auto* planeGeo = dynamic_cast<const PlaneGeometry*>(pf->GetPlaneGeometry());
if (planeGeo != nullptr)
{
// Write parameters of IndexToWorldTransform of the PlaneGeometry
typedef mitk::Geometry3D::TransformType TransformType;
const TransformType* affineGeometry = planeGeo->GetIndexToWorldTransform();
const TransformType::ParametersType& parameters = affineGeometry->GetParameters();
- auto vElement = new TiXmlElement("transformParam");
+ auto *vElement = document.NewElement("transformParam");
for (unsigned int i = 0; i < affineGeometry->GetNumberOfParameters(); ++i)
{
std::stringstream paramName;
paramName << "param" << i;
- vElement->SetDoubleAttribute(paramName.str().c_str(), parameters.GetElement(i));
+ vElement->SetAttribute(paramName.str().c_str(), parameters.GetElement(i));
}
- geoElement->LinkEndChild(vElement);
+ geoElement->InsertEndChild(vElement);
// Write bounds of the PlaneGeometry
typedef mitk::Geometry3D::BoundsArrayType BoundsArrayType;
const BoundsArrayType& bounds = planeGeo->GetBounds();
- vElement = new TiXmlElement("boundsParam");
+ vElement = document.NewElement("boundsParam");
for (unsigned int i = 0; i < 6; ++i)
{
std::stringstream boundName;
boundName << "bound" << i;
- vElement->SetDoubleAttribute(boundName.str().c_str(), bounds.GetElement(i));
+ vElement->SetAttribute(boundName.str().c_str(), bounds.GetElement(i));
}
- geoElement->LinkEndChild(vElement);
+ geoElement->InsertEndChild(vElement);
// Write spacing and origin of the PlaneGeometry
Vector3D spacing = planeGeo->GetSpacing();
Point3D origin = planeGeo->GetOrigin();
- geoElement->LinkEndChild(this->CreateXMLVectorElement("Spacing", spacing));
- geoElement->LinkEndChild(this->CreateXMLVectorElement("Origin", origin));
+ geoElement->InsertEndChild(this->CreateXMLVectorElement(document, "Spacing", spacing));
+ geoElement->InsertEndChild(this->CreateXMLVectorElement(document, "Origin", origin));
- pfElement->LinkEndChild(geoElement);
+ pfElement->InsertEndChild(geoElement);
}
if (this->GetOutputStream() != nullptr)
{
- *(this->GetOutputStream()) << document;
+ tinyxml2::XMLPrinter printer;
+ document.Print(&printer);
+ *(this->GetOutputStream()) << printer.CStr();
}
else
{
- if (document.SaveFile(this->GetOutputLocation()) == false)
+ if (document.SaveFile(this->GetOutputLocation().c_str()) != tinyxml2::XML_SUCCESS)
{
- MITK_ERROR << "Could not write planar figures to " << this->GetOutputLocation() << "\nTinyXML reports '" << document.ErrorDesc()
+ MITK_ERROR << "Could not write planar figures to " << this->GetOutputLocation() << "\nTinyXML reports '" << document.ErrorStr()
<< "'";
throw std::ios_base::failure("Error during writing of planar figure xml file.");
}
}
}
- TiXmlElement* mitk::PlanarFigureIO::CreateXMLVectorElement(const char* name, itk::FixedArray<mitk::ScalarType, 3> v)
+ tinyxml2::XMLElement* mitk::PlanarFigureIO::CreateXMLVectorElement(tinyxml2::XMLDocument& doc, const char* name, itk::FixedArray<mitk::ScalarType, 3> v)
{
- auto vElement = new TiXmlElement(name);
- vElement->SetDoubleAttribute("x", v.GetElement(0));
- vElement->SetDoubleAttribute("y", v.GetElement(1));
- vElement->SetDoubleAttribute("z", v.GetElement(2));
+ auto vElement = doc.NewElement(name);
+ vElement->SetAttribute("x", v.GetElement(0));
+ vElement->SetAttribute("y", v.GetElement(1));
+ vElement->SetAttribute("z", v.GetElement(2));
return vElement;
}
IFileIO::ConfidenceLevel PlanarFigureIO::GetReaderConfidenceLevel() const
{
if (AbstractFileIO::GetReaderConfidenceLevel() == Unsupported)
return Unsupported;
return Supported;
//Remark: The original reader code assumed that al pf files can be read.
//So no content checking was done. Thus was not implemented while refactoring
//to services yet. But I think it would make sense.
}
std::vector<BaseData::Pointer> PlanarFigureIO::DoRead()
{
mitk::LocaleSwitch localeSwitch("C");
std::vector<BaseData::Pointer> results;
- TiXmlDocument document;
+ tinyxml2::XMLDocument document;
if (this->GetInputStream() != nullptr)
{
std::string s(std::istreambuf_iterator<char>(*(this->GetInputStream())), {});
document.Parse(s.c_str());
//Remark: didn't use *(this->GetInputStream()) >> document;
//because our PlanarFigure files version 1 are illformed (multiple top level elements)
//and therefor tinyxml does not read them completly when streamed directly.
//only the first (version element) is read.
}
else
{
- if (!document.LoadFile(this->GetInputLocation()))
+ if (tinyxml2::XML_SUCCESS != document.LoadFile(this->GetInputLocation().c_str()))
{
- MITK_ERROR << "Could not open/read/parse " << this->GetInputLocation() << ". TinyXML reports: '" << document.ErrorDesc()
- << "'. "
- << "The error occurred in row " << document.ErrorRow() << ", column " << document.ErrorCol() << ".";
+ MITK_ERROR << "Could not open/read/parse " << this->GetInputLocation() << ". TinyXML reports: '" << document.ErrorStr() << "'.";
return {};
}
}
int fileVersion = 1;
- TiXmlElement* versionObject = document.FirstChildElement("Version");
+ auto* versionObject = document.FirstChildElement("Version");
if (versionObject != nullptr)
{
- if (versionObject->QueryIntAttribute("FileVersion", &fileVersion) != TIXML_SUCCESS)
+ if (versionObject->QueryIntAttribute("FileVersion", &fileVersion) != tinyxml2::XML_SUCCESS)
{
MITK_WARN << this->GetInputLocation() << " does not contain version information! Trying version 1 format." << std::endl;
}
}
else
{
MITK_WARN << this->GetInputLocation() << " does not contain version information! Trying version 1 format." << std::endl;
}
if (fileVersion !=
1) // add file version selection and version specific file parsing here, if newer file versions are created
{
MITK_WARN << "File version > 1 is not supported by this reader.";
return {};
}
/* file version 1 reader code */
- for (TiXmlElement* pfElement = document.FirstChildElement("PlanarFigure"); pfElement != nullptr;
+ for (auto* pfElement = document.FirstChildElement("PlanarFigure"); pfElement != nullptr;
pfElement = pfElement->NextSiblingElement("PlanarFigure"))
{
- std::string type = pfElement->Attribute("type");
+ const char* typeC = pfElement->Attribute("type");
+ std::string type = nullptr != typeC
+ ? typeC
+ : "";
mitk::PlanarFigure::Pointer planarFigure = nullptr;
if (type == "PlanarAngle")
{
planarFigure = mitk::PlanarAngle::New();
}
else if (type == "PlanarCircle")
{
planarFigure = mitk::PlanarCircle::New();
}
else if (type == "PlanarEllipse")
{
planarFigure = mitk::PlanarEllipse::New();
}
else if (type == "PlanarCross")
{
planarFigure = mitk::PlanarCross::New();
}
else if (type == "PlanarFourPointAngle")
{
planarFigure = mitk::PlanarFourPointAngle::New();
}
else if (type == "PlanarLine")
{
planarFigure = mitk::PlanarLine::New();
}
else if (type == "PlanarPolygon")
{
planarFigure = mitk::PlanarPolygon::New();
}
else if (type == "PlanarSubdivisionPolygon")
{
planarFigure = mitk::PlanarSubdivisionPolygon::New();
}
else if (type == "PlanarRectangle")
{
planarFigure = mitk::PlanarRectangle::New();
}
else if (type == "PlanarArrow")
{
planarFigure = mitk::PlanarArrow::New();
}
else if (type == "PlanarDoubleEllipse")
{
planarFigure = mitk::PlanarDoubleEllipse::New();
}
else if (type == "PlanarBezierCurve")
{
planarFigure = mitk::PlanarBezierCurve::New();
}
else
{
// unknown type
MITK_WARN << "encountered unknown planar figure type '" << type << "'. Skipping this element.";
continue;
}
// Read properties of the planar figure
- for (TiXmlElement* propertyElement = pfElement->FirstChildElement("property"); propertyElement != nullptr;
+ for (auto* propertyElement = pfElement->FirstChildElement("property"); propertyElement != nullptr;
propertyElement = propertyElement->NextSiblingElement("property"))
{
const char* keya = propertyElement->Attribute("key");
const std::string key(keya ? keya : "");
const char* typea = propertyElement->Attribute("type");
const std::string type(typea ? typea : "");
// hand propertyElement to specific reader
std::stringstream propertyDeserializerClassName;
propertyDeserializerClassName << type << "Serializer";
const std::list<itk::LightObject::Pointer> readers =
itk::ObjectFactoryBase::CreateAllInstance(propertyDeserializerClassName.str().c_str());
if (readers.size() < 1)
{
MITK_ERROR << "No property reader found for " << type;
}
if (readers.size() > 1)
{
MITK_WARN << "Multiple property readers found for " << type << ". Using arbitrary first one.";
}
for (auto iter = readers.cbegin(); iter != readers.cend(); ++iter)
{
if (auto* reader = dynamic_cast<BasePropertySerializer*>(iter->GetPointer()))
{
const BaseProperty::Pointer property = reader->Deserialize(propertyElement->FirstChildElement());
if (property.IsNotNull())
{
planarFigure->GetPropertyList()->ReplaceProperty(key, property);
}
else
{
MITK_ERROR << "There were errors while loading property '" << key << "' of type " << type
<< ". Your data may be corrupted";
}
break;
}
}
}
// If we load a planarFigure, it has definitely been placed correctly.
// If we do not set this property here, we cannot load old planarFigures
// without messing up the interaction (PF-Interactor needs this property.
planarFigure->GetPropertyList()->SetBoolProperty("initiallyplaced", true);
// Which features (length or circumference etc) a figure has is decided by whether it is closed or not
// the function SetClosed has to be called in case of PlanarPolygons to ensure they hold the correct feature
auto* planarPolygon = dynamic_cast<PlanarPolygon*>(planarFigure.GetPointer());
if (planarPolygon != nullptr)
{
bool isClosed = false;
planarFigure->GetPropertyList()->GetBoolProperty("closed", isClosed);
planarPolygon->SetClosed(isClosed);
}
// Read geometry of containing plane
- TiXmlElement* geoElement = pfElement->FirstChildElement("Geometry");
+ auto* geoElement = pfElement->FirstChildElement("Geometry");
if (geoElement != nullptr)
{
try
{
// Create plane geometry
mitk::PlaneGeometry::Pointer planeGeo = mitk::PlaneGeometry::New();
// Extract and set plane transform parameters
const DoubleList transformList =
this->GetDoubleAttributeListFromXMLNode(geoElement->FirstChildElement("transformParam"), "param", 12);
typedef mitk::BaseGeometry::TransformType TransformType;
TransformType::ParametersType parameters;
parameters.SetSize(12);
unsigned int i;
DoubleList::const_iterator it;
for (it = transformList.cbegin(), i = 0; it != transformList.cend(); ++it, ++i)
{
parameters.SetElement(i, *it);
}
typedef mitk::BaseGeometry::TransformType TransformType;
TransformType::Pointer affineGeometry = TransformType::New();
affineGeometry->SetParameters(parameters);
planeGeo->SetIndexToWorldTransform(affineGeometry);
// Extract and set plane bounds
const DoubleList boundsList =
this->GetDoubleAttributeListFromXMLNode(geoElement->FirstChildElement("boundsParam"), "bound", 6);
typedef mitk::BaseGeometry::BoundsArrayType BoundsArrayType;
BoundsArrayType bounds;
for (it = boundsList.cbegin(), i = 0; it != boundsList.cend(); ++it, ++i)
{
bounds[i] = *it;
}
planeGeo->SetBounds(bounds);
// Extract and set spacing and origin
const Vector3D spacing = this->GetVectorFromXMLNode(geoElement->FirstChildElement("Spacing"));
planeGeo->SetSpacing(spacing);
const Point3D origin = this->GetPointFromXMLNode(geoElement->FirstChildElement("Origin"));
planeGeo->SetOrigin(origin);
planarFigure->SetPlaneGeometry(planeGeo);
}
catch (...)
{
}
}
- TiXmlElement* cpElement = pfElement->FirstChildElement("ControlPoints");
+ auto* cpElement = pfElement->FirstChildElement("ControlPoints");
bool first = true;
if (cpElement != nullptr)
- for (TiXmlElement* vertElement = cpElement->FirstChildElement("Vertex"); vertElement != nullptr;
+ for (auto* vertElement = cpElement->FirstChildElement("Vertex"); vertElement != nullptr;
vertElement = vertElement->NextSiblingElement("Vertex"))
{
int id = 0;
mitk::Point2D::ValueType x = 0.0;
mitk::Point2D::ValueType y = 0.0;
- if (vertElement->QueryIntAttribute("id", &id) == TIXML_WRONG_TYPE)
+ if (vertElement->QueryIntAttribute("id", &id) != tinyxml2::XML_SUCCESS)
return{}; // TODO: can we do a better error handling?
- if (vertElement->QueryDoubleAttribute("x", &x) == TIXML_WRONG_TYPE)
+ if (vertElement->QueryDoubleAttribute("x", &x) != tinyxml2::XML_SUCCESS)
return{}; // TODO: can we do a better error handling?
- if (vertElement->QueryDoubleAttribute("y", &y) == TIXML_WRONG_TYPE)
+ if (vertElement->QueryDoubleAttribute("y", &y) != tinyxml2::XML_SUCCESS)
return{}; // TODO: can we do a better error handling?
Point2D p;
p.SetElement(0, x);
p.SetElement(1, y);
if (first == true) // needed to set m_FigurePlaced to true
{
planarFigure->PlaceFigure(p);
first = false;
}
planarFigure->SetControlPoint(id, p, true);
}
// Calculate feature quantities of this PlanarFigure
planarFigure->EvaluateFeatures();
// Make sure that no control point is currently selected
planarFigure->DeselectControlPoint();
if (planarFigure.IsNotNull())
{
results.emplace_back(planarFigure);
}
}
return results;
}
mitk::PlanarFigureIO::DoubleList mitk::PlanarFigureIO::GetDoubleAttributeListFromXMLNode(
- TiXmlElement* e, const char* attributeNameBase, unsigned int count)
+ const tinyxml2::XMLElement* e, const char* attributeNameBase, unsigned int count)
{
DoubleList list;
if (e == nullptr)
throw std::invalid_argument("node invalid"); // TODO: can we do a better error handling?
for (unsigned int i = 0; i < count; ++i)
{
mitk::ScalarType p(-1.0);
std::stringstream attributeName;
attributeName << attributeNameBase << i;
- if (e->QueryDoubleAttribute(attributeName.str().c_str(), &p) == TIXML_WRONG_TYPE)
+ if (e->QueryDoubleAttribute(attributeName.str().c_str(), &p) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
list.push_back(p);
}
return list;
}
- mitk::Point3D mitk::PlanarFigureIO::GetPointFromXMLNode(TiXmlElement* e)
+ mitk::Point3D mitk::PlanarFigureIO::GetPointFromXMLNode(const tinyxml2::XMLElement* e)
{
if (e == nullptr)
throw std::invalid_argument("node invalid"); // TODO: can we do a better error handling?
mitk::Point3D point;
mitk::ScalarType p(-1.0);
- if (e->QueryDoubleAttribute("x", &p) == TIXML_WRONG_TYPE)
+ if (e->QueryDoubleAttribute("x", &p) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
point.SetElement(0, p);
- if (e->QueryDoubleAttribute("y", &p) == TIXML_WRONG_TYPE)
+ if (e->QueryDoubleAttribute("y", &p) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
point.SetElement(1, p);
- if (e->QueryDoubleAttribute("z", &p) == TIXML_WRONG_TYPE)
+ if (e->QueryDoubleAttribute("z", &p) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
point.SetElement(2, p);
return point;
}
- mitk::Vector3D mitk::PlanarFigureIO::GetVectorFromXMLNode(TiXmlElement* e)
+ mitk::Vector3D mitk::PlanarFigureIO::GetVectorFromXMLNode(const tinyxml2::XMLElement* e)
{
if (e == nullptr)
throw std::invalid_argument("node invalid"); // TODO: can we do a better error handling?
mitk::Vector3D vector;
mitk::ScalarType p(-1.0);
- if (e->QueryDoubleAttribute("x", &p) == TIXML_WRONG_TYPE)
+ if (e->QueryDoubleAttribute("x", &p) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
vector.SetElement(0, p);
- if (e->QueryDoubleAttribute("y", &p) == TIXML_WRONG_TYPE)
+ if (e->QueryDoubleAttribute("y", &p) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
vector.SetElement(1, p);
- if (e->QueryDoubleAttribute("z", &p) == TIXML_WRONG_TYPE)
+ if (e->QueryDoubleAttribute("z", &p) != tinyxml2::XML_SUCCESS)
throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
vector.SetElement(2, p);
return vector;
}
PlanarFigureIO *PlanarFigureIO::IOClone() const { return new PlanarFigureIO(*this); }
} // namespace
diff --git a/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.h b/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.h
index 215ca99134..2033cfd0a4 100644
--- a/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.h
+++ b/Modules/PlanarFigure/autoload/IO/mitkPlanarFigureIO.h
@@ -1,92 +1,97 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITK_PLANAR_FIGURE_IO_H
#define MITK_PLANAR_FIGURE_IO_H
#include <mitkAbstractFileIO.h>
#include <mitkPlanarFigure.h>
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
/**
* Reads/Writes a PlanarFigure to a file
* @ingroup Process
*/
class PlanarFigureIO : public mitk::AbstractFileIO
{
public:
typedef mitk::PlanarFigure InputType;
PlanarFigureIO();
// -------------- AbstractFileReader -------------
using AbstractFileReader::Read;
ConfidenceLevel GetReaderConfidenceLevel() const override;
// -------------- AbstractFileWriter -------------
void Write() override;
ConfidenceLevel GetWriterConfidenceLevel() const override;
protected:
/**
* @brief Reads a number of mitk::PlanarFigures from the file system
* @return a vector of mitk::PlanarFigures
* @throws throws an mitk::Exception if an error ocurrs during parsing the nrrd header
*/
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
using DoubleList = std::list<double>;
/**
* \brief parses the element for the attributes name0 to nameN, where "name" and the number of attributes
* to read are passed as argument. Returns a list of double vales.
- * \param[in] e the TiXmlElement that will be parsed
+ * \param[in] e the XML element that will be parsed
* \param[in] attributeNameBase the basic name of the parameters
* \param[in] count the number of parameters
* \return returns a mitk::Point3D with the values x,y,z
*/
- DoubleList GetDoubleAttributeListFromXMLNode(TiXmlElement* e, const char* attributeNameBase, unsigned int count);
+ DoubleList GetDoubleAttributeListFromXMLNode(const tinyxml2::XMLElement* e, const char* attributeNameBase, unsigned int count);
/**
* \brief parses the element for the attributes x,y,z and returns a mitk::Vector3D filled with these values
- * \param[in] e the TiXmlElement that will be parsed
+ * \param[in] e the XML element that will be parsed
* \return returns a mitk::Vector3D with the values x,y,z
*/
- static mitk::Vector3D GetVectorFromXMLNode(TiXmlElement* e);
+ static mitk::Vector3D GetVectorFromXMLNode(const tinyxml2::XMLElement* e);
/**
* \brief parses the element for the attributes x,y,z and returns a mitk::Point3D filled with these values
- * \param[in] e the TiXmlElement that will be parsed
+ * \param[in] e the XML element that will be parsed
* \return returns a mitk::Point3D with the values x,y,z
*/
- static mitk::Point3D GetPointFromXMLNode(TiXmlElement* e);
+ static mitk::Point3D GetPointFromXMLNode(const tinyxml2::XMLElement* e);
/**Documentation
* \brief creates a TinyXML element that contains x, y, and z values
*
+ * \param[in] doc
* \param[in] name the name of the XML element
* \param[in] v the vector or point that contains the x, y and z values
- * \return returns a TiXmlElement named name and three attributes x, y and z.
+ * \return returns a XML element named name and three attributes x, y and z.
*/
- static TiXmlElement* CreateXMLVectorElement(const char* name, itk::FixedArray<mitk::ScalarType, 3> v);
+ static tinyxml2::XMLElement* CreateXMLVectorElement(tinyxml2::XMLDocument& doc, const char* name, itk::FixedArray<mitk::ScalarType, 3> v);
private:
PlanarFigureIO *IOClone() const override;
};
} // end of namespace mitk
#endif // MITK_PLANAR_FIGURE_IO_H
diff --git a/Modules/Python/autoload/PythonService/CMakeLists.txt b/Modules/Python/autoload/PythonService/CMakeLists.txt
index 57455c3863..c0b5d4f8f6 100644
--- a/Modules/Python/autoload/PythonService/CMakeLists.txt
+++ b/Modules/Python/autoload/PythonService/CMakeLists.txt
@@ -1,15 +1,15 @@
mitkFunctionCheckCompilerFlags("-Wno-cpp" CMAKE_CXX_FLAGS)
mitk_create_module(PythonService
INCLUDE_DIRS
PRIVATE src/PythonService
DEPENDS PUBLIC MitkPython
PACKAGE_DEPENDS
PUBLIC Qt5|Widgets CTK|CTKScriptingPythonCore+CTKScriptingPythonWidgets
- AUTOLOAD_WITH MitkPython
+ PRIVATE Python3|NumPy
+ AUTOLOAD_WITH MitkPython
)
if(TARGET ${MODULE_TARGET})
- target_link_libraries(${MODULE_TARGET} PUBLIC Python3::NumPy)
configure_file(PythonPath.h.in "${CMAKE_CURRENT_BINARY_DIR}/PythonPath.h" @ONLY)
endif()
diff --git a/Modules/QtWidgets/CMakeLists.txt b/Modules/QtWidgets/CMakeLists.txt
index f383232898..7d4c22415b 100644
--- a/Modules/QtWidgets/CMakeLists.txt
+++ b/Modules/QtWidgets/CMakeLists.txt
@@ -1,8 +1,8 @@
MITK_CREATE_MODULE(
INCLUDE_DIRS PRIVATE resource # for xpm includes
DEPENDS MitkPlanarFigure MitkAnnotation
PACKAGE_DEPENDS
- PUBLIC ITK|ITKIOImageBase VTK|GUISupportQt+RenderingQt Qt5|Widgets+OpenGL+Core
+ PUBLIC VTK|GUISupportQt+RenderingQt Qt5|Widgets+OpenGL+Core
)
add_subdirectory(test)
diff --git a/Modules/QtWidgets/include/QmitkRenderWindow.h b/Modules/QtWidgets/include/QmitkRenderWindow.h
index 308235e392..124352da5a 100644
--- a/Modules/QtWidgets/include/QmitkRenderWindow.h
+++ b/Modules/QtWidgets/include/QmitkRenderWindow.h
@@ -1,154 +1,158 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QMITKRENDERWINDOW_H
#define QMITKRENDERWINDOW_H
#include "mitkRenderWindowBase.h"
#include "QmitkRenderWindowMenu.h"
#include <MitkQtWidgetsExports.h>
#include <vtkGenericOpenGLRenderWindow.h>
#include <QVTKOpenGLNativeWidget.h>
#include "mitkBaseRenderer.h"
#include "mitkInteractionEventConst.h"
class QDragEnterEvent;
class QDropEvent;
class QInputEvent;
class QMouseEvent;
/**
* \ingroup QmitkModule
* \brief MITK implementation of the QVTKWidget
*/
class MITKQTWIDGETS_EXPORT QmitkRenderWindow : public QVTKOpenGLNativeWidget, public mitk::RenderWindowBase
{
Q_OBJECT
public:
QmitkRenderWindow(
QWidget *parent = nullptr,
const QString &name = "unnamed renderwindow",
mitk::VtkPropRenderer *renderer = nullptr);
~QmitkRenderWindow() override;
/**
* \brief Whether Qt events should be passed to parent (default: true)
*
* With introduction of the QVTKWidget the behaviour regarding Qt events changed.
* QVTKWidget "accepts" Qt events like mouse clicks (i.e. set an "accepted" flag).
* When this flag is set, Qt fininshed handling of this event -- otherwise it is
* reached through to the widget's parent.
*
* This reaching through to the parent was implicitly required by QmitkMaterialWidget / QmitkMaterialShowCase.
*
* The default behaviour of QmitkRenderWindow is now to clear the "accepted" flag
* of Qt events after they were handled by QVTKWidget. This way parents can also
* handle events.
*
* If you don't want this behaviour, call SetResendQtEvents(true) on your render window.
*/
virtual void SetResendQtEvents(bool resend);
// Set Layout Index to define the Layout Type
void SetLayoutIndex(QmitkRenderWindowMenu::LayoutIndex layoutIndex);
// Get Layout Index to define the Layout Type
QmitkRenderWindowMenu::LayoutIndex GetLayoutIndex();
// MenuWidget need to update the Layout Design List when Layout had changed
- void LayoutDesignListChanged(QmitkRenderWindowMenu::LayoutDesign layoutDesign);
+ void UpdateLayoutDesignList(QmitkRenderWindowMenu::LayoutDesign layoutDesign);
+
+ void UpdateCrosshairVisibility(bool);
+
+ void UpdateCrosshairRotationMode(int);
// Activate or Deactivate MenuWidget.
void ActivateMenuWidget(bool state);
bool GetActivateMenuWidgetFlag() { return m_MenuWidgetActivated; }
// Get it from the QVTKWidget parent
vtkRenderWindow *GetVtkRenderWindow() override { return this->renderWindow(); }
vtkRenderWindowInteractor *GetVtkRenderWindowInteractor() override { return nullptr; }
protected:
// catch-all event handler
bool event(QEvent *e) override;
// overloaded move handler
void moveEvent(QMoveEvent *event) override;
// overloaded show handler
void showEvent(QShowEvent *event) override;
// overloaded enter handler
void enterEvent(QEvent *) override;
// overloaded leave handler
void leaveEvent(QEvent *) override;
// Overloaded resize handler, see decs in QVTKOpenGLWidget.
// Basically, we have to ensure the VTK rendering is updated for each change in window size.
void resizeGL(int w, int h) override;
/// \brief Simply says we accept the event type.
void dragEnterEvent(QDragEnterEvent *event) override;
/// \brief If the dropped type is application/x-mitk-datanodes we process the request by converting to mitk::DataNode
/// pointers and emitting the NodesDropped signal.
void dropEvent(QDropEvent *event) override;
void AdjustRenderWindowMenuVisibility(const QPoint &pos);
Q_SIGNALS:
void LayoutDesignChanged(QmitkRenderWindowMenu::LayoutDesign);
void ResetView();
void CrosshairRotationModeChanged(int);
void CrosshairVisibilityChanged(bool);
void moved();
/// \brief Emits a signal to say that this window has had the following nodes dropped on it.
void NodesDropped(QmitkRenderWindow *thisWindow, std::vector<mitk::DataNode *> nodes);
void mouseEvent(QMouseEvent *);
private Q_SLOTS:
void DeferredHideMenu();
private:
// Helper Functions to Convert Qt-Events to Mitk-Events
mitk::Point2D GetMousePosition(QMouseEvent *me) const;
mitk::Point2D GetMousePosition(QWheelEvent *we) const;
mitk::InteractionEvent::MouseButtons GetEventButton(QMouseEvent *me) const;
mitk::InteractionEvent::MouseButtons GetButtonState(QMouseEvent *me) const;
mitk::InteractionEvent::ModifierKeys GetModifiers(QInputEvent *me) const;
mitk::InteractionEvent::MouseButtons GetButtonState(QWheelEvent *we) const;
std::string GetKeyLetter(QKeyEvent *ke) const;
int GetDelta(QWheelEvent *we) const;
bool m_ResendQtEvents;
QmitkRenderWindowMenu *m_MenuWidget;
bool m_MenuWidgetActivated;
QmitkRenderWindowMenu::LayoutIndex m_LayoutIndex;
vtkSmartPointer<vtkGenericOpenGLRenderWindow> m_InternalRenderWindow;
};
#endif // QMITKRENDERWINDOW_H
diff --git a/Modules/QtWidgets/include/QmitkRenderWindowMenu.h b/Modules/QtWidgets/include/QmitkRenderWindowMenu.h
index c01bbf9449..705ffc8a19 100644
--- a/Modules/QtWidgets/include/QmitkRenderWindowMenu.h
+++ b/Modules/QtWidgets/include/QmitkRenderWindowMenu.h
@@ -1,210 +1,214 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QMITKRENDERWINDOWMENU_H
#define QMITKRENDERWINDOWMENU_H
#if defined(_WIN32) || defined(__APPLE__)
#define QMITK_USE_EXTERNAL_RENDERWINDOW_MENU
#endif
// mitk qtwidgets module
#include "MitkQtWidgetsExports.h"
#include "QmitkMultiWidgetLayoutManager.h"
// mitk core
#include <mitkBaseRenderer.h>
// qt
#include <QAction>
#include <QEvent>
#include <QLabel>
#include <QMenuBar>
#include <QPushButton>
#include <QTimer>
#include <QToolButton>
#include <QWidget>
/**
* \ingroup QmitkModule
* \brief The QmitkRenderWindowMenu is a popup Widget which shows
* up when the mouse cursor enter a QmitkRenderWindow.
* The Menu Widget is located in the right top corner of each
* RenderWindow. It includes different settings. For example
* the layout design can be changed with the setting button. Switching
* between full-screen mode and layout design can be done
* with the full-screen button.
* The popup Widget can be deactivated with ActivateMenuWidget(false) in
* QmitkRenderWindow.
*
* \sa QmitkRenderWindow
*
*/
class MITKQTWIDGETS_EXPORT QmitkRenderWindowMenu : public QWidget
{
Q_OBJECT
public:
using LayoutIndex = mitk::BaseRenderer::ViewDirection;
using LayoutDesign = QmitkMultiWidgetLayoutManager::LayoutDesign;
QmitkRenderWindowMenu(QWidget *parent = nullptr,
Qt::WindowFlags f = nullptr,
mitk::BaseRenderer *b = nullptr);
~QmitkRenderWindowMenu() override;
/*! Return visibility of settings menu. The menu is connected with m_SettingsButton and includes
layout direction (axial, coronal .. ) and layout design (standard layout, 2D images top,
3D bottom ... ). */
bool GetSettingsMenuVisibilty()
{
if (m_LayoutActionsMenu == nullptr)
return false;
else
return m_LayoutActionsMenu->isVisible();
}
/*! Set layout index. Defines layout direction (axial, coronal, sagital or threeD) of the parent. */
void SetLayoutIndex(LayoutIndex layoutIndex);
/*! Return layout direction of parent (axial, coronal, sagital or threeD) */
LayoutIndex GetLayoutIndex() { return m_Layout; }
/*! Update list of layout design (standard layout, 2D images top, 3D bottom ..). Set action of current layout design
to disable and all other to enable. */
void UpdateLayoutDesignList(LayoutDesign layoutDesign);
+ void UpdateCrosshairVisibility(bool visible);
+
+ void UpdateCrosshairRotationMode(int mode);
+
/*! Move menu widget to correct position (right upper corner). E.g. it is necessary when the full-screen mode
is activated.*/
#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU
void MoveWidgetToCorrectPos(float opacity);
#else
void MoveWidgetToCorrectPos(float /*opacity*/);
#endif
void ShowMenu();
void HideMenu();
protected:
/*! Reimplemented from QWidget. The paint event is a request to repaint all or part of a widget.*/
void paintEvent(QPaintEvent *event) override;
void CreateMenuWidget();
/*! Create settings menu which contains layout direction and the different layout designs. */
void CreateSettingsWidget();
/*! Change Icon of full-screen button depending on full-screen mode. */
void ChangeFullScreenIcon();
Q_SIGNALS:
void ResetView(); // == "global reinit"
void CrosshairVisibilityChanged(bool);
// \brief int parameters are enum from QmitkStdMultiWidget
void CrosshairRotationModeChanged(int);
/*! emit signal, when layout design changed by the setting menu.*/
void LayoutDesignChanged(LayoutDesign layoutDesign);
public Q_SLOTS:
void DeferredShowMenu();
void DeferredHideMenu();
/*! This method is responsible for non fluttering of
the renderWindowMenu when mouse cursor moves along the renderWindowMenu*/
void smoothHide();
protected Q_SLOTS:
void enterEvent(QEvent * /*e*/) override;
void leaveEvent(QEvent * /*e*/) override;
/// this function is continuously called by a timer
/// to do the auto rotation
void AutoRotateNextStep();
/// this function is invoked when the auto-rotate action
/// is clicked
void OnAutoRotationActionTriggered();
void OnTSNumChanged(int);
void OnCrosshairMenuAboutToShow();
void OnCrosshairVisibilityChanged(bool);
void OnCrosshairRotationModeSelected(QAction *);
/*! slot for activating/deactivating the full-screen mode. The slot is connected to the clicked() event of
m_FullScreenButton.
Activating the full-screen maximize the current widget, deactivating restore If layout design changed by the settings
menu, the full-Screen mode is automatically switched to false. */
void OnFullScreenButton(bool checked);
/*! Slot for opening setting menu. The slot is connected to the clicked() event of m_SettingsButton.
The settings menu includes different layout directions (axial, coronal, sagittal and 3D) as well all layout design
(standard layout, 2D images top, 3D bottom ..)*/
void OnLayoutDesignButton(bool checked);
void OnSetLayout(LayoutDesign layoutDesign);
protected:
QToolButton* m_CrosshairModeButton;
QToolButton* m_FullScreenButton;
QToolButton* m_LayoutDesignButton;
QMenu* m_LayoutActionsMenu;
QAction* m_DefaultLayoutAction;
QAction* m_All2DTop3DBottomLayoutAction;
QAction* m_All2DLeft3DRightLayoutAction;
QAction* m_OneBigLayoutAction;
QAction* m_Only2DHorizontalLayoutAction;
QAction* m_Only2DVerticalLayoutAction;
QAction* m_OneTop3DBottomLayoutAction;
QAction* m_OneLeft3DRightLayoutAction;
QAction* m_AllHorizontalLayoutAction;
QAction* m_AllVerticalLayoutAction;
QAction* m_RemoveOneLayoutAction;
QLabel *m_TSLabel;
QMenu *m_CrosshairMenu;
/*! Flag if full-screen mode is activated or deactivated. */
bool m_FullScreenMode;
private:
mitk::BaseRenderer::Pointer m_Renderer;
QTimer* m_AutoRotationTimer;
QTimer* m_HideTimer;
QWidget *m_Parent;
//memory because mode is set to default for slice num = 1
static unsigned int m_DefaultThickMode;
int m_CrosshairRotationMode;
bool m_CrosshairVisibility;
LayoutIndex m_Layout;
LayoutDesign m_LayoutDesign;
LayoutDesign m_OldLayoutDesign;
};
#endif // QMITKRENDERWINDOWMENU_H
diff --git a/Modules/QtWidgets/include/QmitkStdMultiWidget.h b/Modules/QtWidgets/include/QmitkStdMultiWidget.h
index fcd57a81b2..7d1cca97a8 100644
--- a/Modules/QtWidgets/include/QmitkStdMultiWidget.h
+++ b/Modules/QtWidgets/include/QmitkStdMultiWidget.h
@@ -1,158 +1,161 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QMITKSTDMULTIWIDGET_H
#define QMITKSTDMULTIWIDGET_H
// qt widgets module
#include "MitkQtWidgetsExports.h"
#include "QmitkAbstractMultiWidget.h"
/**
* @brief The 'QmitkStdMultiWidget' is a 'QmitkAbstractMultiWidget' that is used to display multiple render windows at once.
* Render windows are predefined in a 2x2 design with 3 different 2D view planes and a 3D render window.
*/
class MITKQTWIDGETS_EXPORT QmitkStdMultiWidget : public QmitkAbstractMultiWidget
{
Q_OBJECT
public:
QmitkStdMultiWidget(
QWidget *parent = nullptr,
Qt::WindowFlags f = nullptr,
const QString &name = "stdmulti");
~QmitkStdMultiWidget() override;
virtual void InitializeMultiWidget() override;
virtual QmitkRenderWindow* GetRenderWindow(const QString& widgetName) const override;
virtual QmitkRenderWindow* GetRenderWindow(const mitk::BaseRenderer::ViewDirection& viewDirection) const override;
virtual void SetSelectedPosition(const mitk::Point3D& newPosition, const QString& widgetName) override;
virtual const mitk::Point3D GetSelectedPosition(const QString& widgetName) const override;
virtual void SetCrosshairVisibility(bool) override;
virtual bool GetCrosshairVisibility() const override;
virtual void ResetCrosshair() override;
virtual void SetWidgetPlaneMode(int mode) override;
mitk::SliceNavigationController* GetTimeNavigationController();
void AddPlanesToDataStorage();
void RemovePlanesFromDataStorage();
/** \brief Listener to the CrosshairPositionEvent
Ensures the CrosshairPositionEvent is handled only once and at the end of the Qt-Event loop
*/
void HandleCrosshairPositionEvent();
/**
* @brief Convenience method to get a render window widget.
* @param number of the widget (0-3)
* @return The render window widget
*/
QmitkRenderWindow* GetRenderWindow(unsigned int number) const;
QmitkRenderWindow* GetRenderWindow1() const;
QmitkRenderWindow* GetRenderWindow2() const;
QmitkRenderWindow* GetRenderWindow3() const;
QmitkRenderWindow* GetRenderWindow4() const;
/**
* @brief Convenience method to get a widget plane.
* @param number of the widget plane (1-3)
* @return The widget plane as data node
*/
mitk::DataNode::Pointer GetWidgetPlane(unsigned int number) const;
mitk::DataNode::Pointer GetWidgetPlane1() const;
mitk::DataNode::Pointer GetWidgetPlane2() const;
mitk::DataNode::Pointer GetWidgetPlane3() const;
/**
* @brief SetDecorationColor Set the color of the decoration of the 4 widgets.
*
* This is used to color the frame of the renderwindow and the corner annatation.
* For the first 3 widgets, this color is a property of the helper object nodes
* which contain the respective plane geometry. For widget 4, this is a member,
* since there is no data node for this widget.
*/
void SetDecorationColor(unsigned int widgetNumber, mitk::Color color);
/**
* @brief GetDecorationColorForWidget Get the color for annotation, crosshair and rectangle.
* @param widgetNumber Number of the renderwindow (0-3).
* @return Color in mitk format.
*/
mitk::Color GetDecorationColor(unsigned int widgetNumber);
public Q_SLOTS:
// mouse events
virtual void mousePressEvent(QMouseEvent*) override;
virtual void moveEvent(QMoveEvent* e) override;
virtual void wheelEvent(QWheelEvent* e) override;
/// Receives the signal from HandleCrosshairPositionEvent, executes the StatusBar update
void HandleCrosshairPositionEventDelayed();
void Fit();
void AddDisplayPlaneSubTree();
void EnsureDisplayContainsPoint(mitk::BaseRenderer *renderer, const mitk::Point3D &p);
void SetWidgetPlaneVisibility(const char *widgetName, bool visible, mitk::BaseRenderer *renderer = nullptr);
void SetWidgetPlanesVisibility(bool visible, mitk::BaseRenderer *renderer = nullptr);
Q_SIGNALS:
+ void NotifyCrosshairVisibilityChanged(bool visible);
+ void NotifyCrosshairRotationModeChanged(int mode);
+
void WheelMoved(QWheelEvent *);
void Moved();
private:
virtual void SetLayoutImpl() override;
virtual void SetInteractionSchemeImpl() override { }
void CreateRenderWindowWidgets();
mitk::SliceNavigationController* m_TimeNavigationController;
/**
* @brief The 3 helper objects which contain the plane geometry.
*/
mitk::DataNode::Pointer m_PlaneNode1;
mitk::DataNode::Pointer m_PlaneNode2;
mitk::DataNode::Pointer m_PlaneNode3;
/**
* @brief m_ParentNodeForGeometryPlanes This helper object is added to the datastorage
* and contains the 3 planes for displaying the image geometry (crosshair and 3D planes).
*/
mitk::DataNode::Pointer m_ParentNodeForGeometryPlanes;
/**
* @brief m_DecorationColorWidget4 color for annotation and rectangle of widget 4.
*
* For other widgets1-3, the color is a property of the respective data node.
* There is no node for widget 4, hence, we need an extra member.
*/
mitk::Color m_DecorationColorWidget4;
bool m_PendingCrosshairPositionEvent;
};
#endif // QMITKSTDMULTIWIDGET_H
diff --git a/Modules/QtWidgets/src/QmitkMultiWidgetLayoutManager.cpp b/Modules/QtWidgets/src/QmitkMultiWidgetLayoutManager.cpp
index 522f7bcdc1..0c5a1111cc 100644
--- a/Modules/QtWidgets/src/QmitkMultiWidgetLayoutManager.cpp
+++ b/Modules/QtWidgets/src/QmitkMultiWidgetLayoutManager.cpp
@@ -1,541 +1,541 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkMultiWidgetLayoutManager.h"
#include <mitkLogMacros.h>
#include <QmitkAbstractMultiWidget.h>
#include <QmitkRenderWindow.h>
#include <QmitkRenderWindowWidget.h>
// qt
#include <QHBoxLayout>
#include <qsplitter.h>
QmitkMultiWidgetLayoutManager::QmitkMultiWidgetLayoutManager(QmitkAbstractMultiWidget* multiwidget)
: QObject(multiwidget)
, m_MultiWidget(multiwidget)
, m_CurrentRenderWindowWidget(nullptr)
{
// nothing here
}
void QmitkMultiWidgetLayoutManager::SetLayoutDesign(LayoutDesign layoutDesign)
{
if (nullptr == m_MultiWidget)
{
return;
}
// retrieve the render window name from the sending render window
auto renderWindow = dynamic_cast<QmitkRenderWindow*>(QObject::sender());
m_CurrentRenderWindowWidget = m_MultiWidget->GetRenderWindowWidget(renderWindow).get();
switch (layoutDesign)
{
case LayoutDesign::DEFAULT:
{
SetDefaultLayout();
break;
}
case LayoutDesign::ALL_2D_TOP_3D_BOTTOM:
{
SetAll2DTop3DBottomLayout();
break;
}
case LayoutDesign::ALL_2D_LEFT_3D_RIGHT:
{
SetAll2DLeft3DRightLayout();
break;
}
case LayoutDesign::ONE_BIG:
{
SetOneBigLayout();
break;
}
case LayoutDesign::ONLY_2D_HORIZONTAL:
{
SetOnly2DHorizontalLayout();
break;
}
case LayoutDesign::ONLY_2D_VERTICAL:
{
SetOnly2DVerticalLayout();
break;
}
case LayoutDesign::ONE_TOP_3D_BOTTOM:
{
SetOneTop3DBottomLayout();
break;
}
case LayoutDesign::ONE_LEFT_3D_RIGHT:
{
SetOneLeft3DRightLayout();
break;
}
case LayoutDesign::ALL_HORIZONTAL:
{
SetAllHorizontalLayout();
break;
}
case LayoutDesign::ALL_VERTICAL:
{
SetAllVerticalLayout();
break;
}
case LayoutDesign::REMOVE_ONE:
{
RemoveOneLayout();
break;
}
case LayoutDesign::NONE:
{
break;
}
};
}
void QmitkMultiWidgetLayoutManager::SetCurrentRenderWindowWidget(QmitkRenderWindowWidget* renderWindowWidget)
{
m_CurrentRenderWindowWidget = renderWindowWidget;
}
void QmitkMultiWidgetLayoutManager::SetDefaultLayout()
{
MITK_INFO << "Set default layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(Qt::Vertical, m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
QList<int> splitterSizeRow;
for (int row = 0; row < m_MultiWidget->GetRowCount(); ++row)
{
splitterSizeRow.push_back(1000);
QList<int> splitterSizeColumn;
auto splitter = new QSplitter(mainSplit);
for (int column = 0; column < m_MultiWidget->GetColumnCount(); ++column)
{
splitterSizeColumn.push_back(1000);
auto renderWindowWidget = m_MultiWidget->GetRenderWindowWidget(row, column);
splitter->addWidget(renderWindowWidget.get());
renderWindowWidget->show();
}
splitter->setSizes(splitterSizeColumn);
}
mainSplit->setSizes(splitterSizeRow);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::DEFAULT);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::DEFAULT);
}
}
void QmitkMultiWidgetLayoutManager::SetAll2DTop3DBottomLayout()
{
MITK_INFO << "Set all 2D top and 3D bottom layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(Qt::Vertical, m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
auto subSplit2D = new QSplitter(mainSplit);
QList<int> splitterSize;
auto all2DRenderWindowWidgets = m_MultiWidget->Get2DRenderWindowWidgets();
for (const auto& renderWindowWidget : all2DRenderWindowWidgets)
{
subSplit2D->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
subSplit2D->setSizes(splitterSize);
auto subSplit3D = new QSplitter(mainSplit);
splitterSize.clear();
auto all3DRenderWindowWidgets = m_MultiWidget->Get3DRenderWindowWidgets();
for (const auto& renderWindowWidget : all3DRenderWindowWidgets)
{
subSplit3D->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
subSplit3D->setSizes(splitterSize);
// set size for main splitter
splitterSize.clear();
splitterSize.push_back(600);
splitterSize.push_back(1000);
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ALL_2D_TOP_3D_BOTTOM);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ALL_2D_TOP_3D_BOTTOM);
}
}
void QmitkMultiWidgetLayoutManager::SetAll2DLeft3DRightLayout()
{
MITK_INFO << "Set all 2D left and 3D right layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
auto subSplit2D = new QSplitter(Qt::Vertical, mainSplit);
QList<int> splitterSize;
auto all2DRenderWindowWidgets = m_MultiWidget->Get2DRenderWindowWidgets();
for (const auto& renderWindowWidget : all2DRenderWindowWidgets)
{
subSplit2D->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
subSplit2D->setSizes(splitterSize);
auto subSplit3D = new QSplitter(mainSplit);
splitterSize.clear();
auto all3DRenderWindowWidgets = m_MultiWidget->Get3DRenderWindowWidgets();
for (const auto& renderWindowWidget : all3DRenderWindowWidgets)
{
subSplit3D->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
subSplit3D->setSizes(splitterSize);
// set size for main splitter
splitterSize.clear();
splitterSize.push_back(600);
splitterSize.push_back(1000);
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ALL_2D_LEFT_3D_RIGHT);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ALL_2D_LEFT_3D_RIGHT);
}
}
void QmitkMultiWidgetLayoutManager::SetOneBigLayout()
{
MITK_INFO << "Set single 2D layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
mainSplit->addWidget(m_CurrentRenderWindowWidget);
m_CurrentRenderWindowWidget->show();
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ONE_BIG);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ONE_BIG);
}
}
void QmitkMultiWidgetLayoutManager::SetOnly2DHorizontalLayout()
{
MITK_INFO << "Set only 2D layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
QList<int> splitterSize;
auto all2DRenderWindowWidgets = m_MultiWidget->Get2DRenderWindowWidgets();
for (const auto& renderWindowWidget : all2DRenderWindowWidgets)
{
mainSplit->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ONLY_2D_HORIZONTAL);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ONLY_2D_HORIZONTAL);
}
}
void QmitkMultiWidgetLayoutManager::SetOnly2DVerticalLayout()
{
MITK_INFO << "Set only 2D layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(Qt::Vertical, m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
QList<int> splitterSize;
auto all2DRenderWindowWidgets = m_MultiWidget->Get2DRenderWindowWidgets();
for (const auto& renderWindowWidget : all2DRenderWindowWidgets)
{
mainSplit->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ONLY_2D_VERTICAL);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ONLY_2D_VERTICAL);
}
}
void QmitkMultiWidgetLayoutManager::SetOneTop3DBottomLayout()
{
MITK_INFO << "Set one top and all 3D bottom layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(Qt::Vertical, m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
mainSplit->addWidget(m_CurrentRenderWindowWidget);
m_CurrentRenderWindowWidget->show();
auto subSplit3D = new QSplitter(mainSplit);
QList<int> splitterSize;
auto all3DRenderWindowWidgets = m_MultiWidget->Get3DRenderWindowWidgets();
for (const auto& renderWindowWidget : all3DRenderWindowWidgets)
{
subSplit3D->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
subSplit3D->setSizes(splitterSize);
// set size for main splitter
splitterSize.clear();
splitterSize.push_back(1000);
splitterSize.push_back(1000);
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ONE_TOP_3D_BOTTOM);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ONE_TOP_3D_BOTTOM);
}
}
void QmitkMultiWidgetLayoutManager::SetOneLeft3DRightLayout()
{
MITK_INFO << "Set one left and all 3D right layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
mainSplit->addWidget(m_CurrentRenderWindowWidget);
m_CurrentRenderWindowWidget->show();
auto subSplit3D = new QSplitter(Qt::Vertical, mainSplit);
QList<int> splitterSize;
auto all3DRenderWindowWidgets = m_MultiWidget->Get3DRenderWindowWidgets();
for (const auto& renderWindowWidget : all3DRenderWindowWidgets)
{
subSplit3D->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
subSplit3D->setSizes(splitterSize);
// set size for main splitter
splitterSize.clear();
splitterSize.push_back(1000);
splitterSize.push_back(1000);
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ONE_LEFT_3D_RIGHT);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ONE_LEFT_3D_RIGHT);
}
}
void QmitkMultiWidgetLayoutManager::SetAllHorizontalLayout()
{
MITK_INFO << "Set default layout" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
QList<int> splitterSize;
auto allRenderWindowWidgets = m_MultiWidget->GetRenderWindowWidgets();
for (const auto& renderWindowWidget : allRenderWindowWidgets)
{
if (nullptr != renderWindowWidget.second)
{
mainSplit->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
}
// set size for main splitter
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ALL_HORIZONTAL);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ALL_HORIZONTAL);
}
}
void QmitkMultiWidgetLayoutManager::SetAllVerticalLayout()
{
MITK_INFO << "Set all vertical" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
delete m_MultiWidget->layout();
auto hBoxLayout = new QHBoxLayout(m_MultiWidget);
hBoxLayout->setContentsMargins(0, 0, 0, 0);
m_MultiWidget->setLayout(hBoxLayout);
hBoxLayout->setMargin(0);
auto mainSplit = new QSplitter(Qt::Vertical, m_MultiWidget);
hBoxLayout->addWidget(mainSplit);
QList<int> splitterSize;
auto allRenderWindowWidgets = m_MultiWidget->GetRenderWindowWidgets();
for (const auto& renderWindowWidget : allRenderWindowWidgets)
{
mainSplit->addWidget(renderWindowWidget.second.get());
renderWindowWidget.second->show();
splitterSize.push_back(1000);
}
// set size for splitter
mainSplit->setSizes(splitterSize);
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::ALL_VERTICAL);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::ALL_VERTICAL);
}
}
void QmitkMultiWidgetLayoutManager::RemoveOneLayout()
{
MITK_INFO << "Remove single render window" << std::endl;
m_MultiWidget->ActivateMenuWidget(false);
m_CurrentRenderWindowWidget->hide();
m_MultiWidget->ActivateMenuWidget(true);
auto allRenderWindows = m_MultiWidget->GetRenderWindows();
for (auto& renderWindow : allRenderWindows)
{
- renderWindow->LayoutDesignListChanged(LayoutDesign::NONE);
+ renderWindow->UpdateLayoutDesignList(LayoutDesign::NONE);
}
}
diff --git a/Modules/QtWidgets/src/QmitkRenderWindow.cpp b/Modules/QtWidgets/src/QmitkRenderWindow.cpp
index 6405ef419c..bf51c1fc4a 100644
--- a/Modules/QtWidgets/src/QmitkRenderWindow.cpp
+++ b/Modules/QtWidgets/src/QmitkRenderWindow.cpp
@@ -1,458 +1,468 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkRenderWindow.h"
#include "mitkInteractionKeyEvent.h"
#include "mitkInternalEvent.h"
#include "mitkMouseDoubleClickEvent.h"
#include "mitkMouseMoveEvent.h"
#include "mitkMousePressEvent.h"
#include "mitkMouseReleaseEvent.h"
#include "mitkMouseWheelEvent.h"
#include <QCursor>
#include <QDragEnterEvent>
#include <QDropEvent>
#include <QKeyEvent>
#include <QMouseEvent>
#include <QResizeEvent>
#include <QSurfaceFormat>
#include <QTimer>
#include <QWheelEvent>
#include <QWindow>
#include "QmitkMimeTypes.h"
#include "QmitkRenderWindowMenu.h"
QmitkRenderWindow::QmitkRenderWindow(QWidget *parent, const QString &name, mitk::VtkPropRenderer *)
: QVTKOpenGLNativeWidget(parent)
, m_ResendQtEvents(true)
, m_MenuWidget(nullptr)
, m_MenuWidgetActivated(false)
, m_LayoutIndex(QmitkRenderWindowMenu::LayoutIndex::AXIAL)
{
m_InternalRenderWindow = vtkSmartPointer<vtkGenericOpenGLRenderWindow>::New();
m_InternalRenderWindow->SetMultiSamples(0);
m_InternalRenderWindow->SetAlphaBitPlanes(0);
setRenderWindow(m_InternalRenderWindow);
Initialize(name.toStdString().c_str());
setFocusPolicy(Qt::StrongFocus);
setMouseTracking(true);
QSizePolicy sizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
setSizePolicy(sizePolicy);
}
QmitkRenderWindow::~QmitkRenderWindow()
{
Destroy(); // Destroy mitkRenderWindowBase
}
void QmitkRenderWindow::SetResendQtEvents(bool resend)
{
m_ResendQtEvents = resend;
}
void QmitkRenderWindow::SetLayoutIndex(QmitkRenderWindowMenu::LayoutIndex layoutIndex)
{
m_LayoutIndex = layoutIndex;
if (nullptr != m_MenuWidget)
{
m_MenuWidget->SetLayoutIndex(layoutIndex);
}
}
QmitkRenderWindowMenu::LayoutIndex QmitkRenderWindow::GetLayoutIndex()
{
if (nullptr != m_MenuWidget)
{
return m_MenuWidget->GetLayoutIndex();
}
else
{
return QmitkRenderWindowMenu::LayoutIndex::AXIAL;
}
}
-void QmitkRenderWindow::LayoutDesignListChanged(QmitkRenderWindowMenu::LayoutDesign layoutDesign)
+void QmitkRenderWindow::UpdateLayoutDesignList(QmitkRenderWindowMenu::LayoutDesign layoutDesign)
{
if (nullptr != m_MenuWidget)
{
m_MenuWidget->UpdateLayoutDesignList(layoutDesign);
}
}
+void QmitkRenderWindow::UpdateCrosshairVisibility(bool visible)
+{
+ m_MenuWidget->UpdateCrosshairVisibility(visible);
+}
+
+void QmitkRenderWindow::UpdateCrosshairRotationMode(int mode)
+{
+ m_MenuWidget->UpdateCrosshairRotationMode(mode);
+}
+
void QmitkRenderWindow::ActivateMenuWidget(bool state)
{
if (nullptr == m_MenuWidget)
{
m_MenuWidget = new QmitkRenderWindowMenu(this, nullptr, m_Renderer);
m_MenuWidget->SetLayoutIndex(m_LayoutIndex);
}
m_MenuWidgetActivated = state;
if (m_MenuWidgetActivated)
{
connect(m_MenuWidget, &QmitkRenderWindowMenu::LayoutDesignChanged, this, &QmitkRenderWindow::LayoutDesignChanged);
connect(m_MenuWidget, &QmitkRenderWindowMenu::ResetView, this, &QmitkRenderWindow::ResetView);
connect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairVisibilityChanged, this, &QmitkRenderWindow::CrosshairVisibilityChanged);
connect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairRotationModeChanged, this, &QmitkRenderWindow::CrosshairRotationModeChanged);
}
else
{
disconnect(m_MenuWidget, &QmitkRenderWindowMenu::LayoutDesignChanged, this, &QmitkRenderWindow::LayoutDesignChanged);
disconnect(m_MenuWidget, &QmitkRenderWindowMenu::ResetView, this, &QmitkRenderWindow::ResetView);
disconnect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairVisibilityChanged, this, &QmitkRenderWindow::CrosshairVisibilityChanged);
disconnect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairRotationModeChanged, this, &QmitkRenderWindow::CrosshairRotationModeChanged);
m_MenuWidget->hide();
}
}
void QmitkRenderWindow::moveEvent(QMoveEvent *event)
{
QVTKOpenGLNativeWidget::moveEvent(event);
// after a move the overlays need to be positioned
emit moved();
}
void QmitkRenderWindow::showEvent(QShowEvent *event)
{
QVTKOpenGLNativeWidget::showEvent(event);
// this singleshot is necessary to have the overlays positioned correctly after initial show
// simple call of moved() is no use here!!
QTimer::singleShot(0, this, SIGNAL(moved()));
}
bool QmitkRenderWindow::event(QEvent* e)
{
mitk::InteractionEvent::Pointer mitkEvent = nullptr;
switch (e->type())
{
case QEvent::MouseMove:
{
auto me = static_cast<QMouseEvent *>(e);
this->AdjustRenderWindowMenuVisibility(me->pos());
mitkEvent = mitk::MouseMoveEvent::New(m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me));
break;
}
case QEvent::MouseButtonPress:
{
auto me = static_cast<QMouseEvent *>(e);
mitkEvent = mitk::MousePressEvent::New( m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me), GetEventButton(me));
break;
}
case QEvent::MouseButtonRelease:
{
auto me = static_cast<QMouseEvent *>(e);
mitkEvent = mitk::MouseReleaseEvent::New( m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me), GetEventButton(me));
break;
}
case QEvent::MouseButtonDblClick:
{
auto me = static_cast<QMouseEvent *>(e);
mitkEvent = mitk::MouseDoubleClickEvent::New( m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me), GetEventButton(me));
break;
}
case QEvent::Wheel:
{
auto we = static_cast<QWheelEvent *>(e);
mitkEvent = mitk::MouseWheelEvent::New( m_Renderer, GetMousePosition(we), GetButtonState(we), GetModifiers(we), GetDelta(we));
break;
}
case QEvent::KeyPress:
{
auto ke = static_cast<QKeyEvent*>(e);
mitkEvent = mitk::InteractionKeyEvent::New(m_Renderer, GetKeyLetter(ke), GetModifiers(ke));
break;
}
default:
{
break;
}
}
if (mitkEvent != nullptr)
{
if (this->HandleEvent(mitkEvent.GetPointer())) {
return m_ResendQtEvents ? false : true;
}
}
return QVTKOpenGLNativeWidget::event(e);
}
void QmitkRenderWindow::enterEvent(QEvent *e)
{
// TODO implement new event
QVTKOpenGLNativeWidget::enterEvent(e);
}
void QmitkRenderWindow::leaveEvent(QEvent *e)
{
mitk::InternalEvent::Pointer internalEvent = mitk::InternalEvent::New(this->m_Renderer, nullptr, "LeaveRenderWindow");
this->HandleEvent(internalEvent.GetPointer());
if (nullptr != m_MenuWidget)
{
m_MenuWidget->smoothHide();
}
QVTKOpenGLNativeWidget::leaveEvent(e);
}
void QmitkRenderWindow::resizeGL(int w, int h)
{
QVTKOpenGLNativeWidget::resizeGL(w, h);
mitk::RenderingManager::GetInstance()->ForceImmediateUpdate(renderWindow());
}
void QmitkRenderWindow::dragEnterEvent(QDragEnterEvent *event)
{
if (event->mimeData()->hasFormat("application/x-mitk-datanodes"))
{
event->accept();
}
}
void QmitkRenderWindow::dropEvent(QDropEvent *event)
{
QList<mitk::DataNode *> dataNodeList = QmitkMimeTypes::ToDataNodePtrList(event->mimeData());
if (!dataNodeList.empty())
{
emit NodesDropped(this, dataNodeList.toVector().toStdVector());
}
}
void QmitkRenderWindow::AdjustRenderWindowMenuVisibility(const QPoint & /*pos*/)
{
if (nullptr != m_MenuWidget)
{
m_MenuWidget->ShowMenu();
m_MenuWidget->MoveWidgetToCorrectPos(1.0f);
}
}
void QmitkRenderWindow::DeferredHideMenu()
{
MITK_DEBUG << "QmitkRenderWindow::DeferredHideMenu";
if (nullptr != m_MenuWidget)
{
m_MenuWidget->HideMenu();
}
}
mitk::Point2D QmitkRenderWindow::GetMousePosition(QMouseEvent *me) const
{
mitk::Point2D point;
point[0] = me->x();
// We need to convert the y component, as the display and vtk have other definitions for the y direction
point[1] = m_Renderer->GetSizeY() - me->y();
return point;
}
mitk::Point2D QmitkRenderWindow::GetMousePosition(QWheelEvent *we) const
{
mitk::Point2D point;
point[0] = we->x();
// We need to convert the y component, as the display and vtk have other definitions for the y direction
point[1] = m_Renderer->GetSizeY() - we->y();
return point;
}
mitk::InteractionEvent::MouseButtons QmitkRenderWindow::GetEventButton(QMouseEvent *me) const
{
mitk::InteractionEvent::MouseButtons eventButton;
switch (me->button())
{
case Qt::LeftButton:
eventButton = mitk::InteractionEvent::LeftMouseButton;
break;
case Qt::RightButton:
eventButton = mitk::InteractionEvent::RightMouseButton;
break;
case Qt::MidButton:
eventButton = mitk::InteractionEvent::MiddleMouseButton;
break;
default:
eventButton = mitk::InteractionEvent::NoButton;
break;
}
return eventButton;
}
mitk::InteractionEvent::MouseButtons QmitkRenderWindow::GetButtonState(QMouseEvent *me) const
{
mitk::InteractionEvent::MouseButtons buttonState = mitk::InteractionEvent::NoButton;
if (me->buttons() & Qt::LeftButton)
{
buttonState = buttonState | mitk::InteractionEvent::LeftMouseButton;
}
if (me->buttons() & Qt::RightButton)
{
buttonState = buttonState | mitk::InteractionEvent::RightMouseButton;
}
if (me->buttons() & Qt::MidButton)
{
buttonState = buttonState | mitk::InteractionEvent::MiddleMouseButton;
}
return buttonState;
}
mitk::InteractionEvent::ModifierKeys QmitkRenderWindow::GetModifiers(QInputEvent *me) const
{
mitk::InteractionEvent::ModifierKeys modifiers = mitk::InteractionEvent::NoKey;
if (me->modifiers() & Qt::ALT)
{
modifiers = modifiers | mitk::InteractionEvent::AltKey;
}
if (me->modifiers() & Qt::CTRL)
{
modifiers = modifiers | mitk::InteractionEvent::ControlKey;
}
if (me->modifiers() & Qt::SHIFT)
{
modifiers = modifiers | mitk::InteractionEvent::ShiftKey;
}
return modifiers;
}
mitk::InteractionEvent::MouseButtons QmitkRenderWindow::GetButtonState(QWheelEvent *we) const
{
mitk::InteractionEvent::MouseButtons buttonState = mitk::InteractionEvent::NoButton;
if (we->buttons() & Qt::LeftButton)
{
buttonState = buttonState | mitk::InteractionEvent::LeftMouseButton;
}
if (we->buttons() & Qt::RightButton)
{
buttonState = buttonState | mitk::InteractionEvent::RightMouseButton;
}
if (we->buttons() & Qt::MidButton)
{
buttonState = buttonState | mitk::InteractionEvent::MiddleMouseButton;
}
return buttonState;
}
std::string QmitkRenderWindow::GetKeyLetter(QKeyEvent *ke) const
{
// Converting Qt Key Event to string element.
std::string key = "";
int tkey = ke->key();
if (tkey < 128)
{ // standard ascii letter
key = (char)toupper(tkey);
}
else
{ // special keys
switch (tkey)
{
case Qt::Key_Return:
key = mitk::InteractionEvent::KeyReturn;
break;
case Qt::Key_Enter:
key = mitk::InteractionEvent::KeyEnter;
break;
case Qt::Key_Escape:
key = mitk::InteractionEvent::KeyEsc;
break;
case Qt::Key_Delete:
key = mitk::InteractionEvent::KeyDelete;
break;
case Qt::Key_Up:
key = mitk::InteractionEvent::KeyArrowUp;
break;
case Qt::Key_Down:
key = mitk::InteractionEvent::KeyArrowDown;
break;
case Qt::Key_Left:
key = mitk::InteractionEvent::KeyArrowLeft;
break;
case Qt::Key_Right:
key = mitk::InteractionEvent::KeyArrowRight;
break;
case Qt::Key_F1:
key = mitk::InteractionEvent::KeyF1;
break;
case Qt::Key_F2:
key = mitk::InteractionEvent::KeyF2;
break;
case Qt::Key_F3:
key = mitk::InteractionEvent::KeyF3;
break;
case Qt::Key_F4:
key = mitk::InteractionEvent::KeyF4;
break;
case Qt::Key_F5:
key = mitk::InteractionEvent::KeyF5;
break;
case Qt::Key_F6:
key = mitk::InteractionEvent::KeyF6;
break;
case Qt::Key_F7:
key = mitk::InteractionEvent::KeyF7;
break;
case Qt::Key_F8:
key = mitk::InteractionEvent::KeyF8;
break;
case Qt::Key_F9:
key = mitk::InteractionEvent::KeyF9;
break;
case Qt::Key_F10:
key = mitk::InteractionEvent::KeyF10;
break;
case Qt::Key_F11:
key = mitk::InteractionEvent::KeyF11;
break;
case Qt::Key_F12:
key = mitk::InteractionEvent::KeyF12;
break;
case Qt::Key_End:
key = mitk::InteractionEvent::KeyEnd;
break;
case Qt::Key_Home:
key = mitk::InteractionEvent::KeyPos1;
break;
case Qt::Key_Insert:
key = mitk::InteractionEvent::KeyInsert;
break;
case Qt::Key_PageDown:
key = mitk::InteractionEvent::KeyPageDown;
break;
case Qt::Key_PageUp:
key = mitk::InteractionEvent::KeyPageUp;
break;
case Qt::Key_Space:
key = mitk::InteractionEvent::KeySpace;
break;
}
}
return key;
}
int QmitkRenderWindow::GetDelta(QWheelEvent *we) const
{
return we->delta();
}
diff --git a/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp b/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp
index a30529f10d..59c39115ef 100644
--- a/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp
+++ b/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp
@@ -1,648 +1,658 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkRenderWindowMenu.h"
// mitk core
#include "mitkProperties.h"
#include "mitkResliceMethodProperty.h"
// qt
#include <QHBoxLayout>
#include <QPainter>
#include <QSize>
#include <QSpacerItem>
#include <QSlider>
#include <QGroupBox>
#include <QLine>
#include <QRadioButton>
#include <QWidgetAction>
//#include"iconClose.xpm"
#include "iconCrosshairMode.xpm"
#include "iconFullScreen.xpm"
//#include"iconHoriSplit.xpm"
#include "iconSettings.xpm"
//#include"iconVertiSplit.xpm"
#include "iconLeaveFullScreen.xpm"
// c++
#include <cmath>
unsigned int QmitkRenderWindowMenu::m_DefaultThickMode(1);
#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU
QmitkRenderWindowMenu::QmitkRenderWindowMenu(QWidget* parent,
Qt::WindowFlags,
mitk::BaseRenderer* baseRenderer)
: QWidget(nullptr, Qt::Tool | Qt::FramelessWindowHint)
#else
QmitkRenderWindowMenu::QmitkRenderWindowMenu(QWidget* parent,
Qt::WindowFlags flags,
mitk::BaseRenderer* baseRenderer)
: QWidget(parent, flags)
#endif
, m_LayoutActionsMenu(nullptr)
, m_CrosshairMenu(nullptr)
, m_FullScreenMode(false)
, m_Renderer(baseRenderer)
, m_Parent(parent)
, m_CrosshairRotationMode(0)
, m_CrosshairVisibility(true)
, m_Layout(LayoutIndex::AXIAL)
, m_LayoutDesign(LayoutDesign::DEFAULT)
, m_OldLayoutDesign(LayoutDesign::DEFAULT)
{
CreateMenuWidget();
setMinimumWidth(61); // DIRTY.. If you add or remove a button, you need to change the size.
setMaximumWidth(61);
setAutoFillBackground(true);
// Else part fixes the render window menu issue on Linux bug but caused bugs on macOS and Windows
// for macOS see bug 3192
// for Windows see bug 12130
//... so macOS and Windows must be treated differently:
#if defined(Q_OS_MAC)
this->show();
this->setWindowOpacity(0.0f);
#else
this->setVisible(false);
#endif
m_AutoRotationTimer = new QTimer(this);
m_AutoRotationTimer->setInterval(75);
m_HideTimer = new QTimer(this);
m_HideTimer->setSingleShot(true);
connect(m_AutoRotationTimer, &QTimer::timeout, this, &QmitkRenderWindowMenu::AutoRotateNextStep);
connect(m_HideTimer, &QTimer::timeout, this, &QmitkRenderWindowMenu::DeferredHideMenu);
connect(m_Parent, &QObject::destroyed, this, &QmitkRenderWindowMenu::deleteLater);
}
QmitkRenderWindowMenu::~QmitkRenderWindowMenu()
{
if (m_AutoRotationTimer->isActive())
{
m_AutoRotationTimer->stop();
}
}
void QmitkRenderWindowMenu::SetLayoutIndex(LayoutIndex layoutIndex)
{
m_Layout = layoutIndex;
}
void QmitkRenderWindowMenu::UpdateLayoutDesignList(LayoutDesign layoutDesign)
{
m_LayoutDesign = layoutDesign;
if (nullptr == m_LayoutActionsMenu)
{
CreateSettingsWidget();
}
m_DefaultLayoutAction->setEnabled(true);
m_All2DTop3DBottomLayoutAction->setEnabled(true);
m_All2DLeft3DRightLayoutAction->setEnabled(true);
m_OneBigLayoutAction->setEnabled(true);
m_Only2DHorizontalLayoutAction->setEnabled(true);
m_Only2DVerticalLayoutAction->setEnabled(true);
m_OneTop3DBottomLayoutAction->setEnabled(true);
m_OneLeft3DRightLayoutAction->setEnabled(true);
m_AllHorizontalLayoutAction->setEnabled(true);
m_AllVerticalLayoutAction->setEnabled(true);
m_RemoveOneLayoutAction->setEnabled(true);
switch (m_LayoutDesign)
{
case LayoutDesign::DEFAULT:
{
m_DefaultLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ALL_2D_TOP_3D_BOTTOM:
{
m_All2DTop3DBottomLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ALL_2D_LEFT_3D_RIGHT:
{
m_All2DLeft3DRightLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ONE_BIG:
{
m_OneBigLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ONLY_2D_HORIZONTAL:
{
m_Only2DHorizontalLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ONLY_2D_VERTICAL:
{
m_Only2DVerticalLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ONE_TOP_3D_BOTTOM:
{
m_OneTop3DBottomLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ONE_LEFT_3D_RIGHT:
{
m_OneLeft3DRightLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ALL_HORIZONTAL:
{
m_AllHorizontalLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::ALL_VERTICAL:
{
m_AllVerticalLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::REMOVE_ONE:
{
m_RemoveOneLayoutAction->setEnabled(false);
break;
}
case LayoutDesign::NONE:
{
break;
}
}
}
+void QmitkRenderWindowMenu::UpdateCrosshairVisibility(bool visible)
+{
+ m_CrosshairVisibility = visible;
+}
+
+void QmitkRenderWindowMenu::UpdateCrosshairRotationMode(int mode)
+{
+ m_CrosshairRotationMode = mode;
+}
+
#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU
void QmitkRenderWindowMenu::MoveWidgetToCorrectPos(float opacity)
#else
void QmitkRenderWindowMenu::MoveWidgetToCorrectPos(float /*opacity*/)
#endif
{
#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU
int X = floor(double(this->m_Parent->width() - this->width() - 8.0));
int Y = 7;
QPoint pos = this->m_Parent->mapToGlobal(QPoint(0, 0));
this->move(X + pos.x(), Y + pos.y());
if (opacity < 0)
opacity = 0;
else if (opacity > 1)
opacity = 1;
this->setWindowOpacity(opacity);
#else
int moveX = floor(double(this->m_Parent->width() - this->width() - 4.0));
this->move(moveX, 3);
this->show();
#endif
}
void QmitkRenderWindowMenu::ShowMenu()
{
MITK_DEBUG << "menu showMenu";
DeferredShowMenu();
}
void QmitkRenderWindowMenu::HideMenu()
{
MITK_DEBUG << "menu hideEvent";
DeferredHideMenu();
}
void QmitkRenderWindowMenu::paintEvent(QPaintEvent * /*e*/)
{
QPainter painter(this);
QColor semiTransparentColor = Qt::black;
semiTransparentColor.setAlpha(255);
painter.fillRect(rect(), semiTransparentColor);
}
void QmitkRenderWindowMenu::CreateMenuWidget()
{
QHBoxLayout *layout = new QHBoxLayout(this);
layout->setAlignment(Qt::AlignRight);
layout->setContentsMargins(1, 1, 1, 1);
QSize size(13, 13);
m_CrosshairMenu = new QMenu(this);
connect(m_CrosshairMenu, &QMenu::aboutToShow, this, &QmitkRenderWindowMenu::OnCrosshairMenuAboutToShow);
m_CrosshairModeButton = new QToolButton(this);
m_CrosshairModeButton->setMaximumSize(15, 15);
m_CrosshairModeButton->setIconSize(size);
m_CrosshairModeButton->setMenu(m_CrosshairMenu);
m_CrosshairModeButton->setIcon(QIcon(QPixmap(iconCrosshairMode_xpm)));
m_CrosshairModeButton->setPopupMode(QToolButton::InstantPopup);
m_CrosshairModeButton->setStyleSheet("QToolButton::menu-indicator { image: none; }");
m_CrosshairModeButton->setAutoRaise(true);
layout->addWidget(m_CrosshairModeButton);
m_FullScreenButton = new QToolButton(this);
m_FullScreenButton->setMaximumSize(15, 15);
m_FullScreenButton->setIconSize(size);
m_FullScreenButton->setIcon(QIcon(QPixmap(iconFullScreen_xpm)));
m_FullScreenButton->setAutoRaise(true);
layout->addWidget(m_FullScreenButton);
m_LayoutDesignButton = new QToolButton(this);
m_LayoutDesignButton->setMaximumSize(15, 15);
m_LayoutDesignButton->setIconSize(size);
m_LayoutDesignButton->setIcon(QIcon(QPixmap(iconSettings_xpm)));
m_LayoutDesignButton->setAutoRaise(true);
layout->addWidget(m_LayoutDesignButton);
connect(m_FullScreenButton, &QToolButton::clicked, this, &QmitkRenderWindowMenu::OnFullScreenButton);
connect(m_LayoutDesignButton, &QToolButton::clicked, this, &QmitkRenderWindowMenu::OnLayoutDesignButton);
}
void QmitkRenderWindowMenu::CreateSettingsWidget()
{
m_LayoutActionsMenu = new QMenu(this);
m_DefaultLayoutAction = new QAction("Standard layout", m_LayoutActionsMenu);
m_DefaultLayoutAction->setDisabled(true);
m_All2DTop3DBottomLayoutAction = new QAction("All 2D top, 3D bottom", m_LayoutActionsMenu);
m_All2DTop3DBottomLayoutAction->setDisabled(false);
m_All2DLeft3DRightLayoutAction = new QAction("All 2D left, 3D right", m_LayoutActionsMenu);
m_All2DLeft3DRightLayoutAction->setDisabled(false);
m_OneBigLayoutAction = new QAction("This big", m_LayoutActionsMenu);
m_OneBigLayoutAction->setDisabled(false);
m_Only2DHorizontalLayoutAction = new QAction("Only 2D horizontal", m_LayoutActionsMenu);
m_Only2DHorizontalLayoutAction->setDisabled(false);
m_Only2DVerticalLayoutAction = new QAction("Only 2D vertical", m_LayoutActionsMenu);
m_Only2DVerticalLayoutAction->setDisabled(false);
m_OneTop3DBottomLayoutAction = new QAction("This top, 3D bottom", m_LayoutActionsMenu);
m_OneTop3DBottomLayoutAction->setDisabled(false);
m_OneLeft3DRightLayoutAction = new QAction("This left, 3D right", m_LayoutActionsMenu);
m_OneLeft3DRightLayoutAction->setDisabled(false);
m_AllHorizontalLayoutAction = new QAction("All horizontal", m_LayoutActionsMenu);
m_AllHorizontalLayoutAction->setDisabled(false);
m_AllVerticalLayoutAction = new QAction("All vertical", m_LayoutActionsMenu);
m_AllVerticalLayoutAction->setDisabled(false);
m_RemoveOneLayoutAction = new QAction("Remove this", m_LayoutActionsMenu);
m_RemoveOneLayoutAction->setDisabled(false);
m_LayoutActionsMenu->addAction(m_DefaultLayoutAction);
m_LayoutActionsMenu->addAction(m_All2DTop3DBottomLayoutAction);
m_LayoutActionsMenu->addAction(m_All2DLeft3DRightLayoutAction);
m_LayoutActionsMenu->addAction(m_OneBigLayoutAction);
m_LayoutActionsMenu->addAction(m_Only2DHorizontalLayoutAction);
m_LayoutActionsMenu->addAction(m_Only2DVerticalLayoutAction);
m_LayoutActionsMenu->addAction(m_OneTop3DBottomLayoutAction);
m_LayoutActionsMenu->addAction(m_OneLeft3DRightLayoutAction);
m_LayoutActionsMenu->addAction(m_AllHorizontalLayoutAction);
m_LayoutActionsMenu->addAction(m_AllVerticalLayoutAction);
m_LayoutActionsMenu->addAction(m_RemoveOneLayoutAction);
m_LayoutActionsMenu->setVisible(false);
connect(m_DefaultLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::DEFAULT); });
connect(m_All2DTop3DBottomLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_2D_TOP_3D_BOTTOM); });
connect(m_All2DLeft3DRightLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_2D_LEFT_3D_RIGHT); });
connect(m_OneBigLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONE_BIG); });
connect(m_Only2DHorizontalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONLY_2D_HORIZONTAL); });
connect(m_Only2DVerticalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONLY_2D_VERTICAL); });
connect(m_OneTop3DBottomLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONE_TOP_3D_BOTTOM); });
connect(m_OneLeft3DRightLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONE_LEFT_3D_RIGHT); });
connect(m_AllHorizontalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_HORIZONTAL); });
connect(m_AllVerticalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_VERTICAL); });
connect(m_RemoveOneLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::REMOVE_ONE); });
}
void QmitkRenderWindowMenu::ChangeFullScreenIcon()
{
m_FullScreenButton->setIcon(m_FullScreenMode ? QPixmap(iconLeaveFullScreen_xpm) : QPixmap(iconFullScreen_xpm));
}
void QmitkRenderWindowMenu::DeferredShowMenu()
{
MITK_DEBUG << "deferred show menu";
m_HideTimer->stop();
// Else part fixes the render window menu issue on Linux bug but caused bugs on macOS and Windows
// for macOS see bug 3192
// for Windows see bug 12130
//... so macOS and Windows must be treated differently:
#if defined(Q_OS_MAC)
this->setWindowOpacity(1.0f);
#else
this->setVisible(true);
this->raise();
#endif
}
void QmitkRenderWindowMenu::DeferredHideMenu()
{
MITK_DEBUG << "menu deferredhidemenu";
// Else part fixes the render window menu issue on Linux bug but caused bugs on macOS and Windows
// for macOS see bug 3192
// for Windows see bug 12130
//... so macOS and Windows must be treated differently:
#if defined(Q_OS_MAC)
this->setWindowOpacity(0.0f);
#else
this->setVisible(false);
#endif
}
void QmitkRenderWindowMenu::smoothHide()
{
MITK_DEBUG << "menu leaveEvent";
m_HideTimer->start(10);
}
void QmitkRenderWindowMenu::enterEvent(QEvent * /*e*/)
{
MITK_DEBUG << "menu enterEvent";
DeferredShowMenu();
}
void QmitkRenderWindowMenu::leaveEvent(QEvent * /*e*/)
{
MITK_DEBUG << "menu leaveEvent";
smoothHide();
}
void QmitkRenderWindowMenu::AutoRotateNextStep()
{
if (m_Renderer->GetCameraRotationController())
{
m_Renderer->GetCameraRotationController()->GetSlice()->Next();
}
}
void QmitkRenderWindowMenu::OnAutoRotationActionTriggered()
{
if (m_AutoRotationTimer->isActive())
{
m_AutoRotationTimer->stop();
m_Renderer->GetCameraRotationController()->GetSlice()->PingPongOff();
}
else
{
m_Renderer->GetCameraRotationController()->GetSlice()->PingPongOn();
m_AutoRotationTimer->start();
}
}
void QmitkRenderWindowMenu::OnTSNumChanged(int num)
{
MITK_DEBUG << "Thickslices num: " << num << " on renderer " << m_Renderer.GetPointer();
if (m_Renderer.IsNotNull())
{
unsigned int thickSlicesMode = 0;
// determine the state of the thick-slice mode
mitk::ResliceMethodProperty *resliceMethodEnumProperty = nullptr;
if(m_Renderer->GetCurrentWorldPlaneGeometryNode()->GetProperty(resliceMethodEnumProperty, "reslice.thickslices") && resliceMethodEnumProperty)
{
thickSlicesMode = resliceMethodEnumProperty->GetValueAsId();
if(thickSlicesMode!=0)
m_DefaultThickMode = thickSlicesMode;
}
if(thickSlicesMode==0 && num>0) //default mode only for single slices
{
thickSlicesMode = m_DefaultThickMode; //mip default
m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea",
mitk::BoolProperty::New(true));
}
if(num<1)
{
thickSlicesMode = 0;
m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea",
mitk::BoolProperty::New(false));
}
m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices",
mitk::ResliceMethodProperty::New(thickSlicesMode));
m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.num",
mitk::IntProperty::New(num));
m_TSLabel->setText(QString::number(num * 2 + 1));
m_Renderer->SendUpdateSlice();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
}
void QmitkRenderWindowMenu::OnCrosshairMenuAboutToShow()
{
QMenu *crosshairModesMenu = m_CrosshairMenu;
crosshairModesMenu->clear();
QAction *resetViewAction = new QAction(crosshairModesMenu);
resetViewAction->setText("Reset view");
crosshairModesMenu->addAction(resetViewAction);
connect(resetViewAction, &QAction::triggered, this, &QmitkRenderWindowMenu::ResetView);
// Show hide crosshairs
{
QAction *showHideCrosshairVisibilityAction = new QAction(crosshairModesMenu);
showHideCrosshairVisibilityAction->setText("Show crosshair");
showHideCrosshairVisibilityAction->setCheckable(true);
showHideCrosshairVisibilityAction->setChecked(m_CrosshairVisibility);
crosshairModesMenu->addAction(showHideCrosshairVisibilityAction);
connect(showHideCrosshairVisibilityAction, &QAction::toggled, this, &QmitkRenderWindowMenu::OnCrosshairVisibilityChanged);
}
// Rotation mode
{
QAction *rotationGroupSeparator = new QAction(crosshairModesMenu);
rotationGroupSeparator->setSeparator(true);
rotationGroupSeparator->setText("Rotation mode");
crosshairModesMenu->addAction(rotationGroupSeparator);
QActionGroup *rotationModeActionGroup = new QActionGroup(crosshairModesMenu);
rotationModeActionGroup->setExclusive(true);
QAction *noCrosshairRotation = new QAction(crosshairModesMenu);
noCrosshairRotation->setActionGroup(rotationModeActionGroup);
noCrosshairRotation->setText("No crosshair rotation");
noCrosshairRotation->setCheckable(true);
noCrosshairRotation->setChecked(m_CrosshairRotationMode == 0);
noCrosshairRotation->setData(0);
crosshairModesMenu->addAction(noCrosshairRotation);
QAction *singleCrosshairRotation = new QAction(crosshairModesMenu);
singleCrosshairRotation->setActionGroup(rotationModeActionGroup);
singleCrosshairRotation->setText("Crosshair rotation");
singleCrosshairRotation->setCheckable(true);
singleCrosshairRotation->setChecked(m_CrosshairRotationMode == 1);
singleCrosshairRotation->setData(1);
crosshairModesMenu->addAction(singleCrosshairRotation);
QAction *coupledCrosshairRotation = new QAction(crosshairModesMenu);
coupledCrosshairRotation->setActionGroup(rotationModeActionGroup);
coupledCrosshairRotation->setText("Coupled crosshair rotation");
coupledCrosshairRotation->setCheckable(true);
coupledCrosshairRotation->setChecked(m_CrosshairRotationMode == 2);
coupledCrosshairRotation->setData(2);
crosshairModesMenu->addAction(coupledCrosshairRotation);
QAction *swivelMode = new QAction(crosshairModesMenu);
swivelMode->setActionGroup(rotationModeActionGroup);
swivelMode->setText("Swivel mode");
swivelMode->setCheckable(true);
swivelMode->setChecked(m_CrosshairRotationMode == 3);
swivelMode->setData(3);
crosshairModesMenu->addAction(swivelMode);
connect(rotationModeActionGroup, &QActionGroup::triggered, this, &QmitkRenderWindowMenu::OnCrosshairRotationModeSelected);
}
// auto rotation support
if (m_Renderer.IsNotNull() && m_Renderer->GetMapperID() == mitk::BaseRenderer::Standard3D)
{
QAction *autoRotationGroupSeparator = new QAction(crosshairModesMenu);
autoRotationGroupSeparator->setSeparator(true);
crosshairModesMenu->addAction(autoRotationGroupSeparator);
QAction *autoRotationAction = crosshairModesMenu->addAction("Auto Rotation");
autoRotationAction->setCheckable(true);
autoRotationAction->setChecked(m_AutoRotationTimer->isActive());
connect(autoRotationAction, &QAction::triggered, this, &QmitkRenderWindowMenu::OnAutoRotationActionTriggered);
}
// Thickslices support
if (m_Renderer.IsNotNull() && m_Renderer->GetMapperID() == mitk::BaseRenderer::Standard2D)
{
QAction *thickSlicesGroupSeparator = new QAction(crosshairModesMenu);
thickSlicesGroupSeparator->setSeparator(true);
thickSlicesGroupSeparator->setText("ThickSlices mode");
crosshairModesMenu->addAction(thickSlicesGroupSeparator);
QActionGroup *thickSlicesActionGroup = new QActionGroup(crosshairModesMenu);
thickSlicesActionGroup->setExclusive(true);
int currentMode = 0;
{
mitk::ResliceMethodProperty::Pointer m = dynamic_cast<mitk::ResliceMethodProperty *>(
m_Renderer->GetCurrentWorldPlaneGeometryNode()->GetProperty("reslice.thickslices"));
if (m.IsNotNull())
currentMode = m->GetValueAsId();
}
int currentNum = 1;
{
mitk::IntProperty::Pointer m = dynamic_cast<mitk::IntProperty *>(
m_Renderer->GetCurrentWorldPlaneGeometryNode()->GetProperty("reslice.thickslices.num"));
if (m.IsNotNull())
{
currentNum = m->GetValue();
}
}
if (currentMode == 0)
currentNum = 0;
QSlider *m_TSSlider = new QSlider(crosshairModesMenu);
m_TSSlider->setMinimum(0);
m_TSSlider->setMaximum(50);
m_TSSlider->setValue(currentNum);
m_TSSlider->setOrientation(Qt::Horizontal);
connect(m_TSSlider, &QSlider::valueChanged, this, &QmitkRenderWindowMenu::OnTSNumChanged);
QHBoxLayout *tsLayout = new QHBoxLayout;
tsLayout->setContentsMargins(4, 4, 4, 4);
tsLayout->addWidget(new QLabel("TS: "));
tsLayout->addWidget(m_TSSlider);
tsLayout->addWidget(m_TSLabel = new QLabel(QString::number(currentNum * 2 + 1), this));
QWidget *tsWidget = new QWidget;
tsWidget->setLayout(tsLayout);
QWidgetAction *m_TSSliderAction = new QWidgetAction(crosshairModesMenu);
m_TSSliderAction->setDefaultWidget(tsWidget);
crosshairModesMenu->addAction(m_TSSliderAction);
}
}
void QmitkRenderWindowMenu::OnCrosshairVisibilityChanged(bool visible)
{
- m_CrosshairVisibility = visible;
- emit CrosshairVisibilityChanged(visible);
+ UpdateCrosshairVisibility(visible);
+ emit CrosshairVisibilityChanged(m_CrosshairVisibility);
}
void QmitkRenderWindowMenu::OnCrosshairRotationModeSelected(QAction *action)
{
- m_CrosshairRotationMode = action->data().toInt();
+ UpdateCrosshairRotationMode(action->data().toInt());
emit CrosshairRotationModeChanged(m_CrosshairRotationMode);
}
void QmitkRenderWindowMenu::OnFullScreenButton(bool /*checked*/)
{
if (!m_FullScreenMode)
{
m_FullScreenMode = true;
m_OldLayoutDesign = m_LayoutDesign;
emit LayoutDesignChanged(LayoutDesign::ONE_BIG);
}
else
{
m_FullScreenMode = false;
emit LayoutDesignChanged(m_OldLayoutDesign);
}
MoveWidgetToCorrectPos(1.0f);
ChangeFullScreenIcon();
DeferredShowMenu();
}
void QmitkRenderWindowMenu::OnLayoutDesignButton(bool /*checked*/)
{
if (nullptr == m_LayoutActionsMenu)
{
CreateSettingsWidget();
}
QPoint point = mapToGlobal(m_LayoutDesignButton->geometry().topLeft());
m_LayoutActionsMenu->setVisible(true);
m_LayoutActionsMenu->exec(point);
}
void QmitkRenderWindowMenu::OnSetLayout(LayoutDesign layoutDesign)
{
m_FullScreenMode = false;
ChangeFullScreenIcon();
m_LayoutDesign = layoutDesign;
emit LayoutDesignChanged(m_LayoutDesign);
DeferredShowMenu();
}
diff --git a/Modules/QtWidgets/src/QmitkStdMultiWidget.cpp b/Modules/QtWidgets/src/QmitkStdMultiWidget.cpp
index a16e26f56d..2b83c9cb66 100644
--- a/Modules/QtWidgets/src/QmitkStdMultiWidget.cpp
+++ b/Modules/QtWidgets/src/QmitkStdMultiWidget.cpp
@@ -1,811 +1,823 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#define SMW_INFO MITK_INFO("widget.stdmulti")
#include "QmitkStdMultiWidget.h"
#include "QmitkRenderWindowWidget.h"
// mitk core
#include <mitkCameraController.h>
#include <mitkImage.h>
#include <mitkImagePixelReadAccessor.h>
#include <mitkInteractionConst.h>
#include <mitkLine.h>
#include <mitkNodePredicateBase.h>
#include <mitkNodePredicateDataType.h>
#include <mitkNodePredicateNot.h>
#include <mitkNodePredicateProperty.h>
#include <mitkPixelTypeMultiplex.h>
#include <mitkPlaneGeometryDataMapper2D.h>
#include <mitkPointSet.h>
#include <mitkProperties.h>
#include <mitkStatusBar.h>
#include <mitkDisplayActionEventHandlerStd.h>
#include <mitkVtkLayerController.h>
// qt
#include <QList>
#include <QMouseEvent>
#include <QTimer>
// vtk
#include <vtkSmartPointer.h>
// c++
#include <iomanip>
QmitkStdMultiWidget::QmitkStdMultiWidget(QWidget *parent,
Qt::WindowFlags f/* = 0*/,
const QString &name/* = "stdmulti"*/)
: QmitkAbstractMultiWidget(parent, f, name)
, m_TimeNavigationController(nullptr)
, m_PendingCrosshairPositionEvent(false)
{
m_TimeNavigationController = mitk::RenderingManager::GetInstance()->GetTimeNavigationController();
}
QmitkStdMultiWidget::~QmitkStdMultiWidget()
{
m_TimeNavigationController->Disconnect(GetRenderWindow1()->GetSliceNavigationController());
m_TimeNavigationController->Disconnect(GetRenderWindow2()->GetSliceNavigationController());
m_TimeNavigationController->Disconnect(GetRenderWindow3()->GetSliceNavigationController());
m_TimeNavigationController->Disconnect(GetRenderWindow4()->GetSliceNavigationController());
}
void QmitkStdMultiWidget::InitializeMultiWidget()
{
// yellow is default color for widget4
m_DecorationColorWidget4[0] = 1.0f;
m_DecorationColorWidget4[1] = 1.0f;
m_DecorationColorWidget4[2] = 0.0f;
SetLayout(2, 2);
// transfer colors in WorldGeometry-Nodes of the associated Renderer
mitk::IntProperty::Pointer layer;
// of widget 1
m_PlaneNode1 =
mitk::BaseRenderer::GetInstance(GetRenderWindow1()->renderWindow())->GetCurrentWorldPlaneGeometryNode();
m_PlaneNode1->SetColor(GetDecorationColor(0));
layer = mitk::IntProperty::New(1000);
m_PlaneNode1->SetProperty("layer", layer);
// of widget 2
m_PlaneNode2 =
mitk::BaseRenderer::GetInstance(GetRenderWindow2()->renderWindow())->GetCurrentWorldPlaneGeometryNode();
m_PlaneNode2->SetColor(GetDecorationColor(1));
layer = mitk::IntProperty::New(1000);
m_PlaneNode2->SetProperty("layer", layer);
// of widget 3
m_PlaneNode3 =
mitk::BaseRenderer::GetInstance(GetRenderWindow3()->renderWindow())->GetCurrentWorldPlaneGeometryNode();
m_PlaneNode3->SetColor(GetDecorationColor(2));
layer = mitk::IntProperty::New(1000);
m_PlaneNode3->SetProperty("layer", layer);
// the parent node
m_ParentNodeForGeometryPlanes =
mitk::BaseRenderer::GetInstance(GetRenderWindow4()->renderWindow())->GetCurrentWorldPlaneGeometryNode();
layer = mitk::IntProperty::New(1000);
m_ParentNodeForGeometryPlanes->SetProperty("layer", layer);
AddDisplayPlaneSubTree();
SetDisplayActionEventHandler(std::make_unique<mitk::DisplayActionEventHandlerStd>());
auto displayActionEventHandler = GetDisplayActionEventHandler();
if (nullptr != displayActionEventHandler)
{
displayActionEventHandler->InitActions();
}
}
QmitkRenderWindow* QmitkStdMultiWidget::GetRenderWindow(const QString& widgetName) const
{
if ("axial" == widgetName)
{
return GetRenderWindow1();
}
if ("sagittal" == widgetName)
{
return GetRenderWindow2();
}
if ("coronal" == widgetName)
{
return GetRenderWindow3();
}
if ("3d" == widgetName)
{
return GetRenderWindow4();
}
return QmitkAbstractMultiWidget::GetRenderWindow(widgetName);
}
QmitkRenderWindow* QmitkStdMultiWidget::GetRenderWindow(const mitk::BaseRenderer::ViewDirection& viewDirection) const
{
return GetRenderWindow(static_cast<unsigned int>(viewDirection));
}
void QmitkStdMultiWidget::SetSelectedPosition(const mitk::Point3D& newPosition, const QString& /*widgetName*/)
{
GetRenderWindow1()->GetSliceNavigationController()->SelectSliceByPoint(newPosition);
GetRenderWindow2()->GetSliceNavigationController()->SelectSliceByPoint(newPosition);
GetRenderWindow3()->GetSliceNavigationController()->SelectSliceByPoint(newPosition);
RequestUpdateAll();
}
const mitk::Point3D QmitkStdMultiWidget::GetSelectedPosition(const QString& /*widgetName*/) const
{
const mitk::PlaneGeometry* plane1 = GetRenderWindow1()->GetSliceNavigationController()->GetCurrentPlaneGeometry();
const mitk::PlaneGeometry* plane2 = GetRenderWindow2()->GetSliceNavigationController()->GetCurrentPlaneGeometry();
const mitk::PlaneGeometry* plane3 = GetRenderWindow3()->GetSliceNavigationController()->GetCurrentPlaneGeometry();
mitk::Line3D line;
if ((plane1 != nullptr) && (plane2 != nullptr)
&& (plane1->IntersectionLine(plane2, line)))
{
mitk::Point3D point;
if ((plane3 != nullptr) && (plane3->IntersectionPoint(line, point)))
{
return point;
}
}
return mitk::Point3D();
}
void QmitkStdMultiWidget::SetCrosshairVisibility(bool visible)
{
if (m_PlaneNode1.IsNotNull())
{
m_PlaneNode1->SetVisibility(visible);
}
if (m_PlaneNode2.IsNotNull())
{
m_PlaneNode2->SetVisibility(visible);
}
if (m_PlaneNode3.IsNotNull())
{
m_PlaneNode3->SetVisibility(visible);
}
+ emit NotifyCrosshairVisibilityChanged(visible);
+
RequestUpdateAll();
}
bool QmitkStdMultiWidget::GetCrosshairVisibility() const
{
bool crosshairVisibility = true;
if (m_PlaneNode1.IsNotNull())
{
bool visibilityProperty = false;
m_PlaneNode1->GetVisibility(visibilityProperty, nullptr);
crosshairVisibility &= visibilityProperty;
}
if (m_PlaneNode2.IsNotNull())
{
bool visibilityProperty = false;
crosshairVisibility &= m_PlaneNode2->GetVisibility(visibilityProperty, nullptr);
crosshairVisibility &= visibilityProperty;
}
if (m_PlaneNode3.IsNotNull())
{
bool visibilityProperty = false;
crosshairVisibility &= m_PlaneNode3->GetVisibility(visibilityProperty, nullptr);
crosshairVisibility &= visibilityProperty;
}
return crosshairVisibility;
}
void QmitkStdMultiWidget::ResetCrosshair()
{
auto dataStorage = GetDataStorage();
if (nullptr == dataStorage)
{
return;
}
mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(dataStorage);
SetWidgetPlaneMode(mitk::InteractionSchemeSwitcher::MITKStandard);
}
void QmitkStdMultiWidget::SetWidgetPlaneMode(int userMode)
{
MITK_DEBUG << "Changing crosshair mode to " << userMode;
switch (userMode)
{
case 0:
SetInteractionScheme(mitk::InteractionSchemeSwitcher::MITKStandard);
break;
case 1:
SetInteractionScheme(mitk::InteractionSchemeSwitcher::MITKRotationUncoupled);
break;
case 2:
SetInteractionScheme(mitk::InteractionSchemeSwitcher::MITKRotationCoupled);
break;
case 3:
SetInteractionScheme(mitk::InteractionSchemeSwitcher::MITKSwivel);
break;
}
+
+ emit NotifyCrosshairRotationModeChanged(userMode);
}
mitk::SliceNavigationController* QmitkStdMultiWidget::GetTimeNavigationController()
{
return m_TimeNavigationController;
}
void QmitkStdMultiWidget::AddPlanesToDataStorage()
{
auto dataStorage = GetDataStorage();
if (nullptr == dataStorage)
{
return;
}
if (m_PlaneNode1.IsNotNull() && m_PlaneNode2.IsNotNull()
&& m_PlaneNode3.IsNotNull() && m_ParentNodeForGeometryPlanes.IsNotNull())
{
dataStorage->Add(m_ParentNodeForGeometryPlanes);
dataStorage->Add(m_PlaneNode1, m_ParentNodeForGeometryPlanes);
dataStorage->Add(m_PlaneNode2, m_ParentNodeForGeometryPlanes);
dataStorage->Add(m_PlaneNode3, m_ParentNodeForGeometryPlanes);
}
}
void QmitkStdMultiWidget::RemovePlanesFromDataStorage()
{
auto dataStorage = GetDataStorage();
if (nullptr == dataStorage)
{
return;
}
if (m_PlaneNode1.IsNotNull() && m_PlaneNode2.IsNotNull()
&& m_PlaneNode3.IsNotNull() && m_ParentNodeForGeometryPlanes.IsNotNull())
{
dataStorage->Remove(m_PlaneNode1);
dataStorage->Remove(m_PlaneNode2);
dataStorage->Remove(m_PlaneNode3);
dataStorage->Remove(m_ParentNodeForGeometryPlanes);
}
}
void QmitkStdMultiWidget::HandleCrosshairPositionEvent()
{
if (!m_PendingCrosshairPositionEvent)
{
m_PendingCrosshairPositionEvent = true;
QTimer::singleShot(0, this, SLOT(HandleCrosshairPositionEventDelayed()));
}
}
QmitkRenderWindow* QmitkStdMultiWidget::GetRenderWindow(unsigned int number) const
{
switch (number)
{
case 0:
return GetRenderWindow1();
case 1:
return GetRenderWindow2();
case 2:
return GetRenderWindow3();
case 3:
return GetRenderWindow4();
default:
MITK_ERROR << "Requested unknown render window";
break;
}
return nullptr;
}
QmitkRenderWindow* QmitkStdMultiWidget::GetRenderWindow1() const
{
return QmitkAbstractMultiWidget::GetRenderWindow(GetNameFromIndex(0, 0));
}
QmitkRenderWindow* QmitkStdMultiWidget::GetRenderWindow2() const
{
return QmitkAbstractMultiWidget::GetRenderWindow(GetNameFromIndex(0, 1));
}
QmitkRenderWindow* QmitkStdMultiWidget::GetRenderWindow3() const
{
return QmitkAbstractMultiWidget::GetRenderWindow(GetNameFromIndex(1, 0));
}
QmitkRenderWindow* QmitkStdMultiWidget::GetRenderWindow4() const
{
return QmitkAbstractMultiWidget::GetRenderWindow(GetNameFromIndex(1, 1));
}
mitk::DataNode::Pointer QmitkStdMultiWidget::GetWidgetPlane1() const
{
return m_PlaneNode1;
}
mitk::DataNode::Pointer QmitkStdMultiWidget::GetWidgetPlane2() const
{
return m_PlaneNode2;
}
mitk::DataNode::Pointer QmitkStdMultiWidget::GetWidgetPlane3() const
{
return m_PlaneNode3;
}
mitk::DataNode::Pointer QmitkStdMultiWidget::GetWidgetPlane(unsigned number) const
{
switch (number)
{
case 1:
return m_PlaneNode1;
case 2:
return m_PlaneNode2;
case 3:
return m_PlaneNode3;
default:
MITK_ERROR << "Requested unknown render window";
break;
}
return nullptr;
}
void QmitkStdMultiWidget::SetDecorationColor(unsigned int widgetNumber, mitk::Color color)
{
switch (widgetNumber)
{
case 0:
if (m_PlaneNode1.IsNotNull())
{
m_PlaneNode1->SetColor(color);
}
break;
case 1:
if (m_PlaneNode2.IsNotNull())
{
m_PlaneNode2->SetColor(color);
}
break;
case 2:
if (m_PlaneNode3.IsNotNull())
{
m_PlaneNode3->SetColor(color);
}
break;
case 3:
m_DecorationColorWidget4 = color;
break;
default:
MITK_ERROR << "Decoration color for unknown widget!";
break;
}
}
mitk::Color QmitkStdMultiWidget::GetDecorationColor(unsigned int widgetNumber)
{
// The implementation looks a bit messy here, but it avoids
// synchronization of the color of the geometry nodes and an
// internal member here.
// Default colors were chosen for decent visibility.
// Feel free to change your preferences in the workbench.
float tmp[3] = { 0.0f, 0.0f, 0.0f };
switch (widgetNumber)
{
case 0:
{
if (m_PlaneNode1.IsNotNull())
{
if (m_PlaneNode1->GetColor(tmp))
{
return dynamic_cast<mitk::ColorProperty *>(m_PlaneNode1->GetProperty("color"))->GetColor();
}
}
float red[3] = { 0.753f, 0.0f, 0.0f }; // This is #C00000 in hex
return mitk::Color(red);
}
case 1:
{
if (m_PlaneNode2.IsNotNull())
{
if (m_PlaneNode2->GetColor(tmp))
{
return dynamic_cast<mitk::ColorProperty *>(m_PlaneNode2->GetProperty("color"))->GetColor();
}
}
float green[3] = { 0.0f, 0.69f, 0.0f }; // This is #00B000 in hex
return mitk::Color(green);
}
case 2:
{
if (m_PlaneNode3.IsNotNull())
{
if (m_PlaneNode3->GetColor(tmp))
{
return dynamic_cast<mitk::ColorProperty *>(m_PlaneNode3->GetProperty("color"))->GetColor();
}
}
float blue[3] = { 0.0, 0.502f, 1.0f }; // This is #0080FF in hex
return mitk::Color(blue);
}
case 3:
{
return m_DecorationColorWidget4;
}
default:
MITK_ERROR << "Decoration color for unknown widget!";
float black[3] = { 0.0f, 0.0f, 0.0f };
return mitk::Color(black);
}
}
void QmitkStdMultiWidget::mousePressEvent(QMouseEvent* e)
{
if (QEvent::MouseButtonPress != e->type())
{
return;
}
auto renderWindowWidget = dynamic_cast<QmitkRenderWindowWidget*>(this->sender());
if (nullptr == renderWindowWidget)
{
return;
}
auto renderWindowWidgetPointer = GetRenderWindowWidget(renderWindowWidget->GetWidgetName());
SetActiveRenderWindowWidget(renderWindowWidgetPointer);
}
void QmitkStdMultiWidget::moveEvent(QMoveEvent* e)
{
QWidget::moveEvent(e);
// it is necessary to readjust the position of the Annotation as the StdMultiWidget has moved
// unfortunately it's not done by QmitkRenderWindow::moveEvent -> must be done here
emit Moved();
}
void QmitkStdMultiWidget::wheelEvent(QWheelEvent* e)
{
emit WheelMoved(e);
}
void QmitkStdMultiWidget::HandleCrosshairPositionEventDelayed()
{
auto dataStorage = GetDataStorage();
if (nullptr == dataStorage)
{
return;
}
m_PendingCrosshairPositionEvent = false;
// find image with highest layer
mitk::TNodePredicateDataType<mitk::Image>::Pointer isImageData = mitk::TNodePredicateDataType<mitk::Image>::New();
mitk::DataStorage::SetOfObjects::ConstPointer nodes = dataStorage->GetSubset(isImageData).GetPointer();
mitk::Point3D crosshairPos = GetSelectedPosition("");
mitk::BaseRenderer* baseRenderer = GetRenderWindow1()->GetSliceNavigationController()->GetRenderer();
auto globalCurrentTimePoint = baseRenderer->GetTime();
mitk::DataNode::Pointer node = mitk::FindTopmostVisibleNode(nodes, crosshairPos, globalCurrentTimePoint, baseRenderer);
mitk::DataNode::Pointer topSourceNode;
mitk::Image::Pointer image;
bool isBinary = false;
int component = 0;
if (node.IsNotNull())
{
node->GetBoolProperty("binary", isBinary);
if (isBinary)
{
mitk::DataStorage::SetOfObjects::ConstPointer sourcenodes = dataStorage->GetSources(node, nullptr, true);
if (!sourcenodes->empty())
{
topSourceNode = mitk::FindTopmostVisibleNode(sourcenodes, crosshairPos, globalCurrentTimePoint, baseRenderer);
}
if (topSourceNode.IsNotNull())
{
image = dynamic_cast<mitk::Image *>(topSourceNode->GetData());
topSourceNode->GetIntProperty("Image.Displayed Component", component);
}
else
{
image = dynamic_cast<mitk::Image *>(node->GetData());
node->GetIntProperty("Image.Displayed Component", component);
}
}
else
{
image = dynamic_cast<mitk::Image *>(node->GetData());
node->GetIntProperty("Image.Displayed Component", component);
}
}
std::string statusText;
std::stringstream stream;
itk::Index<3> p;
unsigned int timestep = baseRenderer->GetTimeStep();
if (image.IsNotNull() && (image->GetTimeSteps() > timestep))
{
image->GetGeometry()->WorldToIndex(crosshairPos, p);
stream.precision(2);
stream << "Position: <" << std::fixed << crosshairPos[0] << ", " << std::fixed << crosshairPos[1] << ", "
<< std::fixed << crosshairPos[2] << "> mm";
stream << "; Index: <" << p[0] << ", " << p[1] << ", " << p[2] << "> ";
mitk::ScalarType pixelValue;
mitkPixelTypeMultiplex5(mitk::FastSinglePixelAccess,
image->GetChannelDescriptor().GetPixelType(),
image,
image->GetVolumeData(image->GetTimeGeometry()->TimePointToTimeStep(globalCurrentTimePoint)),
p,
pixelValue,
component);
if (fabs(pixelValue) > 1000000 || fabs(pixelValue) < 0.01)
{
stream << "; Time: " << globalCurrentTimePoint << " ms; Pixelvalue: " << std::scientific << pixelValue << " ";
}
else
{
stream << "; Time: " << globalCurrentTimePoint << " ms; Pixelvalue: " << pixelValue << " ";
}
}
else
{
stream << "No image information at this position!";
}
statusText = stream.str();
mitk::StatusBar::GetInstance()->DisplayGreyValueText(statusText.c_str());
}
void QmitkStdMultiWidget::Fit()
{
vtkSmartPointer<vtkRenderer> vtkrenderer;
vtkrenderer = mitk::BaseRenderer::GetInstance(GetRenderWindow1()->renderWindow())->GetVtkRenderer();
if (nullptr != vtkrenderer)
{
vtkrenderer->ResetCamera();
}
vtkrenderer = mitk::BaseRenderer::GetInstance(GetRenderWindow2()->renderWindow())->GetVtkRenderer();
if (nullptr != vtkrenderer)
{
vtkrenderer->ResetCamera();
}
vtkrenderer = mitk::BaseRenderer::GetInstance(GetRenderWindow3()->renderWindow())->GetVtkRenderer();
if (nullptr != vtkrenderer)
{
vtkrenderer->ResetCamera();
}
vtkrenderer = mitk::BaseRenderer::GetInstance(GetRenderWindow4()->renderWindow())->GetVtkRenderer();
if (nullptr != vtkrenderer)
{
vtkrenderer->ResetCamera();
}
mitk::BaseRenderer::GetInstance(GetRenderWindow1()->renderWindow())->GetCameraController()->Fit();
mitk::BaseRenderer::GetInstance(GetRenderWindow2()->renderWindow())->GetCameraController()->Fit();
mitk::BaseRenderer::GetInstance(GetRenderWindow3()->renderWindow())->GetCameraController()->Fit();
mitk::BaseRenderer::GetInstance(GetRenderWindow4()->renderWindow())->GetCameraController()->Fit();
int w = vtkObject::GetGlobalWarningDisplay();
vtkObject::GlobalWarningDisplayOff();
vtkObject::SetGlobalWarningDisplay(w);
}
void QmitkStdMultiWidget::AddDisplayPlaneSubTree()
{
// add the displayed planes of the multiwidget to a node to which the subtree
// @a planesSubTree points ...
mitk::PlaneGeometryDataMapper2D::Pointer mapper;
// ... of widget 1
mitk::BaseRenderer* renderer1 = mitk::BaseRenderer::GetInstance(GetRenderWindow1()->renderWindow());
m_PlaneNode1 = renderer1->GetCurrentWorldPlaneGeometryNode();
m_PlaneNode1->SetProperty("visible", mitk::BoolProperty::New(true));
m_PlaneNode1->SetProperty("name", mitk::StringProperty::New(std::string(renderer1->GetName()) + ".plane"));
m_PlaneNode1->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false));
m_PlaneNode1->SetProperty("helper object", mitk::BoolProperty::New(true));
mapper = mitk::PlaneGeometryDataMapper2D::New();
m_PlaneNode1->SetMapper(mitk::BaseRenderer::Standard2D, mapper);
// ... of widget 2
mitk::BaseRenderer* renderer2 = mitk::BaseRenderer::GetInstance(GetRenderWindow2()->renderWindow());
m_PlaneNode2 = renderer2->GetCurrentWorldPlaneGeometryNode();
m_PlaneNode2->SetProperty("visible", mitk::BoolProperty::New(true));
m_PlaneNode2->SetProperty("name", mitk::StringProperty::New(std::string(renderer2->GetName()) + ".plane"));
m_PlaneNode2->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false));
m_PlaneNode2->SetProperty("helper object", mitk::BoolProperty::New(true));
mapper = mitk::PlaneGeometryDataMapper2D::New();
m_PlaneNode2->SetMapper(mitk::BaseRenderer::Standard2D, mapper);
// ... of widget 3
mitk::BaseRenderer *renderer3 = mitk::BaseRenderer::GetInstance(GetRenderWindow3()->renderWindow());
m_PlaneNode3 = renderer3->GetCurrentWorldPlaneGeometryNode();
m_PlaneNode3->SetProperty("visible", mitk::BoolProperty::New(true));
m_PlaneNode3->SetProperty("name", mitk::StringProperty::New(std::string(renderer3->GetName()) + ".plane"));
m_PlaneNode3->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false));
m_PlaneNode3->SetProperty("helper object", mitk::BoolProperty::New(true));
mapper = mitk::PlaneGeometryDataMapper2D::New();
m_PlaneNode3->SetMapper(mitk::BaseRenderer::Standard2D, mapper);
m_ParentNodeForGeometryPlanes = mitk::DataNode::New();
m_ParentNodeForGeometryPlanes->SetProperty("name", mitk::StringProperty::New("Widgets"));
m_ParentNodeForGeometryPlanes->SetProperty("helper object", mitk::BoolProperty::New(true));
}
void QmitkStdMultiWidget::EnsureDisplayContainsPoint(mitk::BaseRenderer *renderer, const mitk::Point3D &p)
{
mitk::Point2D pointOnDisplay;
renderer->WorldToDisplay(p, pointOnDisplay);
if (pointOnDisplay[0] < renderer->GetVtkRenderer()->GetOrigin()[0] ||
pointOnDisplay[1] < renderer->GetVtkRenderer()->GetOrigin()[1] ||
pointOnDisplay[0] > renderer->GetVtkRenderer()->GetOrigin()[0] + renderer->GetViewportSize()[0] ||
pointOnDisplay[1] > renderer->GetVtkRenderer()->GetOrigin()[1] + renderer->GetViewportSize()[1])
{
mitk::Point2D pointOnPlane;
renderer->GetCurrentWorldPlaneGeometry()->Map(p, pointOnPlane);
renderer->GetCameraController()->MoveCameraToPoint(pointOnPlane);
}
}
void QmitkStdMultiWidget::SetWidgetPlaneVisibility(const char *widgetName, bool visible, mitk::BaseRenderer *renderer)
{
auto dataStorage = GetDataStorage();
if (nullptr != dataStorage)
{
mitk::DataNode* dataNode = dataStorage->GetNamedNode(widgetName);
if (dataNode != nullptr)
{
dataNode->SetVisibility(visible, renderer);
}
}
}
void QmitkStdMultiWidget::SetWidgetPlanesVisibility(bool visible, mitk::BaseRenderer *renderer)
{
if (m_PlaneNode1.IsNotNull())
{
m_PlaneNode1->SetVisibility(visible, renderer);
}
if (m_PlaneNode2.IsNotNull())
{
m_PlaneNode2->SetVisibility(visible, renderer);
}
if (m_PlaneNode3.IsNotNull())
{
m_PlaneNode3->SetVisibility(visible, renderer);
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
//////////////////////////////////////////////////////////////////////////
// PRIVATE
//////////////////////////////////////////////////////////////////////////
void QmitkStdMultiWidget::SetLayoutImpl()
{
CreateRenderWindowWidgets();
GetMultiWidgetLayoutManager()->SetLayoutDesign(QmitkMultiWidgetLayoutManager::LayoutDesign::DEFAULT);
// Initialize views as axial, sagittal, coronal to all data objects in DataStorage
auto geo = GetDataStorage()->ComputeBoundingGeometry3D(GetDataStorage()->GetAll());
mitk::RenderingManager::GetInstance()->InitializeViews(geo);
}
void QmitkStdMultiWidget::CreateRenderWindowWidgets()
{
// create axial render window (widget)
QString renderWindowWidgetName = GetNameFromIndex(0, 0);
RenderWindowWidgetPointer renderWindowWidget1 = std::make_shared<QmitkRenderWindowWidget>(this, renderWindowWidgetName, GetDataStorage());
auto renderWindow1 = renderWindowWidget1->GetRenderWindow();
renderWindow1->GetSliceNavigationController()->SetDefaultViewDirection(mitk::SliceNavigationController::Axial);
renderWindowWidget1->SetDecorationColor(GetDecorationColor(0));
renderWindowWidget1->SetCornerAnnotationText("Axial");
renderWindowWidget1->GetRenderWindow()->SetLayoutIndex(ViewDirection::AXIAL);
AddRenderWindowWidget(renderWindowWidgetName, renderWindowWidget1);
// create sagittal render window (widget)
renderWindowWidgetName = GetNameFromIndex(0, 1);
RenderWindowWidgetPointer renderWindowWidget2 = std::make_shared<QmitkRenderWindowWidget>(this, renderWindowWidgetName, GetDataStorage());
auto renderWindow2 = renderWindowWidget2->GetRenderWindow();
renderWindow2->GetSliceNavigationController()->SetDefaultViewDirection(mitk::SliceNavigationController::Sagittal);
renderWindowWidget2->SetDecorationColor(GetDecorationColor(1));
renderWindowWidget2->setStyleSheet("border: 0px");
renderWindowWidget2->SetCornerAnnotationText("Sagittal");
renderWindowWidget2->GetRenderWindow()->SetLayoutIndex(ViewDirection::SAGITTAL);
AddRenderWindowWidget(renderWindowWidgetName, renderWindowWidget2);
// create coronal render window (widget)
renderWindowWidgetName = GetNameFromIndex(1, 0);
RenderWindowWidgetPointer renderWindowWidget3 = std::make_shared<QmitkRenderWindowWidget>(this, renderWindowWidgetName, GetDataStorage());
auto renderWindow3 = renderWindowWidget3->GetRenderWindow();
renderWindow3->GetSliceNavigationController()->SetDefaultViewDirection(mitk::SliceNavigationController::Frontal);
renderWindowWidget3->SetDecorationColor(GetDecorationColor(2));
renderWindowWidget3->SetCornerAnnotationText("Coronal");
renderWindowWidget3->GetRenderWindow()->SetLayoutIndex(ViewDirection::CORONAL);
AddRenderWindowWidget(renderWindowWidgetName, renderWindowWidget3);
// create 3D render window (widget)
renderWindowWidgetName = GetNameFromIndex(1, 1);
RenderWindowWidgetPointer renderWindowWidget4 = std::make_shared<QmitkRenderWindowWidget>(this, renderWindowWidgetName, GetDataStorage());
auto renderWindow4 = renderWindowWidget4->GetRenderWindow();
renderWindow4->GetSliceNavigationController()->SetDefaultViewDirection(mitk::SliceNavigationController::Original);
renderWindowWidget4->SetDecorationColor(GetDecorationColor(3));
renderWindowWidget4->SetCornerAnnotationText("3D");
renderWindowWidget4->GetRenderWindow()->SetLayoutIndex(ViewDirection::THREE_D);
mitk::BaseRenderer::GetInstance(renderWindowWidget4->GetRenderWindow()->renderWindow())->SetMapperID(mitk::BaseRenderer::Standard3D);
AddRenderWindowWidget(renderWindowWidgetName, renderWindowWidget4);
SetActiveRenderWindowWidget(renderWindowWidget1);
// connect to the "time navigation controller": send time via sliceNavigationControllers
m_TimeNavigationController->ConnectGeometryTimeEvent(renderWindow1->GetSliceNavigationController(), false);
m_TimeNavigationController->ConnectGeometryTimeEvent(renderWindow2->GetSliceNavigationController(), false);
m_TimeNavigationController->ConnectGeometryTimeEvent(renderWindow3->GetSliceNavigationController(), false);
m_TimeNavigationController->ConnectGeometryTimeEvent(renderWindow4->GetSliceNavigationController(), false);
renderWindow1->GetSliceNavigationController()->ConnectGeometrySendEvent(
mitk::BaseRenderer::GetInstance(renderWindow4->renderWindow()));
// reverse connection between sliceNavigationControllers and timeNavigationController
renderWindow1->GetSliceNavigationController()->ConnectGeometryTimeEvent(m_TimeNavigationController, false);
renderWindow2->GetSliceNavigationController()->ConnectGeometryTimeEvent(m_TimeNavigationController, false);
renderWindow3->GetSliceNavigationController()->ConnectGeometryTimeEvent(m_TimeNavigationController, false);
//renderWindow4->GetSliceNavigationController()->ConnectGeometryTimeEvent(m_TimeNavigationController, false);
auto layoutManager = GetMultiWidgetLayoutManager();
connect(renderWindowWidget1.get(), &QmitkRenderWindowWidget::MouseEvent, this, &QmitkStdMultiWidget::mousePressEvent);
connect(renderWindow1, &QmitkRenderWindow::ResetView, this, &QmitkStdMultiWidget::ResetCrosshair);
connect(renderWindow1, &QmitkRenderWindow::CrosshairVisibilityChanged, this, &QmitkStdMultiWidget::SetCrosshairVisibility);
connect(renderWindow1, &QmitkRenderWindow::CrosshairRotationModeChanged, this, &QmitkStdMultiWidget::SetWidgetPlaneMode);
connect(renderWindow1, &QmitkRenderWindow::LayoutDesignChanged, layoutManager, &QmitkMultiWidgetLayoutManager::SetLayoutDesign);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairVisibilityChanged, renderWindow1, &QmitkRenderWindow::UpdateCrosshairVisibility);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairRotationModeChanged, renderWindow1, &QmitkRenderWindow::UpdateCrosshairRotationMode);
connect(renderWindowWidget2.get(), &QmitkRenderWindowWidget::MouseEvent, this, &QmitkStdMultiWidget::mousePressEvent);
connect(renderWindow2, &QmitkRenderWindow::ResetView, this, &QmitkStdMultiWidget::ResetCrosshair);
connect(renderWindow2, &QmitkRenderWindow::CrosshairVisibilityChanged, this, &QmitkStdMultiWidget::SetCrosshairVisibility);
connect(renderWindow2, &QmitkRenderWindow::CrosshairRotationModeChanged, this, &QmitkStdMultiWidget::SetWidgetPlaneMode);
connect(renderWindow2, &QmitkRenderWindow::LayoutDesignChanged, layoutManager, &QmitkMultiWidgetLayoutManager::SetLayoutDesign);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairVisibilityChanged, renderWindow2, &QmitkRenderWindow::UpdateCrosshairVisibility);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairRotationModeChanged, renderWindow2, &QmitkRenderWindow::UpdateCrosshairRotationMode);
connect(renderWindowWidget3.get(), &QmitkRenderWindowWidget::MouseEvent, this, &QmitkStdMultiWidget::mousePressEvent);
connect(renderWindow3, &QmitkRenderWindow::ResetView, this, &QmitkStdMultiWidget::ResetCrosshair);
connect(renderWindow3, &QmitkRenderWindow::CrosshairVisibilityChanged, this, &QmitkStdMultiWidget::SetCrosshairVisibility);
connect(renderWindow3, &QmitkRenderWindow::CrosshairRotationModeChanged, this, &QmitkStdMultiWidget::SetWidgetPlaneMode);
connect(renderWindow3, &QmitkRenderWindow::LayoutDesignChanged, layoutManager, &QmitkMultiWidgetLayoutManager::SetLayoutDesign);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairVisibilityChanged, renderWindow3, &QmitkRenderWindow::UpdateCrosshairVisibility);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairRotationModeChanged, renderWindow3, &QmitkRenderWindow::UpdateCrosshairRotationMode);
connect(renderWindowWidget4.get(), &QmitkRenderWindowWidget::MouseEvent, this, &QmitkStdMultiWidget::mousePressEvent);
connect(renderWindow4, &QmitkRenderWindow::ResetView, this, &QmitkStdMultiWidget::ResetCrosshair);
connect(renderWindow4, &QmitkRenderWindow::CrosshairVisibilityChanged, this, &QmitkStdMultiWidget::SetCrosshairVisibility);
connect(renderWindow4, &QmitkRenderWindow::CrosshairRotationModeChanged, this, &QmitkStdMultiWidget::SetWidgetPlaneMode);
connect(renderWindow4, &QmitkRenderWindow::LayoutDesignChanged, layoutManager, &QmitkMultiWidgetLayoutManager::SetLayoutDesign);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairVisibilityChanged, renderWindow4, &QmitkRenderWindow::UpdateCrosshairVisibility);
+ connect(this, &QmitkStdMultiWidget::NotifyCrosshairRotationModeChanged, renderWindow4, &QmitkRenderWindow::UpdateCrosshairRotationMode);
}
diff --git a/Modules/REST/CMakeLists.txt b/Modules/REST/CMakeLists.txt
index 2b0286b6b6..09e301a39e 100644
--- a/Modules/REST/CMakeLists.txt
+++ b/Modules/REST/CMakeLists.txt
@@ -1,13 +1,14 @@
-if(MITK_USE_cpprestsdk)
+set(boost_depends "Boost|date_time+regex+system")
- mitk_create_module(
- DEPENDS MitkCore
- )
+if(UNIX)
+ set(boost_depends "${boost_depends}+atomic+chrono+filesystem+random+thread")
+endif()
- if(TARGET ${MODULE_TARGET})
- target_link_libraries(${MODULE_TARGET} PUBLIC cpprestsdk::cpprest OpenSSL::SSL)
- endif()
+mitk_create_module(
+ DEPENDS MitkCore
+ PACKAGE_DEPENDS PUBLIC cpprestsdk OpenSSL|SSL ${boost_depends}
+)
+if(TARGET ${MODULE_TARGET})
add_subdirectory(test)
-
endif()
diff --git a/Modules/REST/test/mitkRESTClientTest.cpp b/Modules/REST/test/mitkRESTClientTest.cpp
index 4c68032e0d..cad9e820a8 100644
--- a/Modules/REST/test/mitkRESTClientTest.cpp
+++ b/Modules/REST/test/mitkRESTClientTest.cpp
@@ -1,262 +1,264 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <mitkTestFixture.h>
#include <mitkTestingMacros.h>
#include <mitkIRESTManager.h>
#include <mitkIRESTObserver.h>
#include <mitkRESTClient.h>
#include <mitkRESTUtil.h>
#include <usGetModuleContext.h>
#include <usModuleContext.h>
#include <usServiceReference.h>
#include <vtkDebugLeaks.h>
+#include <atomic>
+
class mitkRESTClientTestSuite : public mitk::TestFixture, mitk::IRESTObserver
{
CPPUNIT_TEST_SUITE(mitkRESTClientTestSuite);
// MITK_TEST(GetRequestValidURI_ReturnsExpectedJSON); GET requests do not support content yet?
MITK_TEST(MultipleGetRequestValidURI_AllTasksFinish);
// MITK_TEST(PutRequestValidURI_ReturnsExpectedJSON); Does not work reliably on dart clients
// MITK_TEST(PostRequestValidURI_ReturnsExpectedJSON); -- " --
MITK_TEST(GetRequestInvalidURI_ThrowsException);
MITK_TEST(PutRequestInvalidURI_ThrowsException);
MITK_TEST(PostRequestInvalidURI_ThrowsException);
CPPUNIT_TEST_SUITE_END();
public:
mitk::IRESTManager *m_Service;
web::json::value m_Data;
web::http::http_response Notify(const web::uri &,
const web::json::value &,
const web::http::method &,
const mitk::RESTUtil::ParamMap &) override
{
auto response = web::http::http_response();
response.set_body(m_Data);
response.set_status_code(web::http::status_codes::OK);
return response;
}
/**
* @brief Setup Always call this method before each Test-case to ensure correct and new intialization of the used
* members for a new test case. (If the members are not used in a test, the method does not need to be called).
*/
void setUp() override
{
m_Data = web::json::value();
m_Data[U("userId")] = web::json::value(1);
m_Data[U("id")] = web::json::value(1);
m_Data[U("title")] = web::json::value(U("this is a title"));
m_Data[U("body")] = web::json::value(U("this is a body"));
us::ServiceReference<mitk::IRESTManager> serviceRef =
us::GetModuleContext()->GetServiceReference<mitk::IRESTManager>();
if (serviceRef)
{
m_Service = us::GetModuleContext()->GetService(serviceRef);
}
if (!m_Service)
{
CPPUNIT_FAIL("Getting Service in setUp() failed");
}
m_Service->ReceiveRequest(U("http://localhost:8080/clienttest"), this);
}
void tearDown() override { m_Service->HandleDeleteObserver(this); }
void GetRequestValidURI_ReturnsExpectedJSON()
{
web::json::value result;
m_Service->SendRequest(U("http://localhost:8080/clienttest"))
.then([&](pplx::task<web::json::value> resultTask) {
try
{
result = resultTask.get();
}
catch (const mitk::Exception &exception)
{
MITK_ERROR << exception.what();
return;
}
})
.wait();
CPPUNIT_ASSERT_MESSAGE("Result is the expected JSON value", result == m_Data);
}
void MultipleGetRequestValidURI_AllTasksFinish()
{
- int count = 0;
+ std::atomic<int> count {0};
// Create multiple tasks e.g. as shown below
std::vector<pplx::task<void>> tasks;
for (int i = 0; i < 20; ++i)
{
pplx::task<void> singleTask = m_Service->SendRequest(U("http://localhost:8080/clienttest"))
.then([&](pplx::task<web::json::value> resultTask) {
// Do something when a single task is done
try
{
resultTask.get();
count += 1;
}
catch (const mitk::Exception &exception)
{
MITK_ERROR << exception.what();
return;
}
});
tasks.emplace_back(singleTask);
}
// Create a joinTask which includes all tasks you've created
auto joinTask = pplx::when_all(begin(tasks), end(tasks));
// Run asynchonously
joinTask
.then([&](pplx::task<void> resultTask) {
// Do something when all tasks are finished
try
{
resultTask.get();
count += 1;
}
catch (const mitk::Exception &exception)
{
MITK_ERROR << exception.what();
return;
}
})
.wait();
CPPUNIT_ASSERT_MESSAGE("Multiple Requests", 21 == count);
}
void PutRequestValidURI_ReturnsExpectedJSON()
{
// optional: link might get invalid or content is changed
web::json::value result;
m_Service
->SendJSONRequest(
U("https://jsonplaceholder.typicode.com/posts/1"), mitk::IRESTManager::RequestType::Put)
.then([&](pplx::task<web::json::value> resultTask) {
try
{
result = resultTask.get();
}
catch (const mitk::Exception &exception)
{
MITK_ERROR << exception.what();
return;
}
})
.wait();
CPPUNIT_ASSERT_MESSAGE(
"Result is the expected JSON value, check if the link is still valid since this is an optional test",
result == m_Data);
}
void PostRequestValidURI_ReturnsExpectedJSON()
{
// optional: link might get invalid or content is changed
web::json::value result;
web::json::value data;
data[U("userId")] = m_Data[U("userId")];
data[U("title")] = m_Data[U("title")];
data[U("body")] = m_Data[U("body")];
m_Service
->SendJSONRequest(U("https://jsonplaceholder.typicode.com/posts"), mitk::IRESTManager::RequestType::Post, &data)
.then([&](pplx::task<web::json::value> resultTask) {
try
{
result = resultTask.get();
}
catch (const mitk::Exception &exception)
{
MITK_ERROR << exception.what();
return;
}
})
.wait();
data[U("id")] = web::json::value(101);
CPPUNIT_ASSERT_MESSAGE(
"Result is the expected JSON value, check if the link is still valid since this is an optional test",
result == data);
}
void PostRequestHeaders_Success()
{
mitk::RESTUtil::ParamMap headers;
headers.insert(mitk::RESTUtil::ParamMap::value_type(
U("Content-Type"), U("multipart/related; type=\"application/dicom\"; boundary=boundary")));
m_Service->SendRequest(U("http://localhost:8080/clienttest")).then([&](pplx::task<web::json::value> resultTask) {
// Do something when a single task is done
try
{
resultTask.get();
}
catch (const mitk::Exception &exception)
{
MITK_ERROR << exception.what();
return;
}
});
}
void GetException()
{
// Method which makes a get request to an invalid uri
web::json::value result;
m_Service->SendRequest(U("http://localhost:1234/invalid"))
.then([&](pplx::task<web::json::value> resultTask) { result = resultTask.get(); })
.wait();
}
void GetRequestInvalidURI_ThrowsException() { CPPUNIT_ASSERT_THROW(GetException(), mitk::Exception); }
void PutException()
{
// Method which makes a put request to an invalid uri
web::json::value result;
m_Service->SendJSONRequest(U("http://localhost:1234/invalid"), mitk::IRESTManager::RequestType::Put, &m_Data)
.then([&](pplx::task<web::json::value> resultTask) { result = resultTask.get(); })
.wait();
}
void PutRequestInvalidURI_ThrowsException() { CPPUNIT_ASSERT_THROW(PutException(), mitk::Exception); }
void PostException()
{
// Method which makes a post request to an invalid uri
web::json::value result;
m_Service->SendJSONRequest(U("http://localhost:1234/invalid"), mitk::IRESTManager::RequestType::Post, &m_Data)
.then([&](pplx::task<web::json::value> resultTask) { result = resultTask.get(); })
.wait();
}
void PostRequestInvalidURI_ThrowsException() { CPPUNIT_ASSERT_THROW(PostException(), mitk::Exception); }
};
MITK_TEST_SUITE_REGISTRATION(mitkRESTClient)
diff --git a/Modules/Remeshing/CMakeLists.txt b/Modules/Remeshing/CMakeLists.txt
index 2697e18603..91db053ef8 100644
--- a/Modules/Remeshing/CMakeLists.txt
+++ b/Modules/Remeshing/CMakeLists.txt
@@ -1,9 +1,4 @@
mitk_create_module(
DEPENDS MitkCore
- PACKAGE_DEPENDS OpenMesh|OpenMeshTools
+ PACKAGE_DEPENDS OpenMesh|Tools
)
-
-if(TARGET ${MODULE_TARGET})
- target_link_libraries(${MODULE_TARGET} PRIVATE OpenMeshTools)
- target_compile_definitions(${MODULE_TARGET} PRIVATE -D_USE_MATH_DEFINES)
-endif()
diff --git a/Modules/SceneSerialization/include/mitkSceneIO.h b/Modules/SceneSerialization/include/mitkSceneIO.h
index 66be8b16f1..588090a2b3 100644
--- a/Modules/SceneSerialization/include/mitkSceneIO.h
+++ b/Modules/SceneSerialization/include/mitkSceneIO.h
@@ -1,134 +1,138 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkSceneIO_h_included
#define mitkSceneIO_h_included
#include <MitkSceneSerializationExports.h>
#include "mitkDataStorage.h"
#include "mitkNodePredicateBase.h"
#include <Poco/Zip/ZipLocalFileHeader.h>
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
class BaseData;
class PropertyList;
class MITKSCENESERIALIZATION_EXPORT SceneIO : public itk::Object
{
public:
mitkClassMacroItkParent(SceneIO, itk::Object);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
typedef DataStorage::SetOfObjects FailedBaseDataListType;
/**
* \brief Load a scene of objects from file
* \return DataStorage with all scene objects and their relations. If loading failed, query GetFailedNodes() and
* GetFailedProperties() for more detail.
*
* Attempts to read the provided file and create objects with
* parent/child relations into a DataStorage.
*
* \param filename full filename of the scene file
* \param storage If given, this DataStorage is used instead of a newly created one
* \param clearStorageFirst If set, the provided DataStorage will be cleared before populating it with the loaded
* objects
*/
virtual DataStorage::Pointer LoadScene(const std::string &filename,
DataStorage *storage = nullptr,
bool clearStorageFirst = false);
/**
* \brief Load a scene of objects from directory.
* \return DataStorage with all scene objects and their relations. If loading failed, query GetFailedNodes() and
* GetFailedProperties() for more detail.
*
* Does the same like LoadScene, but assumes that the given filename is the index.xml of the scene and the working directory
* is the directory of the given filename. This function can be used to load an already unpacked scene and create objects with
* parent/child relations into a DataStorage.
*
* \param indexfilename full filename of the scene index file
* \param storage If given, this DataStorage is used instead of a newly created one
* \param clearStorageFirst If set, the provided DataStorage will be cleared before populating it with the loaded
* objects
*/
virtual DataStorage::Pointer LoadSceneUnzipped(const std::string &indexfilename,
DataStorage *storage = nullptr,
bool clearStorageFirst = false);
/**
* \brief Save a scene of objects to file
* \return True if complete success, false if any problem occurred. Note that a scene file might still be written if
false is returned,
it just will not contain every node/property. If writing failed, query GetFailedNodes() and
GetFailedProperties() for more detail.
*
* Attempts to write a scene file, which contains the nodes of the
* provided DataStorage, their parent/child relations, and properties.
*
* \param sceneNodes
* \param storage a DataStorage containing all nodes that should be saved
* \param filename
*/
virtual bool SaveScene(DataStorage::SetOfObjects::ConstPointer sceneNodes,
const DataStorage *storage,
const std::string &filename);
/**
* \brief Get a list of nodes (BaseData containers) that failed to be read/written.
*
* FailedBaseDataListType hold all those nodes that contain BaseData objects
* which could not be read or written during the last call to LoadScene or SaveScene.
*/
const FailedBaseDataListType *GetFailedNodes();
/**
* \brief Get a list of properties that failed to be read/written.
*
* Each entry corresponds to a property which could not
* be (de)serialized. The properties may come from either of
* <ul>
* <li> The BaseData's PropertyList
* <li> The DataNodes's PropertyList
* <li> Any of a DataNodes's render window specific PropertyLists
* </ul>
*/
const PropertyList *GetFailedProperties();
protected:
SceneIO();
~SceneIO() override;
std::string CreateEmptyTempDirectory();
- TiXmlElement *SaveBaseData(BaseData *data, const std::string &filenamehint, bool &error);
- TiXmlElement *SavePropertyList(PropertyList *propertyList, const std::string &filenamehint);
+ tinyxml2::XMLElement *SaveBaseData(tinyxml2::XMLDocument &doc, BaseData *data, const std::string &filenamehint, bool &error);
+ tinyxml2::XMLElement *SavePropertyList(tinyxml2::XMLDocument &doc, PropertyList *propertyList, const std::string &filenamehint);
void OnUnzipError(const void *pSender, std::pair<const Poco::Zip::ZipLocalFileHeader, const std::string> &info);
void OnUnzipOk(const void *pSender, std::pair<const Poco::Zip::ZipLocalFileHeader, const Poco::Path> &info);
FailedBaseDataListType::Pointer m_FailedNodes;
PropertyList::Pointer m_FailedProperties;
std::string m_WorkingDirectory;
unsigned int m_UnzipErrors;
};
}
#endif
diff --git a/Modules/SceneSerialization/include/mitkSceneReader.h b/Modules/SceneSerialization/include/mitkSceneReader.h
index e01c62bab3..e3d790dc4f 100644
--- a/Modules/SceneSerialization/include/mitkSceneReader.h
+++ b/Modules/SceneSerialization/include/mitkSceneReader.h
@@ -1,32 +1,35 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <MitkSceneSerializationExports.h>
-#include <tinyxml.h>
-
#include <itkObjectFactory.h>
#include "mitkDataStorage.h"
+namespace tinyxml2
+{
+ class XMLDocument;
+}
+
namespace mitk
{
class MITKSCENESERIALIZATION_EXPORT SceneReader : public itk::Object
{
public:
mitkClassMacroItkParent(SceneReader, itk::Object);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- virtual bool LoadScene(TiXmlDocument &document, const std::string &workingDirectory, DataStorage *storage);
+ virtual bool LoadScene(tinyxml2::XMLDocument &document, const std::string &workingDirectory, DataStorage *storage);
};
}
diff --git a/Modules/SceneSerialization/src/mitkGeometryDataSerializer.cpp b/Modules/SceneSerialization/src/mitkGeometryDataSerializer.cpp
index fcf615bab7..8c4bd9854b 100644
--- a/Modules/SceneSerialization/src/mitkGeometryDataSerializer.cpp
+++ b/Modules/SceneSerialization/src/mitkGeometryDataSerializer.cpp
@@ -1,63 +1,61 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkGeometryDataSerializer.h"
#include "mitkGeometry3D.h"
#include "mitkGeometryData.h"
#include "mitkIOUtil.h"
-#include <tinyxml.h>
-
MITK_REGISTER_SERIALIZER(GeometryDataSerializer)
mitk::GeometryDataSerializer::GeometryDataSerializer()
{
}
mitk::GeometryDataSerializer::~GeometryDataSerializer()
{
}
std::string mitk::GeometryDataSerializer::Serialize()
{
// Verify good input data type
const auto *ps = dynamic_cast<const GeometryData *>(m_Data.GetPointer());
if (ps == nullptr)
{
MITK_ERROR << " Object at " << (const void *)this->m_Data << " is not an mitk::GeometryData. Cannot serialize...";
return "";
}
// Construct the full filename to store the geometry
std::string filename(this->GetUniqueFilenameInWorkingDirectory());
filename += "_";
filename += m_FilenameHint;
filename += ".mitkgeometry";
std::string fullname(m_WorkingDirectory);
fullname += IOUtil::GetDirectorySeparator();
fullname += filename;
try
{
IOUtil::Save(ps, fullname);
// in case of success, return only the relative filename part
return filename;
}
catch (const std::exception &e)
{
MITK_ERROR << "Unable to serialize GeometryData object: " << e.what();
}
// when failed, return empty string
return "";
}
diff --git a/Modules/SceneSerialization/src/mitkPropertyListDeserializer.cpp b/Modules/SceneSerialization/src/mitkPropertyListDeserializer.cpp
index 0e7f5501a0..2cde291477 100644
--- a/Modules/SceneSerialization/src/mitkPropertyListDeserializer.cpp
+++ b/Modules/SceneSerialization/src/mitkPropertyListDeserializer.cpp
@@ -1,88 +1,88 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPropertyListDeserializer.h"
-#include <tinyxml.h>
+#include <tinyxml2.h>
mitk::PropertyListDeserializer::PropertyListDeserializer()
{
}
mitk::PropertyListDeserializer::~PropertyListDeserializer()
{
}
bool mitk::PropertyListDeserializer::Deserialize()
{
bool error(false);
- TiXmlDocument document(m_Filename);
- if (!document.LoadFile())
+ tinyxml2::XMLDocument document;
+ if (tinyxml2::XML_SUCCESS != document.LoadFile(m_Filename.c_str()))
{
- MITK_ERROR << "Could not open/read/parse " << m_Filename << "\nTinyXML reports: " << document.ErrorDesc()
+ MITK_ERROR << "Could not open/read/parse " << m_Filename << "\nTinyXML reports: " << document.ErrorStr()
<< std::endl;
return false;
}
// find version node --> note version in some variable
int fileVersion = 1;
- TiXmlElement *versionObject = document.FirstChildElement("Version");
+ auto *versionObject = document.FirstChildElement("Version");
if (versionObject)
{
- if (versionObject->QueryIntAttribute("FileVersion", &fileVersion) != TIXML_SUCCESS)
+ if (versionObject->QueryIntAttribute("FileVersion", &fileVersion) != tinyxml2::XML_SUCCESS)
{
MITK_ERROR << "Property file " << m_Filename << " does not contain version information! Trying version 1 format."
<< std::endl;
}
}
std::stringstream propertyListDeserializerClassName;
propertyListDeserializerClassName << "PropertyListDeserializerV" << fileVersion;
std::list<itk::LightObject::Pointer> readers =
itk::ObjectFactoryBase::CreateAllInstance(propertyListDeserializerClassName.str().c_str());
if (readers.size() < 1)
{
MITK_ERROR << "No property list reader found for file version " << fileVersion;
}
if (readers.size() > 1)
{
MITK_WARN << "Multiple property list readers found for file version " << fileVersion
<< ". Using arbitrary first one.";
}
for (auto iter = readers.begin(); iter != readers.end(); ++iter)
{
if (auto *reader = dynamic_cast<PropertyListDeserializer *>(iter->GetPointer()))
{
reader->SetFilename(m_Filename);
bool success = reader->Deserialize();
error |= !success;
m_PropertyList = reader->GetOutput();
if (error)
{
MITK_ERROR << "There were errors while loading property list file " << m_Filename
<< ". Your data may be corrupted";
}
break;
}
}
return !error;
}
mitk::PropertyList::Pointer mitk::PropertyListDeserializer::GetOutput()
{
return m_PropertyList;
}
diff --git a/Modules/SceneSerialization/src/mitkPropertyListDeserializerV1.cpp b/Modules/SceneSerialization/src/mitkPropertyListDeserializerV1.cpp
index 4eafaa51f8..bca359e64d 100644
--- a/Modules/SceneSerialization/src/mitkPropertyListDeserializerV1.cpp
+++ b/Modules/SceneSerialization/src/mitkPropertyListDeserializerV1.cpp
@@ -1,87 +1,87 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPropertyListDeserializerV1.h"
#include "mitkBasePropertySerializer.h"
#include "mitkSerializerMacros.h"
-#include <tinyxml.h>
+#include <tinyxml2.h>
MITK_REGISTER_SERIALIZER(PropertyListDeserializerV1)
mitk::PropertyListDeserializerV1::PropertyListDeserializerV1()
{
}
mitk::PropertyListDeserializerV1::~PropertyListDeserializerV1()
{
}
bool mitk::PropertyListDeserializerV1::Deserialize()
{
bool error(false);
m_PropertyList = PropertyList::New();
- TiXmlDocument document(m_Filename);
- if (!document.LoadFile())
+ tinyxml2::XMLDocument document;
+ if (tinyxml2::XML_SUCCESS != document.LoadFile(m_Filename.c_str()))
{
- MITK_ERROR << "Could not open/read/parse " << m_Filename << "\nTinyXML reports: " << document.ErrorDesc()
+ MITK_ERROR << "Could not open/read/parse " << m_Filename << "\nTinyXML reports: " << document.ErrorStr()
<< std::endl;
return false;
}
- for (TiXmlElement *propertyElement = document.FirstChildElement("property"); propertyElement != nullptr;
+ for (auto *propertyElement = document.FirstChildElement("property"); propertyElement != nullptr;
propertyElement = propertyElement->NextSiblingElement("property"))
{
const char *keya = propertyElement->Attribute("key");
std::string key(keya ? keya : "");
const char *typea = propertyElement->Attribute("type");
std::string type(typea ? typea : "");
// hand propertyElement to specific reader
std::stringstream propertyDeserializerClassName;
propertyDeserializerClassName << type << "Serializer";
std::list<itk::LightObject::Pointer> readers =
itk::ObjectFactoryBase::CreateAllInstance(propertyDeserializerClassName.str().c_str());
if (readers.size() < 1)
{
MITK_ERROR << "No property reader found for " << type;
error = true;
}
if (readers.size() > 1)
{
MITK_WARN << "Multiple property readers found for " << type << ". Using arbitrary first one.";
}
for (auto iter = readers.begin(); iter != readers.end(); ++iter)
{
if (auto *reader = dynamic_cast<BasePropertySerializer *>(iter->GetPointer()))
{
BaseProperty::Pointer property = reader->Deserialize(propertyElement->FirstChildElement());
if (property.IsNotNull())
{
m_PropertyList->ReplaceProperty(key, property);
}
else
{
MITK_ERROR << "There were errors while loading property '" << key << "' of type " << type
<< ". Your data may be corrupted";
error = true;
}
break;
}
}
}
return !error;
}
diff --git a/Modules/SceneSerialization/src/mitkSceneIO.cpp b/Modules/SceneSerialization/src/mitkSceneIO.cpp
index a6b5c851af..04db6cf399 100644
--- a/Modules/SceneSerialization/src/mitkSceneIO.cpp
+++ b/Modules/SceneSerialization/src/mitkSceneIO.cpp
@@ -1,578 +1,575 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <Poco/Delegate.h>
#include <Poco/Path.h>
#include <Poco/TemporaryFile.h>
#include <Poco/Zip/Compress.h>
#include <Poco/Zip/Decompress.h>
#include "mitkBaseDataSerializer.h"
#include "mitkPropertyListSerializer.h"
#include "mitkSceneIO.h"
#include "mitkSceneReader.h"
#include "mitkBaseRenderer.h"
#include "mitkProgressBar.h"
#include "mitkRenderingManager.h"
#include "mitkStandaloneDataStorage.h"
#include <mitkLocaleSwitch.h>
#include <mitkStandardFileLocations.h>
#include <itkObjectFactoryBase.h>
-#include <tinyxml.h>
-
#include <fstream>
#include <mitkIOUtil.h>
#include <sstream>
#include "itksys/SystemTools.hxx"
+#include <tinyxml2.h>
+
mitk::SceneIO::SceneIO() : m_WorkingDirectory(""), m_UnzipErrors(0)
{
}
mitk::SceneIO::~SceneIO()
{
}
std::string mitk::SceneIO::CreateEmptyTempDirectory()
{
mitk::UIDGenerator uidGen;
// std::string returnValue = mitk::StandardFileLocations::GetInstance()->GetOptionDirectory() +
// Poco::Path::separator() + "SceneIOTemp" + uidGen.GetUID();
std::string returnValue = Poco::Path::temp() + "SceneIOTemp" + uidGen.GetUID();
std::string uniquename = returnValue + Poco::Path::separator();
Poco::File tempdir(uniquename);
try
{
bool existsNot = tempdir.createDirectory();
if (!existsNot)
{
MITK_ERROR << "Warning: Directory already exitsts: " << uniquename << " (choosing another)";
returnValue = mitk::StandardFileLocations::GetInstance()->GetOptionDirectory() + Poco::Path::separator() +
"SceneIOTempDirectory" + uidGen.GetUID();
uniquename = returnValue + Poco::Path::separator();
Poco::File tempdir2(uniquename);
if (!tempdir2.createDirectory())
{
MITK_ERROR << "Warning: Second directory also already exitsts: " << uniquename;
}
}
}
catch (std::exception &e)
{
MITK_ERROR << "Could not create temporary directory " << uniquename << ":" << e.what();
return "";
}
return returnValue;
}
mitk::DataStorage::Pointer mitk::SceneIO::LoadScene(const std::string &filename,
DataStorage *pStorage,
bool clearStorageFirst)
{
mitk::LocaleSwitch localeSwitch("C");
// prepare data storage
DataStorage::Pointer storage = pStorage;
if (storage.IsNull())
{
storage = StandaloneDataStorage::New().GetPointer();
}
// test input filename
if (filename.empty())
{
MITK_ERROR << "No filename given. Not possible to load scene.";
return storage;
}
// test if filename can be read
std::ifstream file(filename.c_str(), std::ios::binary);
if (!file.good())
{
MITK_ERROR << "Cannot open '" << filename << "' for reading";
return storage;
}
// get new temporary directory
m_WorkingDirectory = CreateEmptyTempDirectory();
if (m_WorkingDirectory.empty())
{
MITK_ERROR << "Could not create temporary directory. Cannot open scene files.";
return storage;
}
// unzip all filenames contents to temp dir
m_UnzipErrors = 0;
Poco::Zip::Decompress unzipper(file, Poco::Path(m_WorkingDirectory));
unzipper.EError += Poco::Delegate<SceneIO, std::pair<const Poco::Zip::ZipLocalFileHeader, const std::string>>(
this, &SceneIO::OnUnzipError);
unzipper.EOk += Poco::Delegate<SceneIO, std::pair<const Poco::Zip::ZipLocalFileHeader, const Poco::Path>>(
this, &SceneIO::OnUnzipOk);
unzipper.decompressAllFiles();
unzipper.EError -= Poco::Delegate<SceneIO, std::pair<const Poco::Zip::ZipLocalFileHeader, const std::string>>(
this, &SceneIO::OnUnzipError);
unzipper.EOk -= Poco::Delegate<SceneIO, std::pair<const Poco::Zip::ZipLocalFileHeader, const Poco::Path>>(
this, &SceneIO::OnUnzipOk);
if (m_UnzipErrors)
{
MITK_ERROR << "There were " << m_UnzipErrors << " errors unzipping '" << filename
<< "'. Will attempt to read whatever could be unzipped.";
}
// transcode locale-dependent string
m_WorkingDirectory = Poco::Path::transcode (m_WorkingDirectory);
auto indexFile = m_WorkingDirectory + mitk::IOUtil::GetDirectorySeparator() + "index.xml";
storage = LoadSceneUnzipped(indexFile, storage, clearStorageFirst);
// delete temp directory
try
{
Poco::File deleteDir(m_WorkingDirectory);
deleteDir.remove(true); // recursive
}
catch (...)
{
MITK_ERROR << "Could not delete temporary directory " << m_WorkingDirectory;
}
// return new data storage, even if empty or uncomplete (return as much as possible but notify calling method)
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIO::LoadSceneUnzipped(const std::string &indexfilename,
DataStorage *pStorage,
bool clearStorageFirst)
{
mitk::LocaleSwitch localeSwitch("C");
// prepare data storage
DataStorage::Pointer storage = pStorage;
if (storage.IsNull())
{
storage = StandaloneDataStorage::New().GetPointer();
}
if (clearStorageFirst)
{
try
{
storage->Remove(storage->GetAll());
}
catch (...)
{
MITK_ERROR << "DataStorage cannot be cleared properly.";
}
}
// test input filename
if (indexfilename.empty())
{
MITK_ERROR << "No filename given. Not possible to load scene.";
return storage;
}
// transcode locale-dependent string
std::string tempfilename;
std::string workingDir;
itksys::SystemTools::SplitProgramPath(indexfilename, workingDir, tempfilename);
// test if index.xml exists
// parse index.xml with TinyXML
- TiXmlDocument document(indexfilename);
- if (!document.LoadFile())
+ tinyxml2::XMLDocument document;
+ if (tinyxml2::XML_SUCCESS != document.LoadFile(indexfilename.c_str()))
{
MITK_ERROR << "Could not open/read/parse " << workingDir << mitk::IOUtil::GetDirectorySeparator()
- << "index.xml\nTinyXML reports: " << document.ErrorDesc() << std::endl;
+ << "index.xml\nTinyXML reports: " << document.ErrorStr() << std::endl;
return storage;
}
SceneReader::Pointer reader = SceneReader::New();
if (!reader->LoadScene(document, workingDir, storage))
{
MITK_ERROR << "There were errors while loading scene file " << indexfilename << ". Your data may be corrupted";
}
// return new data storage, even if empty or uncomplete (return as much as possible but notify calling method)
return storage;
}
bool mitk::SceneIO::SaveScene(DataStorage::SetOfObjects::ConstPointer sceneNodes,
const DataStorage *storage,
const std::string &filename)
{
if (!sceneNodes)
{
MITK_ERROR << "No set of nodes given. Not possible to save scene.";
return false;
}
if (!storage)
{
MITK_ERROR << "No data storage given. Not possible to save scene."; // \TODO: Technically, it would be possible to
// save the nodes without their relation
return false;
}
if (filename.empty())
{
MITK_ERROR << "No filename given. Not possible to save scene.";
return false;
}
mitk::LocaleSwitch localeSwitch("C");
try
{
m_FailedNodes = DataStorage::SetOfObjects::New();
m_FailedProperties = PropertyList::New();
// start XML DOM
- TiXmlDocument document;
- auto *decl = new TiXmlDeclaration(
- "1.0",
- "UTF-8",
- ""); // TODO what to write here? encoding? standalone would mean that we provide a DTD somewhere...
- document.LinkEndChild(decl);
-
- auto *version = new TiXmlElement("Version");
+ tinyxml2::XMLDocument document;
+ document.InsertEndChild(document.NewDeclaration());
+
+ auto *version = document.NewElement("Version");
version->SetAttribute("Writer", __FILE__);
version->SetAttribute("Revision", "$Revision: 17055 $");
version->SetAttribute("FileVersion", 1);
- document.LinkEndChild(version);
+ document.InsertEndChild(version);
// DataStorage::SetOfObjects::ConstPointer sceneNodes = storage->GetSubset( predicate );
if (sceneNodes.IsNull())
{
MITK_WARN << "Saving empty scene to " << filename;
}
else
{
if (sceneNodes->size() == 0)
{
MITK_WARN << "Saving empty scene to " << filename;
}
MITK_INFO << "Storing scene with " << sceneNodes->size() << " objects to " << filename;
m_WorkingDirectory = CreateEmptyTempDirectory();
if (m_WorkingDirectory.empty())
{
MITK_ERROR << "Could not create temporary directory. Cannot create scene files.";
return false;
}
ProgressBar::GetInstance()->AddStepsToDo(sceneNodes->size());
// find out about dependencies
typedef std::map<DataNode *, std::string> UIDMapType;
typedef std::map<DataNode *, std::list<std::string>> SourcesMapType;
UIDMapType nodeUIDs; // for dependencies: ID of each node
SourcesMapType sourceUIDs; // for dependencies: IDs of a node's parent nodes
UIDGenerator nodeUIDGen("OBJECT_");
for (auto iter = sceneNodes->begin(); iter != sceneNodes->end(); ++iter)
{
DataNode *node = iter->GetPointer();
if (!node)
continue; // unlikely event that we get a nullptr pointer as an object for saving. just ignore
// generate UIDs for all source objects
DataStorage::SetOfObjects::ConstPointer sourceObjects = storage->GetSources(node);
for (auto sourceIter = sourceObjects->begin();
sourceIter != sourceObjects->end();
++sourceIter)
{
if (std::find(sceneNodes->begin(), sceneNodes->end(), *sourceIter) == sceneNodes->end())
continue; // source is not saved, so don't generate a UID for this source
// create a uid for the parent object
if (nodeUIDs[*sourceIter].empty())
{
nodeUIDs[*sourceIter] = nodeUIDGen.GetUID();
}
// store this dependency for writing
sourceUIDs[node].push_back(nodeUIDs[*sourceIter]);
}
if (nodeUIDs[node].empty())
{
nodeUIDs[node] = nodeUIDGen.GetUID();
}
}
// write out objects, dependencies and properties
for (auto iter = sceneNodes->begin(); iter != sceneNodes->end(); ++iter)
{
DataNode *node = iter->GetPointer();
if (node)
{
- auto *nodeElement = new TiXmlElement("node");
+ auto *nodeElement = document.NewElement("node");
std::string filenameHint(node->GetName());
filenameHint = itksys::SystemTools::MakeCindentifier(
filenameHint.c_str()); // escape filename <-- only allow [A-Za-z0-9_], replace everything else with _
// store dependencies
auto searchUIDIter = nodeUIDs.find(node);
if (searchUIDIter != nodeUIDs.end())
{
// store this node's ID
nodeElement->SetAttribute("UID", searchUIDIter->second.c_str());
}
auto searchSourcesIter = sourceUIDs.find(node);
if (searchSourcesIter != sourceUIDs.end())
{
// store all source IDs
for (auto sourceUIDIter = searchSourcesIter->second.begin();
sourceUIDIter != searchSourcesIter->second.end();
++sourceUIDIter)
{
- auto *uidElement = new TiXmlElement("source");
+ auto *uidElement = document.NewElement("source");
uidElement->SetAttribute("UID", sourceUIDIter->c_str());
- nodeElement->LinkEndChild(uidElement);
+ nodeElement->InsertEndChild(uidElement);
}
}
// store basedata
if (BaseData *data = node->GetData())
{
// std::string filenameHint( node->GetName() );
bool error(false);
- TiXmlElement *dataElement(SaveBaseData(data, filenameHint, error)); // returns a reference to a file
+ auto *dataElement = SaveBaseData(document, data, filenameHint, error); // returns a reference to a file
if (error)
{
m_FailedNodes->push_back(node);
}
// store basedata properties
PropertyList *propertyList = data->GetPropertyList();
if (propertyList && !propertyList->IsEmpty())
{
- TiXmlElement *baseDataPropertiesElement(
- SavePropertyList(propertyList, filenameHint + "-data")); // returns a reference to a file
- dataElement->LinkEndChild(baseDataPropertiesElement);
+ auto *baseDataPropertiesElement =
+ SavePropertyList(document, propertyList, filenameHint + "-data"); // returns a reference to a file
+ dataElement->InsertEndChild(baseDataPropertiesElement);
}
- nodeElement->LinkEndChild(dataElement);
+ nodeElement->InsertEndChild(dataElement);
}
// store all renderwindow specific propertylists
mitk::DataNode::PropertyListKeyNames propertyListKeys = node->GetPropertyListNames();
for (auto renderWindowName : propertyListKeys)
{
PropertyList *propertyList = node->GetPropertyList(renderWindowName);
if (propertyList && !propertyList->IsEmpty())
{
- TiXmlElement *renderWindowPropertiesElement(
- SavePropertyList(propertyList, filenameHint + "-" + renderWindowName)); // returns a reference to a file
- renderWindowPropertiesElement->SetAttribute("renderwindow", renderWindowName);
- nodeElement->LinkEndChild(renderWindowPropertiesElement);
+ auto *renderWindowPropertiesElement =
+ SavePropertyList(document, propertyList, filenameHint + "-" + renderWindowName); // returns a reference to a file
+ renderWindowPropertiesElement->SetAttribute("renderwindow", renderWindowName.c_str());
+ nodeElement->InsertEndChild(renderWindowPropertiesElement);
}
}
// don't forget the renderwindow independent list
PropertyList *propertyList = node->GetPropertyList();
if (propertyList && !propertyList->IsEmpty())
{
- TiXmlElement *propertiesElement(
- SavePropertyList(propertyList, filenameHint + "-node")); // returns a reference to a file
- nodeElement->LinkEndChild(propertiesElement);
+ auto *propertiesElement =
+ SavePropertyList(document, propertyList, filenameHint + "-node"); // returns a reference to a file
+ nodeElement->InsertEndChild(propertiesElement);
}
- document.LinkEndChild(nodeElement);
+ document.InsertEndChild(nodeElement);
}
else
{
MITK_WARN << "Ignoring nullptr node during scene serialization.";
}
ProgressBar::GetInstance()->Progress();
} // end for all nodes
} // end if sceneNodes
std::string defaultLocale_WorkingDirectory = Poco::Path::transcode( m_WorkingDirectory );
- if (!document.SaveFile(defaultLocale_WorkingDirectory + Poco::Path::separator() + "index.xml"))
+ auto xmlFilename = defaultLocale_WorkingDirectory + Poco::Path::separator() + "index.xml";
+ if (tinyxml2::XML_SUCCESS != document.SaveFile(xmlFilename.c_str()))
{
MITK_ERROR << "Could not write scene to " << defaultLocale_WorkingDirectory << Poco::Path::separator() << "index.xml"
- << "\nTinyXML reports '" << document.ErrorDesc() << "'";
+ << "\nTinyXML reports '" << document.ErrorStr() << "'";
return false;
}
else
{
try
{
Poco::File deleteFile(filename.c_str());
if (deleteFile.exists())
{
deleteFile.remove();
}
// create zip at filename
std::ofstream file(filename.c_str(), std::ios::binary | std::ios::out);
if (!file.good())
{
MITK_ERROR << "Could not open a zip file for writing: '" << filename << "'";
return false;
}
else
{
Poco::Zip::Compress zipper(file, true);
Poco::Path tmpdir(m_WorkingDirectory);
zipper.addRecursive(tmpdir);
zipper.close();
}
try
{
Poco::File deleteDir(m_WorkingDirectory);
deleteDir.remove(true); // recursive
}
catch (...)
{
MITK_ERROR << "Could not delete temporary directory " << m_WorkingDirectory;
return false; // ok?
}
}
catch (std::exception &e)
{
MITK_ERROR << "Could not create ZIP file from " << m_WorkingDirectory << "\nReason: " << e.what();
return false;
}
return true;
}
}
catch (std::exception &e)
{
MITK_ERROR << "Caught exception during saving temporary files to disk. Error description: '" << e.what() << "'";
return false;
}
}
-TiXmlElement *mitk::SceneIO::SaveBaseData(BaseData *data, const std::string &filenamehint, bool &error)
+tinyxml2::XMLElement *mitk::SceneIO::SaveBaseData(tinyxml2::XMLDocument &doc, BaseData *data, const std::string &filenamehint, bool &error)
{
assert(data);
error = true;
// find correct serializer
// the serializer must
// - create a file containing all information to recreate the BaseData object --> needs to know where to put this
// file (and a filename?)
// - TODO what to do about writers that creates one file per timestep?
- auto *element = new TiXmlElement("data");
+ auto *element = doc.NewElement("data");
element->SetAttribute("type", data->GetNameOfClass());
// construct name of serializer class
std::string serializername(data->GetNameOfClass());
serializername += "Serializer";
std::list<itk::LightObject::Pointer> thingsThatCanSerializeThis =
itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str());
if (thingsThatCanSerializeThis.size() < 1)
{
MITK_ERROR << "No serializer found for " << data->GetNameOfClass() << ". Skipping object";
}
for (auto iter = thingsThatCanSerializeThis.begin();
iter != thingsThatCanSerializeThis.end();
++iter)
{
if (auto *serializer = dynamic_cast<BaseDataSerializer *>(iter->GetPointer()))
{
serializer->SetData(data);
serializer->SetFilenameHint(filenamehint);
std::string defaultLocale_WorkingDirectory = Poco::Path::transcode( m_WorkingDirectory );
serializer->SetWorkingDirectory(defaultLocale_WorkingDirectory);
try
{
std::string writtenfilename = serializer->Serialize();
- element->SetAttribute("file", writtenfilename);
+ element->SetAttribute("file", writtenfilename.c_str());
error = false;
}
catch (std::exception &e)
{
MITK_ERROR << "Serializer " << serializer->GetNameOfClass() << " failed: " << e.what();
}
break;
}
}
- element->SetAttribute("UID", data->GetUID());
+ element->SetAttribute("UID", data->GetUID().c_str());
return element;
}
-TiXmlElement *mitk::SceneIO::SavePropertyList(PropertyList *propertyList, const std::string &filenamehint)
+tinyxml2::XMLElement *mitk::SceneIO::SavePropertyList(tinyxml2::XMLDocument &doc, PropertyList *propertyList, const std::string &filenamehint)
{
assert(propertyList);
// - TODO what to do about shared properties (same object in two lists or behind several keys)?
- auto *element = new TiXmlElement("properties");
+ auto *element = doc.NewElement("properties");
// construct name of serializer class
PropertyListSerializer::Pointer serializer = PropertyListSerializer::New();
serializer->SetPropertyList(propertyList);
serializer->SetFilenameHint(filenamehint);
std::string defaultLocale_WorkingDirectory = Poco::Path::transcode( m_WorkingDirectory );
serializer->SetWorkingDirectory(defaultLocale_WorkingDirectory);
try
{
std::string writtenfilename = serializer->Serialize();
- element->SetAttribute("file", writtenfilename);
+ element->SetAttribute("file", writtenfilename.c_str());
PropertyList::Pointer failedProperties = serializer->GetFailedProperties();
if (failedProperties.IsNotNull())
{
// move failed properties to global list
m_FailedProperties->ConcatenatePropertyList(failedProperties, true);
}
}
catch (std::exception &e)
{
MITK_ERROR << "Serializer " << serializer->GetNameOfClass() << " failed: " << e.what();
}
return element;
}
const mitk::SceneIO::FailedBaseDataListType *mitk::SceneIO::GetFailedNodes()
{
return m_FailedNodes.GetPointer();
}
const mitk::PropertyList *mitk::SceneIO::GetFailedProperties()
{
return m_FailedProperties;
}
void mitk::SceneIO::OnUnzipError(const void * /*pSender*/,
std::pair<const Poco::Zip::ZipLocalFileHeader, const std::string> &info)
{
++m_UnzipErrors;
MITK_ERROR << "Error while unzipping: " << info.second;
}
void mitk::SceneIO::OnUnzipOk(const void * /*pSender*/,
std::pair<const Poco::Zip::ZipLocalFileHeader, const Poco::Path> & /*info*/)
{
// MITK_INFO << "Unzipped ok: " << info.second.toString();
}
diff --git a/Modules/SceneSerialization/src/mitkSceneReader.cpp b/Modules/SceneSerialization/src/mitkSceneReader.cpp
index 1fb3751a86..e47032c47d 100644
--- a/Modules/SceneSerialization/src/mitkSceneReader.cpp
+++ b/Modules/SceneSerialization/src/mitkSceneReader.cpp
@@ -1,61 +1,62 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkSceneReader.h"
+#include <tinyxml2.h>
-bool mitk::SceneReader::LoadScene(TiXmlDocument &document, const std::string &workingDirectory, DataStorage *storage)
+bool mitk::SceneReader::LoadScene(tinyxml2::XMLDocument &document, const std::string &workingDirectory, DataStorage *storage)
{
// find version node --> note version in some variable
int fileVersion = 1;
- TiXmlElement *versionObject = document.FirstChildElement("Version");
+ auto *versionObject = document.FirstChildElement("Version");
if (versionObject)
{
- if (versionObject->QueryIntAttribute("FileVersion", &fileVersion) != TIXML_SUCCESS)
+ if (versionObject->QueryIntAttribute("FileVersion", &fileVersion) != tinyxml2::XML_SUCCESS)
{
MITK_ERROR << "Scene file " << workingDirectory + "/index.xml"
<< " does not contain version information! Trying version 1 format." << std::endl;
}
}
std::stringstream sceneReaderClassName;
sceneReaderClassName << "SceneReaderV" << fileVersion;
std::list<itk::LightObject::Pointer> sceneReaders =
itk::ObjectFactoryBase::CreateAllInstance(sceneReaderClassName.str().c_str());
if (sceneReaders.size() < 1)
{
MITK_ERROR << "No scene reader found for scene file version " << fileVersion;
}
if (sceneReaders.size() > 1)
{
MITK_WARN << "Multiple scene readers found for scene file version " << fileVersion
<< ". Using arbitrary first one.";
}
for (auto iter = sceneReaders.begin(); iter != sceneReaders.end(); ++iter)
{
if (auto *reader = dynamic_cast<SceneReader *>(iter->GetPointer()))
{
if (!reader->LoadScene(document, workingDirectory, storage))
{
MITK_ERROR << "There were errors while loading scene file "
<< workingDirectory + "/index.xml. Your data may be corrupted";
return false;
}
else
{
return true;
}
}
}
return false;
}
diff --git a/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp b/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp
index 5f349a4d22..155f8f20f4 100644
--- a/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp
+++ b/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp
@@ -1,429 +1,430 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkSceneReaderV1.h"
#include "Poco/Path.h"
#include "mitkBaseRenderer.h"
#include "mitkIOUtil.h"
#include "mitkProgressBar.h"
#include "mitkPropertyListDeserializer.h"
#include "mitkSerializerMacros.h"
#include <mitkUIDManipulator.h>
#include <mitkRenderingModeProperty.h>
+#include <tinyxml2.h>
MITK_REGISTER_SERIALIZER(SceneReaderV1)
namespace
{
typedef std::pair<mitk::DataNode::Pointer, std::list<std::string>> NodesAndParentsPair;
bool NodeSortByLayerIsLessThan(const NodesAndParentsPair &left, const NodesAndParentsPair &right)
{
if (left.first.IsNotNull() && right.first.IsNotNull())
{
int leftLayer;
int rightLayer;
if (left.first->GetIntProperty("layer", leftLayer) && right.first->GetIntProperty("layer", rightLayer))
{
return leftLayer < rightLayer;
}
else
{
// fall back to name sort
return left.first->GetName() < right.first->GetName();
}
}
// in all other cases, fall back to stupid pointer comparison
// this is not reasonable but at least answers the sorting
// question clearly
return left.first.GetPointer() < right.first.GetPointer();
}
}
-bool mitk::SceneReaderV1::LoadScene(TiXmlDocument &document, const std::string &workingDirectory, DataStorage *storage)
+bool mitk::SceneReaderV1::LoadScene(tinyxml2::XMLDocument &document, const std::string &workingDirectory, DataStorage *storage)
{
assert(storage);
bool error(false);
// TODO prepare to detect errors (such as cycles) from wrongly written or edited xml files
// Get number of elements to initialze progress bar
// 1. if there is a <data type="..." file="..."> element,
// - construct a name for the appropriate serializer
// - try to instantiate this serializer via itk object factory
// - if serializer could be created, use it to read the file into a BaseData object
// - if successful, call the new node's SetData(..)
// create a node for the tag "data" and test if node was created
typedef std::vector<mitk::DataNode::Pointer> DataNodeVector;
DataNodeVector DataNodes;
unsigned int listSize = 0;
- for (TiXmlElement *element = document.FirstChildElement("node"); element != nullptr;
+ for (auto *element = document.FirstChildElement("node"); element != nullptr;
element = element->NextSiblingElement("node"))
{
++listSize;
}
ProgressBar::GetInstance()->AddStepsToDo(listSize * 2);
- for (TiXmlElement *element = document.FirstChildElement("node"); element != nullptr;
+ for (auto *element = document.FirstChildElement("node"); element != nullptr;
element = element->NextSiblingElement("node"))
{
DataNodes.push_back(LoadBaseDataFromDataTag(element->FirstChildElement("data"), workingDirectory, error));
ProgressBar::GetInstance()->Progress();
}
// iterate all nodes
// first level nodes should be <node> elements
auto nit = DataNodes.begin();
- for (TiXmlElement *element = document.FirstChildElement("node"); element != nullptr || nit != DataNodes.end();
+ for (auto *element = document.FirstChildElement("node"); element != nullptr || nit != DataNodes.end();
element = element->NextSiblingElement("node"), ++nit)
{
mitk::DataNode::Pointer node = *nit;
// in case dataXmlElement is valid test whether it containts the "properties" child tag
// and process further if and only if yes
- TiXmlElement *dataXmlElement = element->FirstChildElement("data");
+ auto *dataXmlElement = element->FirstChildElement("data");
if (dataXmlElement && dataXmlElement->FirstChildElement("properties"))
{
- TiXmlElement *baseDataElement = dataXmlElement->FirstChildElement("properties");
+ auto *baseDataElement = dataXmlElement->FirstChildElement("properties");
if (node->GetData())
{
DecorateBaseDataWithProperties(node->GetData(), baseDataElement, workingDirectory);
}
else
{
MITK_WARN << "BaseData properties stored in scene file, but BaseData could not be read" << std::endl;
}
}
// 2. check child nodes
const char *uida = element->Attribute("UID");
std::string uid("");
if (uida)
{
uid = uida;
m_NodeForID[uid] = node.GetPointer();
m_IDForNode[node.GetPointer()] = uid;
}
else
{
MITK_ERROR << "No UID found for current node. Node will have no parents.";
error = true;
}
// 3. if there are <properties> nodes,
// - instantiate the appropriate PropertyListDeSerializer
// - use them to construct PropertyList objects
// - add these properties to the node (if necessary, use renderwindow name)
bool success = DecorateNodeWithProperties(node, element, workingDirectory);
if (!success)
{
MITK_ERROR << "Could not load properties for node.";
error = true;
}
// remember node for later adding to DataStorage
m_OrderedNodePairs.push_back(std::make_pair(node, std::list<std::string>()));
// 4. if there are <source> elements, remember parent objects
- for (TiXmlElement *source = element->FirstChildElement("source"); source != nullptr;
+ for (auto *source = element->FirstChildElement("source"); source != nullptr;
source = source->NextSiblingElement("source"))
{
const char *sourceUID = source->Attribute("UID");
if (sourceUID)
{
m_OrderedNodePairs.back().second.push_back(std::string(sourceUID));
}
}
ProgressBar::GetInstance()->Progress();
} // end for all <node>
// sort our nodes by their "layer" property
// (to be inserted in that order)
m_OrderedNodePairs.sort(&NodeSortByLayerIsLessThan);
// remove all unknown parent UIDs
for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
for (auto parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();)
{
if (m_NodeForID.find(*parentsIter) == m_NodeForID.end())
{
parentsIter = nodesIter->second.erase(parentsIter);
MITK_WARN << "Found a DataNode with unknown parents. Will add it to DataStorage without any parent objects.";
error = true;
}
else
{
++parentsIter;
}
}
}
// repeat the following loop ...
// ... for all created nodes
unsigned int lastMapSize(0);
while (lastMapSize !=
m_OrderedNodePairs
.size()) // this is to prevent infinite loops; each iteration must at least add one node to DataStorage
{
lastMapSize = m_OrderedNodePairs.size();
// iterate (layer) ordered nodes backwards
// we insert the highest layers first
for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
bool addThisNode(true);
// if any parent node is not yet in DataStorage, skip node for now and check later
for (auto parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();
++parentsIter)
{
if (!storage->Exists(m_NodeForID[*parentsIter]))
{
addThisNode = false;
break;
}
}
if (addThisNode)
{
DataStorage::SetOfObjects::Pointer parents = DataStorage::SetOfObjects::New();
for (auto parentsIter = nodesIter->second.begin();
parentsIter != nodesIter->second.end();
++parentsIter)
{
parents->push_back(m_NodeForID[*parentsIter]);
}
// if all parents are found in datastorage (or are unknown), add node to DataStorage
storage->Add(nodesIter->first, parents);
// remove this node from m_OrderedNodePairs
m_OrderedNodePairs.erase(nodesIter);
// break this for loop because iterators are probably invalid
break;
}
}
}
// All nodes that are still in m_OrderedNodePairs at this point are not part of a proper directed graph structure.
// We'll add such nodes without any parent information.
for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end();
++nodesIter)
{
storage->Add(nodesIter->first);
MITK_WARN << "Encountered node that is not part of a directed graph structure. Will be added to DataStorage "
"without parents.";
error = true;
}
return !error;
}
-mitk::DataNode::Pointer mitk::SceneReaderV1::LoadBaseDataFromDataTag(TiXmlElement *dataElement,
+mitk::DataNode::Pointer mitk::SceneReaderV1::LoadBaseDataFromDataTag(const tinyxml2::XMLElement *dataElement,
const std::string &workingDirectory,
bool &error)
{
DataNode::Pointer node;
if (dataElement)
{
const char *filename = dataElement->Attribute("file");
if (filename && strlen(filename) != 0)
{
try
{
std::vector<BaseData::Pointer> baseData = IOUtil::Load(workingDirectory + Poco::Path::separator() + filename);
if (baseData.size() > 1)
{
MITK_WARN << "Discarding multiple base data results from " << filename << " except the first one.";
}
node = DataNode::New();
node->SetData(baseData.front());
}
catch (std::exception &e)
{
MITK_ERROR << "Error during attempt to read '" << filename << "'. Exception says: " << e.what();
error = true;
}
if (node.IsNull())
{
MITK_ERROR << "Error during attempt to read '" << filename << "'. Factory returned nullptr object.";
error = true;
}
}
const char* dataUID = dataElement->Attribute("UID");
- if (!error && nullptr != dataUID && 0 != strlen(dataUID))
+ if (!error && dataUID != nullptr)
{
UIDManipulator manip(node->GetData());
manip.SetUID(dataUID);
}
}
// in case there was no <data> element we create a new empty node (for appending a propertylist later)
if (node.IsNull())
{
node = DataNode::New();
}
return node;
}
void mitk::SceneReaderV1::ClearNodePropertyListWithExceptions(DataNode &node, PropertyList &propertyList)
{
// Basically call propertyList.Clear(), but implement exceptions (see bug 19354)
BaseData *data = node.GetData();
PropertyList::Pointer propertiesToKeep = PropertyList::New();
if (dynamic_cast<Image *>(data))
{
/*
Older scene files (before changes of bug 17547) could contain
a RenderingMode property with value "LevelWindow_Color".
Since bug 17547 this value has been removed and replaced by
the default value LookupTable_LevelWindow_Color.
This new default value does only result in "black-to-white"
CT images (or others) if there is a corresponding lookup
table. Such a lookup table is provided as a default value
by the Image mapper. Since that value was never present in
older scene files, we do well in not removing the new
default value here. Otherwise the mapper would fall back
to another default which is all the colors of the rainbow :-(
*/
BaseProperty::Pointer lutProperty = propertyList.GetProperty("LookupTable");
propertiesToKeep->SetProperty("LookupTable", lutProperty);
/*
Older scene files (before changes of T14807) may contain
multi-component images without the "Image.Displayed Component"
property.
As the treatment as multi-component image and the corresponding
visualization options hinges on that property we should not delete
it, if it was added by the mapper.
This is a fix for the issue reported in T19919.
*/
BaseProperty::Pointer compProperty = propertyList.GetProperty("Image.Displayed Component");
if (compProperty.IsNotNull())
{
propertiesToKeep->SetProperty("Image.Displayed Component", compProperty);
}
}
propertyList.Clear();
propertyList.ConcatenatePropertyList(propertiesToKeep);
}
bool mitk::SceneReaderV1::DecorateNodeWithProperties(DataNode *node,
- TiXmlElement *nodeElement,
+ const tinyxml2::XMLElement *nodeElement,
const std::string &workingDirectory)
{
assert(node);
assert(nodeElement);
bool error(false);
- for (TiXmlElement *properties = nodeElement->FirstChildElement("properties"); properties != nullptr;
+ for (auto *properties = nodeElement->FirstChildElement("properties"); properties != nullptr;
properties = properties->NextSiblingElement("properties"))
{
const char *propertiesfilea(properties->Attribute("file"));
std::string propertiesfile(propertiesfilea ? propertiesfilea : "");
const char *renderwindowa(properties->Attribute("renderwindow"));
std::string renderwindow(renderwindowa ? renderwindowa : "");
PropertyList::Pointer propertyList =
node->GetPropertyList(renderwindow); // DataNode implementation always returns a propertylist
ClearNodePropertyListWithExceptions(*node, *propertyList);
// use deserializer to construct new properties
PropertyListDeserializer::Pointer deserializer = PropertyListDeserializer::New();
deserializer->SetFilename(workingDirectory + Poco::Path::separator() + propertiesfile);
bool success = deserializer->Deserialize();
error |= !success;
PropertyList::Pointer readProperties = deserializer->GetOutput();
if (readProperties.IsNotNull())
{
propertyList->ConcatenatePropertyList(readProperties, true); // true = replace
}
else
{
MITK_ERROR << "Property list reader did not return a property list. This is an implementation error. Please tell "
"your developer.";
error = true;
}
}
return !error;
}
bool mitk::SceneReaderV1::DecorateBaseDataWithProperties(BaseData::Pointer data,
- TiXmlElement *baseDataNodeElem,
+ const tinyxml2::XMLElement *baseDataNodeElem,
const std::string &workingDir)
{
// check given variables, initialize error variable
assert(baseDataNodeElem);
bool error(false);
// get the file name stored in the <properties ...> tag
const char *baseDataPropertyFile(baseDataNodeElem->Attribute("file"));
// check if the filename was found
if (baseDataPropertyFile)
{
// PropertyList::Pointer dataPropList = data->GetPropertyList();
PropertyListDeserializer::Pointer propertyDeserializer = PropertyListDeserializer::New();
// initialize the property reader
propertyDeserializer->SetFilename(workingDir + Poco::Path::separator() + baseDataPropertyFile);
bool ioSuccess = propertyDeserializer->Deserialize();
error = !ioSuccess;
// get the output
PropertyList::Pointer inProperties = propertyDeserializer->GetOutput();
// store the read-in properties to the given node or throw error otherwise
if (inProperties.IsNotNull())
{
data->SetPropertyList(inProperties);
}
else
{
MITK_ERROR << "The property deserializer did not return a (valid) property list.";
error = true;
}
}
else
{
- MITK_ERROR << "Function DecorateBaseDataWithProperties(...) called with false TiXmlElement. \n \t ->Given element "
+ MITK_ERROR << "Function DecorateBaseDataWithProperties(...) called with false XML element. \n \t ->Given element "
"does not contain a 'file' attribute. \n";
error = true;
}
return !error;
}
diff --git a/Modules/SceneSerialization/src/mitkSceneReaderV1.h b/Modules/SceneSerialization/src/mitkSceneReaderV1.h
index 9ba5964e93..548fbe428a 100644
--- a/Modules/SceneSerialization/src/mitkSceneReaderV1.h
+++ b/Modules/SceneSerialization/src/mitkSceneReaderV1.h
@@ -1,74 +1,79 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkSceneReader.h"
+namespace tinyxml2
+{
+ class XMLElement;
+}
+
namespace mitk
{
class SceneReaderV1 : public SceneReader
{
public:
mitkClassMacro(SceneReaderV1, SceneReader);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- bool LoadScene(TiXmlDocument &document,
+ bool LoadScene(tinyxml2::XMLDocument &document,
const std::string &workingDirectory,
DataStorage *storage) override;
protected:
/**
\brief tries to create one DataNode from a given XML \<node\> element
*/
- DataNode::Pointer LoadBaseDataFromDataTag(TiXmlElement *dataElement,
+ DataNode::Pointer LoadBaseDataFromDataTag(const tinyxml2::XMLElement *dataElement,
const std::string &workingDirectory,
bool &error);
/**
\brief reads all the properties from the XML document and recreates them in node
*/
- bool DecorateNodeWithProperties(DataNode *node, TiXmlElement *nodeElement, const std::string &workingDirectory);
+ bool DecorateNodeWithProperties(DataNode *node, const tinyxml2::XMLElement *nodeElement, const std::string &workingDirectory);
/**
\brief Clear a default property list and handle some exceptions.
Called after assigning a BaseData object to a fresh DataNode via SetData().
This call to SetData() would create default properties that have not been
there when saving the scene. Since they can produce problems, we clear the
list and use only those properties that we read from the scene file.
This method also handles some exceptions for backwards compatibility.
Those exceptions are documented directly in the code of the method.
*/
void ClearNodePropertyListWithExceptions(DataNode &node, PropertyList &propertyList);
/**
\brief reads all properties assigned to a base data element and assigns the list to the base data object
The baseDataNodeElem is supposed to be the \c \<properties file="..."\> element.
*/
bool DecorateBaseDataWithProperties(BaseData::Pointer data,
- TiXmlElement *baseDataNodeElem,
+ const tinyxml2::XMLElement *baseDataNodeElem,
const std::string &workingDir);
typedef std::pair<DataNode::Pointer, std::list<std::string>> NodesAndParentsPair;
typedef std::list<NodesAndParentsPair> OrderedNodesList;
typedef std::map<std::string, DataNode *> IDToNodeMappingType;
typedef std::map<DataNode *, std::string> NodeToIDMappingType;
OrderedNodesList m_OrderedNodePairs;
IDToNodeMappingType m_NodeForID;
NodeToIDMappingType m_IDForNode;
UIDGenerator m_UIDGen;
};
}
diff --git a/Modules/SceneSerialization/test/mitkSceneIOTest.cpp b/Modules/SceneSerialization/test/mitkSceneIOTest.cpp
index 9644a18111..f37faa9b4f 100644
--- a/Modules/SceneSerialization/test/mitkSceneIOTest.cpp
+++ b/Modules/SceneSerialization/test/mitkSceneIOTest.cpp
@@ -1,373 +1,374 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkTestingConfig.h"
#include "mitkTestingMacros.h"
#include "mitkSceneIO.h"
#include "Poco/File.h"
#include "Poco/TemporaryFile.h"
#include "mitkBaseData.h"
#include "mitkCoreObjectFactory.h"
#include "mitkGeometryData.h"
#include "mitkIOUtil.h"
#include "mitkImage.h"
#include "mitkPointSet.h"
#include "mitkStandaloneDataStorage.h"
#include "mitkStandardFileLocations.h"
#include "mitkSurface.h"
#ifndef WIN32
#include <cerrno>
#include <ulimit.h>
#endif
class SceneIOTestClass
{
public:
static mitk::Image::Pointer LoadImage(const std::string &filename)
{
mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(filename);
if (image.IsNull())
{
MITK_TEST_FAILED_MSG(<< "Test image '" << filename << "' was not loaded as an mitk::Image");
}
return image;
}
static mitk::Surface::Pointer LoadSurface(const std::string &filename)
{
mitk::Surface::Pointer surface = mitk::IOUtil::Load<mitk::Surface>(filename);
if (surface.IsNull())
{
MITK_TEST_FAILED_MSG(<< "Test surface '" << filename << "' was not loaded as an mitk::Surface");
}
return surface;
}
static mitk::PointSet::Pointer CreatePointSet()
{
mitk::PointSet::Pointer ps = mitk::PointSet::New();
mitk::PointSet::PointType p;
mitk::FillVector3D(p, 1.0, -2.0, 33.0);
ps->SetPoint(0, p);
mitk::FillVector3D(p, 100.0, -200.0, 3300.0);
ps->SetPoint(1, p);
mitk::FillVector3D(p, 2.0, -3.0, 22.0);
ps->SetPoint(2, p, mitk::PTCORNER); // add point spec
// mitk::FillVector3D(p, -2.0, -2.0, -2.22);
// ps->SetPoint(0, p, 1); // ID 0 in timestep 1
// mitk::FillVector3D(p, -1.0, -1.0, -11.22);
// ps->SetPoint(1, p, 1); // ID 1 in timestep 1
// mitk::FillVector3D(p, 1000.0, 1000.0, 1122.22);
// ps->SetPoint(11, p, mitk::PTCORNER, 2); // ID 11, point spec, timestep 2
return ps;
}
static mitk::GeometryData::Pointer CreateGeometryDataObject()
{
mitk::GeometryData::Pointer gdata = mitk::GeometryData::New();
// define Geometry3D parameters
mitk::AffineTransform3D::MatrixType matrix;
matrix[0][0] = 1.1;
matrix[1][1] = 2.2;
matrix[2][2] = 3.3;
mitk::AffineTransform3D::OffsetType offset;
mitk::FillVector3D(offset, 0.1, 0.2, 0.3);
bool isImageGeometry(false);
unsigned int frameOfReferenceID(47);
mitk::BaseGeometry::BoundsArrayType bounds;
+ bounds.Fill(1.1);
mitk::Point3D origin;
mitk::FillVector3D(origin, 5.1, 5.2, 5.3);
mitk::Vector3D spacing;
mitk::FillVector3D(spacing, 2.1, 2.2, 2.3);
// build GeometryData from matrix/offset/etc.
mitk::AffineTransform3D::Pointer newTransform = mitk::AffineTransform3D::New();
newTransform->SetMatrix(matrix);
newTransform->SetOffset(offset);
mitk::Geometry3D::Pointer newGeometry = mitk::Geometry3D::New();
newGeometry->SetFrameOfReferenceID(frameOfReferenceID);
newGeometry->SetImageGeometry(isImageGeometry);
newGeometry->SetIndexToWorldTransform(newTransform);
newGeometry->SetBounds(bounds);
newGeometry->SetOrigin(origin);
newGeometry->SetSpacing(spacing);
mitk::GeometryData::Pointer newGeometryData = mitk::GeometryData::New();
gdata->SetGeometry(newGeometry);
return gdata;
}
static void FillStorage(mitk::DataStorage *storage, std::string imageName, std::string surfaceName)
{
mitk::Image::Pointer image = LoadImage(imageName);
MITK_TEST_CONDITION_REQUIRED(image.IsNotNull(), "Loading test image" + imageName);
image->SetProperty("image type", mitk::StringProperty::New("test image"));
image->SetProperty("greetings", mitk::StringProperty::New("to mom"));
image->SetProperty("test_float_property", mitk::FloatProperty::New(-2.57f));
mitk::DataNode::Pointer imagenode = mitk::DataNode::New();
imagenode->SetData(image);
imagenode->SetName("Pic3D");
storage->Add(imagenode);
mitk::DataNode::Pointer imagechildnode = mitk::DataNode::New();
imagechildnode->SetData(image);
imagechildnode->SetName("Pic3D again");
storage->Add(imagechildnode, imagenode);
mitk::Surface::Pointer surface = LoadSurface(surfaceName);
MITK_TEST_CONDITION_REQUIRED(surface.IsNotNull(), "Loading test surface binary.stl");
surface->SetProperty("surface type", mitk::StringProperty::New("test surface"));
surface->SetProperty("greetings", mitk::StringProperty::New("to dad"));
mitk::DataNode::Pointer surfacenode = mitk::DataNode::New();
surfacenode->SetData(surface);
surfacenode->SetName("binary");
storage->Add(surfacenode);
mitk::PointSet::Pointer ps = CreatePointSet();
mitk::DataNode::Pointer psenode = mitk::DataNode::New();
psenode->SetData(ps);
psenode->SetName("points");
storage->Add(psenode);
mitk::GeometryData::Pointer gdo = CreateGeometryDataObject();
mitk::DataNode::Pointer geomNode = mitk::DataNode::New();
geomNode->SetData(gdo);
geomNode->SetName("geometry3d");
storage->Add(geomNode);
}
static void VerifyStorage(mitk::DataStorage *storage)
{
mitk::DataNode::Pointer imagenode = storage->GetNamedNode("Pic3D");
MITK_TEST_CONDITION_REQUIRED(imagenode.IsNotNull(), "Get previously stored image node");
mitk::Image::Pointer image = dynamic_cast<mitk::Image *>(imagenode->GetData());
MITK_TEST_CONDITION_REQUIRED(image.IsNotNull(), "Loading test image from Datastorage");
// Image
std::string testString("");
float testFloatValue = 0.0f;
mitk::PropertyList::Pointer imagePropList = image->GetPropertyList();
imagePropList->GetStringProperty("image type", testString);
MITK_TEST_CONDITION(testString == "test image", "Get StringProperty from previously stored image");
imagePropList->GetStringProperty("greetings", testString);
MITK_TEST_CONDITION(testString == "to mom", "Get another StringProperty from previously stored image");
imagePropList->GetFloatProperty("test_float_property", testFloatValue);
MITK_TEST_CONDITION(testFloatValue == -2.57f, "Get FloatProperty from previously stored image.")
// Get Image child node
mitk::DataNode::Pointer imagechildnode = storage->GetNamedNode("Pic3D again");
mitk::DataStorage::SetOfObjects::ConstPointer objects = storage->GetSources(imagechildnode);
MITK_TEST_CONDITION_REQUIRED(objects->Size() == 1, "Check size of image child nodes source list");
MITK_TEST_CONDITION_REQUIRED(objects->ElementAt(0) == imagenode, "Check for right parent node");
mitk::Image::Pointer imagechild = dynamic_cast<mitk::Image *>(imagechildnode->GetData());
MITK_TEST_CONDITION_REQUIRED(imagechild.IsNotNull(), "Loading child test image from Datastorage");
// Surface
mitk::DataNode::Pointer surfacenode = storage->GetNamedNode("binary");
MITK_TEST_CONDITION_REQUIRED(surfacenode.IsNotNull(), "Get previously stored surface node");
mitk::Surface::Pointer surface = dynamic_cast<mitk::Surface *>(surfacenode->GetData());
MITK_TEST_CONDITION_REQUIRED(surface.IsNotNull(), "Loading test surface from Datastorage");
// Get the property list and test the properties
mitk::PropertyList::Pointer surfacePropList = surface->GetPropertyList();
surfacePropList->GetStringProperty("surface type", testString);
MITK_TEST_CONDITION((testString.compare("test surface") == 0),
"Get StringProperty from previously stored surface node");
surfacePropList->GetStringProperty("greetings", testString);
MITK_TEST_CONDITION((testString.compare("to dad") == 0),
"Get another StringProperty from previously stored surface node");
// PointSet
mitk::DataNode::Pointer pointsnode = storage->GetNamedNode("points");
MITK_TEST_CONDITION_REQUIRED(pointsnode.IsNotNull(), "Get previously stored PointSet node");
mitk::PointSet::Pointer pointset = dynamic_cast<mitk::PointSet *>(pointsnode->GetData());
MITK_TEST_CONDITION_REQUIRED(pointset.IsNotNull(), "Loading test PointSet from Datastorage");
mitk::PointSet::PointType p = pointset->GetPoint(0);
MITK_TEST_CONDITION_REQUIRED(p[0] == 1.0 && p[1] == -2.0 && p[2] == 33.0, "Test Pointset entry 0 after loading");
p = pointset->GetPoint(1);
MITK_TEST_CONDITION_REQUIRED(p[0] == 100.0 && p[1] == -200.0 && p[2] == 3300.0,
"Test Pointset entry 1 after loading");
p = pointset->GetPoint(2);
MITK_TEST_CONDITION_REQUIRED(p[0] == 2.0 && p[1] == -3.0 && p[2] == 22.0, "Test Pointset entry 2 after loading");
// GeometryData
mitk::DataNode::Pointer geomnode = storage->GetNamedNode("geometry3d");
MITK_TEST_CONDITION_REQUIRED(geomnode.IsNotNull(), "Get previously stored GeometryData node");
mitk::GeometryData::Pointer gdata = dynamic_cast<mitk::GeometryData *>(geomnode->GetData());
MITK_TEST_CONDITION_REQUIRED(gdata.IsNotNull(), "Loading test GeometryData from Datastorage");
mitk::Geometry3D::Pointer geom3D = dynamic_cast<mitk::Geometry3D *>(gdata->GetGeometry());
MITK_TEST_CONDITION_REQUIRED(geom3D.IsNotNull(), "Reconstructed a Geometry3D from serialization");
MITK_TEST_CONDITION(geom3D->GetImageGeometry() == false, "Reconstructed Geometry3D 'is image geometry'");
MITK_TEST_CONDITION(geom3D->GetFrameOfReferenceID() == 47, "Reconstructa Geometry3D has frame of reference '47'");
// TODO test other properties, BUT don't test too much, that shall be done in a reader/writer test!
}
}; // end test helper class
int mitkSceneIOTest(int, char *argv[])
{
MITK_TEST_BEGIN("SceneIO")
std::string sceneFileName;
for (unsigned int i = 0; i < 1; ++i) // TODO change to " < 2" to check cases where file system would be full
{
if (i == 1)
{
// call ulimit and restrict maximum file size to something small
#ifndef WIN32
errno = 0;
long int value = ulimit(UL_SETFSIZE, 1);
MITK_TEST_CONDITION_REQUIRED(value != -1, "ulimit() returned with errno = " << errno);
#else
continue;
#endif
}
// create a data storage and fill it with some test data
mitk::SceneIO::Pointer sceneIO = mitk::SceneIO::New();
MITK_TEST_CONDITION_REQUIRED(sceneIO.IsNotNull(), "SceneIO instantiation")
mitk::DataStorage::Pointer storage = mitk::StandaloneDataStorage::New().GetPointer();
MITK_TEST_CONDITION_REQUIRED(storage.IsNotNull(), "StandaloneDataStorage instantiation");
std::cout << "ImageName: " << argv[1] << std::endl;
std::cout << "SurfaceName: " << argv[2] << std::endl;
SceneIOTestClass::FillStorage(storage, argv[1], argv[2]);
// attempt to save it
Poco::Path newname(Poco::TemporaryFile::tempName());
sceneFileName = std::string(MITK_TEST_OUTPUT_DIR) + Poco::Path::separator() + newname.getFileName() + ".zip";
MITK_TEST_CONDITION_REQUIRED(sceneIO->SaveScene(storage->GetAll(), storage, sceneFileName),
"Saving scene file '" << sceneFileName << "'");
// test if no errors were reported
mitk::SceneIO::FailedBaseDataListType::ConstPointer failedNodes = sceneIO->GetFailedNodes();
if (failedNodes.IsNotNull() && !failedNodes->empty())
{
MITK_TEST_OUTPUT(<< "The following nodes could not be serialized:");
for (auto iter = failedNodes->begin();
iter != failedNodes->end();
++iter)
{
MITK_TEST_OUTPUT_NO_ENDL(<< " - ");
if (mitk::BaseData *data = (*iter)->GetData())
{
MITK_TEST_OUTPUT_NO_ENDL(<< data->GetNameOfClass());
}
else
{
MITK_TEST_OUTPUT_NO_ENDL(<< "(nullptr)");
}
MITK_TEST_OUTPUT(<< " contained in node '" << (*iter)->GetName() << "'");
// \TODO: should we fail the test case if failed properties exist?
}
}
mitk::PropertyList::ConstPointer failedProperties = sceneIO->GetFailedProperties();
if (failedProperties.IsNotNull() && !failedProperties->IsEmpty())
{
MITK_TEST_OUTPUT(<< "The following properties could not be serialized:");
const mitk::PropertyList::PropertyMap *propmap = failedProperties->GetMap();
for (auto iter = propmap->begin(); iter != propmap->end(); ++iter)
{
MITK_TEST_OUTPUT(<< " - " << iter->second->GetNameOfClass() << " associated to key '" << iter->first << "'");
// \TODO: should we fail the test case if failed properties exist?
}
}
MITK_TEST_CONDITION_REQUIRED(failedProperties.IsNotNull() && failedProperties->IsEmpty(),
"Checking if all properties have been saved.")
MITK_TEST_CONDITION_REQUIRED(failedNodes.IsNotNull() && failedNodes->empty(),
"Checking if all nodes have been saved.")
// Now do the loading part
sceneIO = mitk::SceneIO::New();
// Load scene into the datastorage and clean the DS first
MITK_TEST_OUTPUT(<< "Loading scene again");
storage = sceneIO->LoadScene(sceneFileName, storage, true);
// test if no errors were reported
failedNodes = sceneIO->GetFailedNodes();
if (failedNodes.IsNotNull() && !failedNodes->empty())
{
MITK_TEST_OUTPUT(<< "The following nodes could not be serialized:");
for (auto iter = failedNodes->begin();
iter != failedNodes->end();
++iter)
{
MITK_TEST_OUTPUT_NO_ENDL(<< " - ");
if (mitk::BaseData *data = (*iter)->GetData())
{
MITK_TEST_OUTPUT_NO_ENDL(<< data->GetNameOfClass());
}
else
{
MITK_TEST_OUTPUT_NO_ENDL(<< "(nullptr)");
}
MITK_TEST_OUTPUT(<< " contained in node '" << (*iter)->GetName() << "'");
// \TODO: should we fail the test case if failed properties exist?
}
}
failedProperties = sceneIO->GetFailedProperties();
if (failedProperties.IsNotNull() && !failedProperties->IsEmpty())
{
MITK_TEST_OUTPUT(<< "The following properties could not be serialized:");
const mitk::PropertyList::PropertyMap *propmap = failedProperties->GetMap();
for (auto iter = propmap->begin(); iter != propmap->end(); ++iter)
{
MITK_TEST_OUTPUT(<< " - " << iter->second->GetNameOfClass() << " associated to key '" << iter->first << "'");
// \TODO: should we fail the test case if failed properties exist?
}
}
// check if data storage content has been restored correctly
SceneIOTestClass::VerifyStorage(storage);
}
// if no sub-test failed remove the scene file, otherwise it is kept for debugging purposes
if (mitk::TestManager::GetInstance()->NumberOfFailedTests() == 0)
{
Poco::File pocoSceneFile(sceneFileName);
MITK_TEST_CONDITION_REQUIRED(pocoSceneFile.exists(), "Checking if scene file still exists before cleaning up.")
pocoSceneFile.remove();
}
MITK_TEST_END();
}
diff --git a/Modules/SceneSerialization/test/mitkSceneIOTest2.cpp b/Modules/SceneSerialization/test/mitkSceneIOTest2.cpp
index 3eb1a9e267..392f0477a7 100644
--- a/Modules/SceneSerialization/test/mitkSceneIOTest2.cpp
+++ b/Modules/SceneSerialization/test/mitkSceneIOTest2.cpp
@@ -1,135 +1,135 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkException.h"
#include "mitkTestFixture.h"
#include "mitkTestingMacros.h"
#include "mitkDataStorageCompare.h"
#include "mitkIOUtil.h"
#include "mitkSceneIO.h"
#include "mitkSceneIOTestScenarioProvider.h"
/**
\brief Test cases for SceneIO.
Tests for SceneIO.
Currently contains:
- I/O tests: write some Storage, read it, compare
Should be enhanced with:
- tests about the interface of SceneIO, providing invalid arguments etc.
- testing the error reporting (needs rework, however)
Original notes on tests for SceneIO (topics to test, details to keep in mind, methods to use):
(this list is a notepad that should be emptied while completing tests)
- SaveScene interface topics:
- all input nodes must be in storage
- no nullptrs (in input parameters, nullptrs as nodes or data can be ok)
- filename must be something valid
- empty file shall be written for empty storage (?)
- failures shall result in return false
- LoadScene interface topics:
- filename must exist
- nullptr storage must be ok
- when storage is given, it shall be returned
- clearStorageFirst flag shall be respected
- existing error reporting should mention failures (create faulty test scene files!)
- Error reporting methods
- why do they return C pointers??
- failed properties are not meaningful, they lack association with a data node (even if it could be deduced from the
input data storage)
- don't test that too much, this is worth re-thinking
- I/O tests:
- data storage could be compared: calculate bounds, get group tags
- reproduction of specific storage situations:
- very long property names (empty ones possible?)
- empty or very long node names
- "historic situations", regression tests, bugs that have been discovered and fixed,
"compatibility tess"
- re-definition of properties to define lookup-tables in image mapper
(gray images turn up in all colors of the rainbow)
- re-definition of size properties from int to float in point or surface mapper
(sizes changed)
- such tests could be implemented as rendering tests:
- create reference scenario manually once, store scene file and expected image in MITK-Data
- keep data small(!)
- describe render setups (2D cuts, 3D perspectives)? better standardize one 2D, one 3D view
- load scene in test, render re-loaded scene, compare
- (ok) Tests scenarios and comparisons should be kept out of
this test for SceneIO because they should be re-used for
a possible re-write!
*/
class mitkSceneIOTest2Suite : public mitk::TestFixture
{
CPPUNIT_TEST_SUITE(mitkSceneIOTest2Suite);
MITK_TEST(Test_SceneIOInterfaces);
MITK_TEST(Test_ReconstructionOfScenes);
CPPUNIT_TEST_SUITE_END();
mitk::SceneIOTestScenarioProvider m_TestCaseProvider;
public:
void Test_SceneIOInterfaces() { CPPUNIT_ASSERT_MESSAGE("Not urgent", true); }
void Test_ReconstructionOfScenes()
{
std::string tempDir = mitk::IOUtil::CreateTemporaryDirectory("SceneIOTest_XXXXXX");
mitk::SceneIOTestScenarioProvider::ScenarioList scenarios = m_TestCaseProvider.GetAllScenarios();
MITK_TEST_OUTPUT(<< "Executing " << scenarios.size() << " test scenarios");
- for (auto scenario : scenarios)
+ for (const auto& scenario : scenarios)
{
MITK_TEST_OUTPUT(<< "\n===== Test_ReconstructionOfScenes, scenario '" << scenario.key << "' =====");
std::string archiveFilename = mitk::IOUtil::CreateTemporaryFile("scene_XXXXXX.mitk", tempDir);
mitk::SceneIO::Pointer writer = mitk::SceneIO::New();
mitk::DataStorage::Pointer originalStorage = scenario.BuildDataStorage();
CPPUNIT_ASSERT_MESSAGE(
std::string("Save test scenario '") + scenario.key + "' to '" + archiveFilename + "'",
scenario.serializable == writer->SaveScene(originalStorage->GetAll(), originalStorage, archiveFilename));
if (scenario.serializable)
{
mitk::SceneIO::Pointer reader = mitk::SceneIO::New();
mitk::DataStorage::Pointer restoredStorage;
CPPUNIT_ASSERT_NO_THROW(restoredStorage = reader->LoadScene(archiveFilename));
CPPUNIT_ASSERT_MESSAGE(
std::string("Comparing restored test scenario '") + scenario.key + "'",
mitk::DataStorageCompare(originalStorage,
restoredStorage,
// TODO make those flags part of the scenario object
// TODO make known/expected failures also part of the
// scenario object (but this needs a way to describe them, first)
mitk::DataStorageCompare::CMP_Hierarchy | mitk::DataStorageCompare::CMP_Data |
mitk::DataStorageCompare::CMP_Properties |
// mappers tested although SceneIO leaves default mappers
mitk::DataStorageCompare::CMP_Mappers,
// mitk::DataStorageCompare::CMP_Interactors
// interactors skipped for now
scenario.comparisonPrecision)
.CompareVerbose());
}
}
}
}; // class
int mitkSceneIOTest2(int /*argc*/, char * /*argv*/ [])
{
CppUnit::TextUi::TestRunner runner;
runner.addTest(mitkSceneIOTest2Suite::suite());
return runner.run() ? 0 : 1;
}
diff --git a/Modules/SceneSerialization/test/mitkSceneIOTestScenarioProvider.cpp b/Modules/SceneSerialization/test/mitkSceneIOTestScenarioProvider.cpp
index acd1515c52..3006fb1a90 100644
--- a/Modules/SceneSerialization/test/mitkSceneIOTestScenarioProvider.cpp
+++ b/Modules/SceneSerialization/test/mitkSceneIOTestScenarioProvider.cpp
@@ -1,434 +1,434 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkSceneIOTestScenarioProvider.h"
#include "mitkGeometryData.h"
#include "mitkImage.h"
#include "mitkImageGenerator.h"
#include "mitkPointSet.h"
#include "mitkProperties.h"
#include "mitkSurface.h"
#include <vtkCellArray.h>
#include <vtkPolyData.h>
#include <vtkPolygon.h>
namespace
{
std::string VeryLongText =
"Lorem ipsum dolor sit amet, consectetur adipiscing elit.Donec a diam lectus.Sed sit amet ipsum mauris.Maecenas "
"congue ligula ac quam viverra nec consectetur ante hendrerit.Donec et mollis dolor.Praesent et diam eget libero "
"egestas mattis sit amet vitae augue.Nam tincidunt congue enim, ut porta lorem lacinia consectetur.Donec ut libero "
"sed arcu vehicula ultricies a non tortor.Lorem ipsum dolor sit amet, consectetur adipiscing elit.Aenean ut "
"gravida lorem.Ut turpis felis, pulvinar a semper sed, adipiscing id dolor.Pellentesque auctor nisi id magna "
"consequat sagittis.Curabitur dapibus enim sit amet elit pharetra tincidunt feugiat nisl imperdiet.Ut convallis "
"libero in urna ultrices accumsan.Donec sed odio eros.Donec viverra mi quis quam pulvinar at malesuada arcu "
"rhoncus.Cum sociis natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.In rutrum accumsan "
"ultricies.Mauris vitae nisi at sem facilisis semper ac in est.\n"
"Vivamus fermentum semper porta.Nunc diam velit, adipiscing ut tristique vitae, sagittis vel odio.Maecenas "
"convallis ullamcorper ultricies.Curabitur ornare, ligula semper consectetur sagittis, nisi diam iaculis velit, id "
"fringilla sem nunc vel mi.Nam dictum, odio nec pretium volutpat, arcu ante placerat erat, non tristique elit urna "
"et turpis.Quisque mi metus, ornare sit amet fermentum et, tincidunt et orci.Fusce eget orci a orci congue "
"vestibulum.Ut dolor diam, elementum et vestibulum eu, porttitor vel elit.Curabitur venenatis pulvinar tellus "
"gravida ornare.Sed et erat faucibus nunc euismod ultricies ut id justo.Nullam cursus suscipit nisi, et ultrices "
"justo sodales nec.Fusce venenatis facilisis lectus ac semper.Aliquam at massa ipsum.Quisque bibendum purus "
"convallis nulla ultrices ultricies.Nullam aliquam, mi eu aliquam tincidunt, purus velit laoreet tortor, viverra "
- "pretium nisi quam vitae mi.Fusce vel volutpat elit.Nam sagittis nisi dui.\r\n"
+ "pretium nisi quam vitae mi.Fusce vel volutpat elit.Nam sagittis nisi dui.\n\n"
"Suspendisse lectus leo, consectetur in tempor sit amet, placerat quis neque.Etiam luctus porttitor lorem, sed "
"suscipit est rutrum non.Curabitur lobortis nisl a enim congue semper.Aenean commodo ultrices imperdiet.Vestibulum "
"ut justo vel sapien venenatis tincidunt.Phasellus eget dolor sit amet ipsum dapibus condimentum vitae quis "
"lectus.Aliquam ut massa in turpis dapibus convallis.Praesent elit lacus, vestibulum at malesuada et, ornare et "
"est.Ut augue nunc, sodales ut euismod non, adipiscing vitae orci.Mauris ut placerat justo.Mauris in ultricies "
"enim.Quisque nec est eleifend nulla ultrices egestas quis ut quam.Donec sollicitudin lectus a mauris pulvinar id "
"aliquam urna cursus.Cras quis ligula sem, vel elementum mi.Phasellus non ullamcorper urna.\t\n"
"Class aptent taciti sociosqu ad litora torquent per conubia nostra, per inceptos himenaeos.In euismod ultrices "
"facilisis.Vestibulum porta sapien adipiscing augue congue id pretium lectus molestie.Proin quis dictum nisl.Morbi "
"id quam sapien, sed vestibulum sem.Duis elementum rutrum mauris sed convallis.Proin vestibulum magna mi.Aenean "
"tristique hendrerit magna, ac facilisis nulla hendrerit ut.Sed non tortor sodales quam auctor elementum.Donec "
"hendrerit nunc eget elit pharetra pulvinar.Suspendisse id tempus tortor.Aenean luctus, elit commodo laoreet "
"commodo, justo nisi consequat massa, sed vulputate quam urna quis eros.Donec vel.";
}
// --------------- SceneIOTestScenarioProvider::Scenario ---------------
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::Scenario::BuildDataStorage() const
{
return (*m_ScenarioProvider.*m_ProviderMethod)(); // calls function
}
mitk::SceneIOTestScenarioProvider::Scenario::Scenario(const std::string &_key,
const SceneIOTestScenarioProvider *_scenarioProvider,
SceneIOTestScenarioProvider::BuilderMethodPointer _providerMethod,
bool _isSerializable,
const std::string &_referenceArchiveFilename,
bool _isReferenceLoadable,
double _comparisonPrecision)
: key(_key),
serializable(_isSerializable),
referenceArchiveFilename(_referenceArchiveFilename),
referenceArchiveLoadable(_isReferenceLoadable),
comparisonPrecision(_comparisonPrecision),
m_ScenarioProvider(_scenarioProvider),
m_ProviderMethod(_providerMethod)
{
}
// --------------- SceneIOTestScenarioProvider ---------------
mitk::SceneIOTestScenarioProvider::ScenarioList mitk::SceneIOTestScenarioProvider::GetAllScenarios() const
{
return m_Scenarios;
}
void mitk::SceneIOTestScenarioProvider::AddScenario(const std::string &key,
BuilderMethodPointer creator,
bool isSerializable,
const std::string &referenceArchiveFilename,
bool isReferenceLoadable,
double comparisonPrecision)
{
Scenario newScenario(
key, this, creator, isSerializable, referenceArchiveFilename, isReferenceLoadable, comparisonPrecision);
m_Scenarios.push_back(newScenario);
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::EmptyStorage() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::OneEmptyNode() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
mitk::DataNode::Pointer node = DataNode::New();
storage->Add(node);
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::OneEmptyNamedNode() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
mitk::DataNode::Pointer node = DataNode::New();
node->SetName("Urmel");
storage->Add(node);
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::ManyTopLevelNodes() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
for (auto i = 0; i < m_HowMuchIsMany; ++i)
{
mitk::DataNode::Pointer node = DataNode::New();
std::stringstream s;
s << "Node #" << i;
node->SetName(s.str());
storage->Add(node);
}
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::LineOfManyOnlyChildren() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
mitk::DataNode::Pointer parent;
for (auto i = 0; i < m_HowMuchIsMany; ++i)
{
mitk::DataNode::Pointer node = DataNode::New();
std::stringstream s;
s << "Node #" << i;
node->SetName(s.str());
storage->Add(node, parent);
parent = node;
}
return storage;
}
#define AddNode(name) storage->Add(name);
#define DefineNode(name) \
mitk::DataNode::Pointer name = mitk::DataNode::New(); \
name->SetName(#name);
#define DefNode0(name) DefineNode(name) AddNode(name)
#define DefNode1(source, name) DefineNode(name) storage->Add(name, source);
#define DefNode2(source1, source2, name) \
DefineNode(name) \
{ \
mitk::DataStorage::SetOfObjects::Pointer sources = mitk::DataStorage::SetOfObjects::New(); \
sources->push_back(source1); \
sources->push_back(source2); \
storage->Add(name, sources); \
}
#define DefNode3(source1, source2, source3, name) \
DefineNode(name) \
{ \
mitk::DataStorage::SetOfObjects::Pointer sources = mitk::DataStorage::SetOfObjects::New(); \
sources->push_back(source1); \
sources->push_back(source2); \
sources->push_back(source3); \
storage->Add(name, sources); \
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::ComplicatedFamilySituation() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
// constructing a hierarchy with multiple levels
// and a couple of multiple parent relations.
// Anybody, feel free to make this something
// meaningful and/or visualize it :-)
DefNode0(Color) DefNode0(White)
DefNode1(Color, Green) DefNode1(Color, Election) DefNode1(Color, Red)
DefNode1(Green, Yellow)
DefNode1(Election, Looser) DefNode1(Election, FreeBeer) DefNode1(Election, Winner)
DefNode1(Looser, Tears) DefNode1(Looser, Anger)
DefNode1(FreeBeer, OpenSource);
DefNode1(White, Sweet)
DefNode2(White, Sweet, Sugar) DefNode2(Red, Sweet, Tomatoe) DefNode2(Tomatoe, Sugar, Ketchup)
DefNode1(Ketchup, BBQSauce) DefNode1(Tomatoe, ATLAS)
DefNode0(Fish) DefNode0(OperatingSystem) DefNode1(Fish, Bird) DefNode1(Bird, Penguin)
DefNode3(Penguin, OperatingSystem, OpenSource, Linux)
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::Image() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
{ // Image of ints
mitk::Image::Pointer image3Dints = mitk::ImageGenerator::GenerateRandomImage<int>(10,
5,
7, // dim
1,
0.5,
0.5, // spacing
1, // time steps
3000,
-1000); // random max / min
mitk::DataNode::Pointer node = DataNode::New();
node->SetName("Image-Int");
node->SetData(image3Dints);
storage->Add(node);
}
{ // Image of doubles
mitk::Image::Pointer image3Ddouble = mitk::ImageGenerator::GenerateRandomImage<double>(5,
10,
8, // dim
1,
0.5,
0.5, // spacing
2, // time steps
3000,
-1000); // random max / min
mitk::DataNode::Pointer node = DataNode::New();
node->SetName("Image-Double");
node->SetData(image3Ddouble);
storage->Add(node);
}
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::Surface() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
{ // Surface
vtkSmartPointer<vtkPoints> points1 = vtkSmartPointer<vtkPoints>::New();
points1->InsertNextPoint(0.0, 0.0, 0.0);
points1->InsertNextPoint(1.0, 0.0, 0.0);
points1->InsertNextPoint(0.0, 1.0, 0.0);
points1->InsertNextPoint(1.0, 1.0, 0.0);
vtkSmartPointer<vtkPolygon> polygon1 = vtkSmartPointer<vtkPolygon>::New();
polygon1->GetPointIds()->SetNumberOfIds(4);
polygon1->GetPointIds()->SetId(0, 0);
polygon1->GetPointIds()->SetId(1, 1);
polygon1->GetPointIds()->SetId(2, 2);
polygon1->GetPointIds()->SetId(3, 3);
vtkSmartPointer<vtkPolygon> polygon2 = vtkSmartPointer<vtkPolygon>::New();
polygon2->GetPointIds()->SetNumberOfIds(4);
polygon2->GetPointIds()->SetId(0, 3);
polygon2->GetPointIds()->SetId(1, 2);
polygon2->GetPointIds()->SetId(2, 0);
polygon2->GetPointIds()->SetId(3, 1);
// generate polydatas
vtkSmartPointer<vtkCellArray> polygonArray1 = vtkSmartPointer<vtkCellArray>::New();
polygonArray1->InsertNextCell(polygon1);
vtkSmartPointer<vtkPolyData> polydata1 = vtkSmartPointer<vtkPolyData>::New();
polydata1->SetPoints(points1);
polydata1->SetPolys(polygonArray1);
vtkSmartPointer<vtkCellArray> polygonArray2 = vtkSmartPointer<vtkCellArray>::New();
polygonArray2->InsertNextCell(polygon2);
vtkSmartPointer<vtkPolyData> polyDataTwo = vtkSmartPointer<vtkPolyData>::New();
polyDataTwo->SetPoints(points1);
polyDataTwo->SetPolys(polygonArray2);
// generate surfaces
mitk::Surface::Pointer surface = mitk::Surface::New();
surface->SetVtkPolyData(polydata1);
mitk::DataNode::Pointer node = DataNode::New();
node->SetName("Surface");
node->SetData(surface);
storage->Add(node);
}
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::PointSet() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
{ // PointSet
mitk::PointSet::Pointer ps = mitk::PointSet::New();
mitk::PointSet::PointType p;
mitk::FillVector3D(p, 1.0, -2.0, 33.0);
ps->SetPoint(0, p);
mitk::FillVector3D(p, 100.0, -200.0, 3300.0);
ps->SetPoint(1, p);
mitk::FillVector3D(p, 2.0, -3.0, 22.0);
ps->SetPoint(2, p, mitk::PTCORNER); // add point spec
mitk::DataNode::Pointer node = DataNode::New();
node->SetName("PointSet");
node->SetData(ps);
storage->Add(node);
}
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::GeometryData() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
{ // GeometryData
mitk::GeometryData::Pointer gdata = mitk::GeometryData::New();
// define Geometry3D parameters
mitk::AffineTransform3D::MatrixType matrix;
matrix[0][0] = 1.1;
matrix[1][1] = 2.2;
matrix[2][2] = 3.3;
mitk::AffineTransform3D::OffsetType offset;
mitk::FillVector3D(offset, 0.1, 0.2, 0.3);
bool isImageGeometry(false);
unsigned int frameOfReferenceID(47);
mitk::BaseGeometry::BoundsArrayType bounds;
bounds[0] = std::numeric_limits<mitk::ScalarType>::min();
bounds[1] = -52.723;
bounds[2] = -0.002;
bounds[3] = 918273645.18293746;
bounds[4] = -0.002;
bounds[5] = +52.723;
mitk::Point3D origin;
mitk::FillVector3D(origin, 5.1, 5.2, 5.3);
mitk::Vector3D spacing;
mitk::FillVector3D(spacing, 2.1, 2.2, 2.3);
// build GeometryData from matrix/offset/etc.
mitk::AffineTransform3D::Pointer newTransform = mitk::AffineTransform3D::New();
newTransform->SetMatrix(matrix);
newTransform->SetOffset(offset);
mitk::Geometry3D::Pointer newGeometry = mitk::Geometry3D::New();
newGeometry->SetFrameOfReferenceID(frameOfReferenceID);
newGeometry->SetImageGeometry(isImageGeometry);
newGeometry->SetIndexToWorldTransform(newTransform);
newGeometry->SetBounds(bounds);
newGeometry->SetOrigin(origin);
newGeometry->SetSpacing(spacing);
mitk::GeometryData::Pointer geometryData = mitk::GeometryData::New();
geometryData->SetGeometry(newGeometry);
mitk::DataNode::Pointer node = DataNode::New();
node->SetName("GeometryData");
node->SetData(geometryData);
storage->Add(node);
}
return storage;
}
mitk::DataStorage::Pointer mitk::SceneIOTestScenarioProvider::SpecialProperties() const
{
mitk::DataStorage::Pointer storage = StandaloneDataStorage::New().GetPointer();
mitk::DataNode::Pointer node = DataNode::New();
node->SetName("Camion");
node->SetProperty("Livre", StringProperty::New(VeryLongText)); // defined at the top of this file
node->SetProperty(VeryLongText.c_str(), StringProperty::New("Shorty"));
node->GetPropertyList("Chapitre1")->SetProperty("Page 1", StringProperty::New(VeryLongText));
node->GetPropertyList("Chapitre1")->SetProperty("Page 2", StringProperty::New(VeryLongText));
node->GetPropertyList("Chapitre 2")->SetProperty("Page", StringProperty::New(VeryLongText));
node->GetPropertyList("Chapitre 3")->SetProperty("Page", StringProperty::New(VeryLongText));
node->GetPropertyList(VeryLongText)->SetProperty("Page", StringProperty::New(VeryLongText));
// not working (NaN etc.)
// node->SetProperty("NotAFloat", FloatProperty::New( sqrt(-1.0) ) );
node->SetProperty("sqrt(2)", FloatProperty::New(-sqrt(2.0)));
node->SetProperty("sqrt(3)", FloatProperty::New(sqrt(3.0)));
// most values work fine, just min/max double produces serialization precision errors
node->SetProperty("sqrt(4)", DoubleProperty::New(-sqrt(4.0)));
node->SetProperty("sqrt(5)", DoubleProperty::New(sqrt(5.0)));
// node->SetProperty("maxd", DoubleProperty::New( std::numeric_limits<double>::max() ) );
node->SetProperty("zero", DoubleProperty::New(0.0));
node->SetProperty("minzero", DoubleProperty::New(-0.0));
// node->SetProperty("mind", DoubleProperty::New( std::numeric_limits<double>::min() ) );
storage->Add(node);
return storage;
}
diff --git a/Modules/SceneSerializationBase/CMakeLists.txt b/Modules/SceneSerializationBase/CMakeLists.txt
index 95aa6b358a..e5ff608f40 100644
--- a/Modules/SceneSerializationBase/CMakeLists.txt
+++ b/Modules/SceneSerializationBase/CMakeLists.txt
@@ -1,6 +1,6 @@
MITK_CREATE_MODULE(
DEPENDS MitkCore
- PACKAGE_DEPENDS PUBLIC tinyxml
+ PACKAGE_DEPENDS PUBLIC tinyxml2
)
-add_subdirectory(test)
+add_subdirectory(test)
diff --git a/Modules/SceneSerializationBase/include/mitkBasePropertySerializer.h b/Modules/SceneSerializationBase/include/mitkBasePropertySerializer.h
index adb01cdaa0..90ba831bbb 100644
--- a/Modules/SceneSerializationBase/include/mitkBasePropertySerializer.h
+++ b/Modules/SceneSerializationBase/include/mitkBasePropertySerializer.h
@@ -1,70 +1,74 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkSerializeBaseProperty_h_included
#define mitkSerializeBaseProperty_h_included
#include "mitkSerializerMacros.h"
#include <MitkSceneSerializationBaseExports.h>
#include "mitkBaseProperty.h"
#include <itkObjectFactoryBase.h>
-#include <tinyxml.h>
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
/**
\brief Base class for objects that serialize BaseProperty types.
The name of sub-classes must be deduced from the class name of the object that should be serialized.
The serialization assumes that
\verbatim
If the class derived from BaseProperty is called GreenProperty
Then the serializer for this class must be called GreenPropertySerializer
\endverbatim
*/
class MITKSCENESERIALIZATIONBASE_EXPORT BasePropertySerializer : public itk::Object
{
public:
mitkClassMacroItkParent(BasePropertySerializer, itk::Object);
itkSetConstObjectMacro(Property, BaseProperty);
/**
\brief Serializes given BaseProperty object.
\return The filename of the newly created file.
This should be overwritten by specific sub-classes.
*/
- virtual TiXmlElement *Serialize();
+ virtual tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument& doc);
/**
- \brief Deserializes given TiXmlElement.
+ \brief Deserializes given XML element.
\return The deserialized Property.
This should be overwritten by specific sub-classes.
*/
- virtual BaseProperty::Pointer Deserialize(TiXmlElement *);
+ virtual BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement*);
protected:
BasePropertySerializer();
~BasePropertySerializer() override;
BaseProperty::ConstPointer m_Property;
};
} // namespace
#endif
diff --git a/Modules/SceneSerializationBase/include/mitkEnumerationPropertySerializer.h b/Modules/SceneSerializationBase/include/mitkEnumerationPropertySerializer.h
index 6ac8da4ca9..16d740f2cf 100644
--- a/Modules/SceneSerializationBase/include/mitkEnumerationPropertySerializer.h
+++ b/Modules/SceneSerializationBase/include/mitkEnumerationPropertySerializer.h
@@ -1,36 +1,36 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkEnumerationPropertySerializer_h_included
#define mitkEnumerationPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkEnumerationProperty.h"
namespace mitk
{
class MITKSCENESERIALIZATIONBASE_EXPORT EnumerationPropertySerializer : public BasePropertySerializer
{
public:
mitkClassMacro(EnumerationPropertySerializer, BasePropertySerializer);
- TiXmlElement *Serialize() override;
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument& doc) override;
protected:
EnumerationPropertySerializer();
~EnumerationPropertySerializer() override;
};
} // namespace
#endif
diff --git a/Modules/SceneSerializationBase/include/mitkLookupTablePropertySerializer.h b/Modules/SceneSerializationBase/include/mitkLookupTablePropertySerializer.h
index 59588423fc..dac01cbcf1 100644
--- a/Modules/SceneSerializationBase/include/mitkLookupTablePropertySerializer.h
+++ b/Modules/SceneSerializationBase/include/mitkLookupTablePropertySerializer.h
@@ -1,57 +1,57 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkLookupTablePropertySerializer_h_included
#define mitkLookupTablePropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include <MitkSceneSerializationBaseExports.h>
namespace mitk
{
/**
\brief Base class for objects that serialize BaseData types.
The name of sub-classes must be deduced from the class name of the object that should be serialized.
The serialization assumes that
\verbatim
If the class derived from BaseData is called GreenData
Then the serializer for this class must be called GreenDataSerializer
\endverbatim
*/
class MITKSCENESERIALIZATIONBASE_EXPORT LookupTablePropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(LookupTablePropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
+ mitkClassMacro(LookupTablePropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- /**
- \brief Serializes given BaseData object.
- \return the filename of the newly created file.
+ /**
+ \brief Serializes given BaseData object.
+ \return the filename of the newly created file.
- This should be overwritten by specific sub-classes.
- */
- TiXmlElement *Serialize() override;
+ This should be overwritten by specific sub-classes.
+ */
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument& doc) override;
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override;
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override;
protected:
LookupTablePropertySerializer(){};
~LookupTablePropertySerializer() override{};
};
}
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(LookupTablePropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/include/mitkPropertyListSerializer.h b/Modules/SceneSerializationBase/include/mitkPropertyListSerializer.h
index ffafeff700..360847a7db 100644
--- a/Modules/SceneSerializationBase/include/mitkPropertyListSerializer.h
+++ b/Modules/SceneSerializationBase/include/mitkPropertyListSerializer.h
@@ -1,66 +1,70 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkPropertyListSerializer_h_included
#define mitkPropertyListSerializer_h_included
#include <MitkSceneSerializationBaseExports.h>
#include "mitkPropertyList.h"
#include <itkObjectFactoryBase.h>
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk
{
/**
\brief Serializes a mitk::PropertyList
*/
class MITKSCENESERIALIZATIONBASE_EXPORT PropertyListSerializer : public itk::Object
{
public:
mitkClassMacroItkParent(PropertyListSerializer, itk::Object);
itkFactorylessNewMacro(Self) // is this needed? should never be instantiated, only subclasses should
itkCloneMacro(Self);
itkSetStringMacro(FilenameHint);
itkGetStringMacro(FilenameHint);
itkSetStringMacro(WorkingDirectory);
itkGetStringMacro(WorkingDirectory);
itkSetObjectMacro(PropertyList, PropertyList);
/**
\brief Serializes given PropertyList object.
\return the filename of the newly created file.
*/
virtual std::string Serialize();
PropertyList *GetFailedProperties();
protected:
PropertyListSerializer();
~PropertyListSerializer() override;
- TiXmlElement *SerializeOneProperty(const std::string &key, const BaseProperty *property);
+ tinyxml2::XMLElement *SerializeOneProperty(tinyxml2::XMLDocument &doc, const std::string &key, const BaseProperty *property);
std::string m_FilenameHint;
std::string m_WorkingDirectory;
PropertyList::Pointer m_PropertyList;
PropertyList::Pointer m_FailedProperties;
};
} // namespace
#endif
diff --git a/Modules/SceneSerializationBase/include/mitkTransferFunctionPropertySerializer.h b/Modules/SceneSerializationBase/include/mitkTransferFunctionPropertySerializer.h
index 786185df13..c064dac33a 100644
--- a/Modules/SceneSerializationBase/include/mitkTransferFunctionPropertySerializer.h
+++ b/Modules/SceneSerializationBase/include/mitkTransferFunctionPropertySerializer.h
@@ -1,35 +1,35 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkBasePropertySerializer.h"
#include "mitkTransferFunctionProperty.h"
namespace mitk
{
class MITKSCENESERIALIZATIONBASE_EXPORT TransferFunctionPropertySerializer : public BasePropertySerializer
{
public:
mitkClassMacro(TransferFunctionPropertySerializer, BasePropertySerializer);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- TiXmlElement *Serialize() override;
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override;
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override;
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override;
static bool SerializeTransferFunction(const char *filename, TransferFunction::Pointer tf);
static TransferFunction::Pointer DeserializeTransferFunction(const char *filePath);
protected:
TransferFunctionPropertySerializer();
~TransferFunctionPropertySerializer() override;
};
} // namespace
diff --git a/Modules/SceneSerializationBase/include/mitkVectorPropertySerializer.h b/Modules/SceneSerializationBase/include/mitkVectorPropertySerializer.h
index 72cf35e431..a2710f1d7b 100644
--- a/Modules/SceneSerializationBase/include/mitkVectorPropertySerializer.h
+++ b/Modules/SceneSerializationBase/include/mitkVectorPropertySerializer.h
@@ -1,153 +1,153 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkVectorPropertySerializer_h
#define mitkVectorPropertySerializer_h
#include "mitkBasePropertySerializer.h"
-
#include "mitkVectorProperty.h"
-
#include <mitkLexicalCast.h>
+#include <tinyxml2.h>
namespace mitk
{
/**
\brief Serializes a VectorProperty
Serializes an instance of VectorProperty into a XML structure like
\verbatim
<Values>
<Value idx="0" value="17.3"/>
<Value idx="1" value="7.2"/>
<Value idx="2" value="-17.3"/>
</Values>
\endverbatim
This class is implemented as a template and makes use of std::stringstream
for necessary conversions of specific data types to and from string.
For numeric types, the class adds a precision token to stringstream that
should usually suffice.
*/
template <typename DATATYPE>
class MITKSCENESERIALIZATIONBASE_EXPORT VectorPropertySerializer : public BasePropertySerializer
{
public:
// Expand manually most of mitkClassMacro:
// mitkClassMacro(VectorProperty<DATATYPE>, mitk::BaseProperty);
// This manual expansion is done to override explicitely
// the GetNameOfClass methods
typedef VectorProperty<DATATYPE> PropertyType;
typedef VectorPropertySerializer<DATATYPE> Self;
typedef BasePropertySerializer SuperClass;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
std::vector<std::string> GetClassHierarchy() const override { return mitk::GetClassHierarchy<Self>(); }
// This function must return different
// strings in function of the template parameter!
// Serialization depends on this feature.
static const char *GetStaticNameOfClass()
{
// concatenate a prefix dependent on the template type and our own classname
static std::string nameOfClass =
std::string(VectorPropertyDataType<DATATYPE>::prefix()) + "VectorPropertySerializer";
return nameOfClass.c_str();
}
const char *GetNameOfClass() const override { return this->GetStaticNameOfClass(); }
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- //! Build an XML version of this property
- TiXmlElement *Serialize() override
+ //! Build an XML version of this property
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
- auto listElement = new TiXmlElement("Values");
+ auto *listElement = doc.NewElement("Values");
if (const PropertyType *prop = dynamic_cast<const PropertyType *>(m_Property.GetPointer()))
{
typename PropertyType::VectorType elements = prop->GetValue();
unsigned int index(0);
for (auto listEntry : elements)
{
std::stringstream indexS;
indexS << index++;
- auto entryElement = new TiXmlElement("Value");
- entryElement->SetAttribute("idx", indexS.str());
- entryElement->SetAttribute("value", boost::lexical_cast<std::string>(listEntry));
- listElement->LinkEndChild(entryElement);
+ auto *entryElement = doc.NewElement("Value");
+ entryElement->SetAttribute("idx", indexS.str().c_str());
+ entryElement->SetAttribute("value", boost::lexical_cast<std::string>(listEntry).c_str());
+ listElement->InsertEndChild(entryElement);
}
return listElement;
}
else
{
return nullptr;
}
}
//! Construct a property from an XML serialization
- BaseProperty::Pointer Deserialize(TiXmlElement *listElement) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *listElement) override
{
typename PropertyType::VectorType datalist;
if (listElement)
{
MITK_DEBUG << "Deserializing " << *listElement;
unsigned int index(0);
std::string valueString;
DATATYPE value;
- for (TiXmlElement *valueElement = listElement->FirstChildElement("Value"); valueElement;
+ for (auto *valueElement = listElement->FirstChildElement("Value"); valueElement;
valueElement = valueElement->NextSiblingElement("Value"))
{
- if (valueElement->QueryValueAttribute("value", &valueString) != TIXML_SUCCESS)
+ valueString = valueElement->Attribute("value");
+ if (valueString.empty())
{
MITK_ERROR << "Missing value attribute in <Values> list";
return nullptr;
}
try
{
value = boost::lexical_cast<DATATYPE>(valueString);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse '" << valueString << "' as number: " << e.what();
return nullptr;
}
datalist.push_back(value);
++index;
}
typename PropertyType::Pointer property = PropertyType::New();
property->SetValue(datalist);
return property.GetPointer();
}
else
{
MITK_ERROR << "Missing <Values> tag.";
}
return nullptr;
}
};
typedef VectorPropertySerializer<double> DoubleVectorPropertySerializer;
typedef VectorPropertySerializer<int> IntVectorPropertySerializer;
} // namespace
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkAnnotationPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkAnnotationPropertySerializer.cpp
index 9368dae2fe..0e1a0b02ac 100644
--- a/Modules/SceneSerializationBase/src/mitkAnnotationPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkAnnotationPropertySerializer.cpp
@@ -1,81 +1,86 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkAnnotationPropertySerializer_h_included
#define mitkAnnotationPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkAnnotationProperty.h"
#include "mitkStringsToNumbers.h"
+#include <array>
+
+#include <tinyxml2.h>
+
namespace mitk
{
class AnnotationPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(AnnotationPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(AnnotationPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument& doc) override
{
if (const AnnotationProperty *prop = dynamic_cast<const AnnotationProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("annotation");
+ auto *element = doc.NewElement("annotation");
element->SetAttribute("label", prop->GetLabel());
Point3D point = prop->GetPosition();
- element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]));
- element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]));
- element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]));
+ element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]).c_str());
+ element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]).c_str());
+ element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
const char *label(element->Attribute("label"));
- std::string p_string[3];
- if (element->QueryStringAttribute("x", &p_string[0]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("y", &p_string[1]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("z", &p_string[2]) != TIXML_SUCCESS)
+ std::array<const char*, 3> p_string = {
+ element->Attribute("x"),
+ element->Attribute("y"),
+ element->Attribute("z")
+ };
+ if (nullptr == p_string[0] || nullptr == p_string[1] || nullptr == p_string[2])
return nullptr;
Point3D p;
try
{
StringsToNumbers<double>(3, p_string, p);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
return AnnotationProperty::New(label, p).GetPointer();
}
protected:
AnnotationPropertySerializer() {}
~AnnotationPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(AnnotationPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkBasePropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkBasePropertySerializer.cpp
index a21cf2889f..de4e87e393 100644
--- a/Modules/SceneSerializationBase/src/mitkBasePropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkBasePropertySerializer.cpp
@@ -1,34 +1,33 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkBasePropertySerializer.h"
mitk::BasePropertySerializer::BasePropertySerializer()
{
}
mitk::BasePropertySerializer::~BasePropertySerializer()
{
}
-TiXmlElement *mitk::BasePropertySerializer::Serialize()
+tinyxml2::XMLElement *mitk::BasePropertySerializer::Serialize(tinyxml2::XMLDocument&)
{
MITK_INFO << this->GetNameOfClass() << " is asked to serialize an object " << (const void *)this->m_Property;
-
return nullptr;
}
-mitk::BaseProperty::Pointer mitk::BasePropertySerializer::Deserialize(TiXmlElement *)
+mitk::BaseProperty::Pointer mitk::BasePropertySerializer::Deserialize(const tinyxml2::XMLElement *)
{
MITK_ERROR << this->GetNameOfClass() << " is asked to deserialize an object but has no implementation. This is bad.";
return nullptr;
}
diff --git a/Modules/SceneSerializationBase/src/mitkBoolLookupTablePropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkBoolLookupTablePropertySerializer.cpp
index 59b9edc80e..eb60909922 100644
--- a/Modules/SceneSerializationBase/src/mitkBoolLookupTablePropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkBoolLookupTablePropertySerializer.cpp
@@ -1,78 +1,78 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkBoolLookupTablePropertySerializer_h_included
#define mitkBoolLookupTablePropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
+#include <tinyxml2.h>
+
namespace mitk
{
class BoolLookupTablePropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(BoolLookupTablePropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(BoolLookupTablePropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override
{
const BoolLookupTableProperty *prop = dynamic_cast<const BoolLookupTableProperty *>(m_Property.GetPointer());
if (prop == nullptr)
return nullptr;
BoolLookupTable lut = prop->GetValue();
// if (lut.IsNull())
// return nullptr; // really?
const BoolLookupTable::LookupTableType &map = lut.GetLookupTable();
- auto element = new TiXmlElement("BoolLookupTable");
+ auto *element = doc.NewElement("BoolLookupTable");
for (auto it = map.begin(); it != map.end(); ++it)
{
- auto tableEntry = new TiXmlElement("LUTValue");
+ auto *tableEntry = doc.NewElement("LUTValue");
tableEntry->SetAttribute("id", it->first);
- if (it->second == true)
- tableEntry->SetAttribute("value", "true");
- else
- tableEntry->SetAttribute("value", "false");
- element->LinkEndChild(tableEntry);
+ tableEntry->SetAttribute("value", it->second);
+ element->InsertEndChild(tableEntry);
}
return element;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
BoolLookupTable lut;
- for (TiXmlElement *child = element->FirstChildElement("LUTValue"); child != nullptr;
+ for (auto *child = element->FirstChildElement("LUTValue"); child != nullptr;
child = child->NextSiblingElement("LUTValue"))
{
int xmlID;
- if (child->QueryIntAttribute("id", &xmlID) == TIXML_WRONG_TYPE)
+ if (child->QueryIntAttribute("id", &xmlID) != tinyxml2::XML_SUCCESS)
return nullptr; // TODO: can we do a better error handling?
BoolLookupTable::IdentifierType id = static_cast<BoolLookupTable::IdentifierType>(xmlID);
BoolLookupTable::ValueType val = std::string(child->Attribute("value")) == std::string("true");
lut.SetTableValue(id, val);
}
return BoolLookupTableProperty::New(lut).GetPointer();
}
protected:
BoolLookupTablePropertySerializer() {}
~BoolLookupTablePropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(BoolLookupTablePropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkBoolPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkBoolPropertySerializer.cpp
index 15da786146..f8e1fc5b32 100644
--- a/Modules/SceneSerializationBase/src/mitkBoolPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkBoolPropertySerializer.cpp
@@ -1,64 +1,58 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkBoolPropertySerializer_h_included
#define mitkBoolPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkProperties.h"
+#include <tinyxml2.h>
namespace mitk
{
class BoolPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(BoolPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(BoolPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const BoolProperty *prop = dynamic_cast<const BoolProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("bool");
- if (prop->GetValue() == true)
- {
- element->SetAttribute("value", "true");
- }
- else
- {
- element->SetAttribute("value", "false");
- }
+ auto element = doc.NewElement("bool");
+ element->SetAttribute("value", prop->GetValue());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
return BoolProperty::New(std::string(element->Attribute("value")) == "true").GetPointer();
}
protected:
BoolPropertySerializer() {}
~BoolPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(BoolPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkClippingPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkClippingPropertySerializer.cpp
index b19fbdb76d..8c9f84f962 100644
--- a/Modules/SceneSerializationBase/src/mitkClippingPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkClippingPropertySerializer.cpp
@@ -1,123 +1,125 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkClippingPropertySerializer_h_included
#define mitkClippingPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkClippingProperty.h"
#include "mitkNumericTypes.h"
#include <mitkLocaleSwitch.h>
#include "mitkStringsToNumbers.h"
+#include <array>
+
+#include <tinyxml2.h>
+
namespace mitk
{
class ClippingPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(ClippingPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(ClippingPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const ClippingProperty *prop = dynamic_cast<const ClippingProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("clipping");
- if (prop->GetClippingEnabled())
- element->SetAttribute("enabled", "true");
- else
- element->SetAttribute("enabled", "false");
- auto originElement = new TiXmlElement("origin");
+ auto *element = doc.NewElement("clipping");
+ element->SetAttribute("enabled", prop->GetClippingEnabled());
+ auto *originElement = doc.NewElement("origin");
const Point3D origin = prop->GetOrigin();
- originElement->SetAttribute("x", boost::lexical_cast<std::string>(origin[0]));
- originElement->SetAttribute("y", boost::lexical_cast<std::string>(origin[1]));
- originElement->SetAttribute("z", boost::lexical_cast<std::string>(origin[2]));
- element->LinkEndChild(originElement);
- auto normalElement = new TiXmlElement("normal");
+ originElement->SetAttribute("x", boost::lexical_cast<std::string>(origin[0]).c_str());
+ originElement->SetAttribute("y", boost::lexical_cast<std::string>(origin[1]).c_str());
+ originElement->SetAttribute("z", boost::lexical_cast<std::string>(origin[2]).c_str());
+ element->InsertEndChild(originElement);
+ auto *normalElement = doc.NewElement("normal");
const Vector3D normal = prop->GetNormal();
- normalElement->SetAttribute("x", boost::lexical_cast<std::string>(normal[0]));
- normalElement->SetAttribute("y", boost::lexical_cast<std::string>(normal[1]));
- normalElement->SetAttribute("z", boost::lexical_cast<std::string>(normal[2]));
- element->LinkEndChild(normalElement);
+ normalElement->SetAttribute("x", boost::lexical_cast<std::string>(normal[0]).c_str());
+ normalElement->SetAttribute("y", boost::lexical_cast<std::string>(normal[1]).c_str());
+ normalElement->SetAttribute("z", boost::lexical_cast<std::string>(normal[2]).c_str());
+ element->InsertEndChild(normalElement);
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
bool enabled = std::string(element->Attribute("enabled")) == "true";
- TiXmlElement *originElement = element->FirstChildElement("origin");
+ auto *originElement = element->FirstChildElement("origin");
if (originElement == nullptr)
return nullptr;
- std::string origin_string[3];
- if (originElement->QueryStringAttribute("x", &origin_string[0]) != TIXML_SUCCESS)
- return nullptr;
- if (originElement->QueryStringAttribute("y", &origin_string[1]) != TIXML_SUCCESS)
- return nullptr;
- if (originElement->QueryStringAttribute("z", &origin_string[2]) != TIXML_SUCCESS)
+ std::array<const char*, 3> origin_string = {
+ originElement->Attribute("x"),
+ originElement->Attribute("y"),
+ originElement->Attribute("z")
+ };
+ if (nullptr == origin_string[0] || nullptr == origin_string[1] || nullptr == origin_string[2])
return nullptr;
Point3D origin;
try
{
StringsToNumbers<ScalarType>(3, origin_string, origin);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
- TiXmlElement *normalElement = element->FirstChildElement("normal");
+ auto *normalElement = element->FirstChildElement("normal");
if (normalElement == nullptr)
return nullptr;
- std::string normal_string[3];
- if (normalElement->QueryStringAttribute("x", &normal_string[0]) != TIXML_SUCCESS)
- return nullptr;
- if (normalElement->QueryStringAttribute("y", &normal_string[1]) != TIXML_SUCCESS)
- return nullptr;
- if (normalElement->QueryStringAttribute("z", &normal_string[2]) != TIXML_SUCCESS)
+ std::array<const char*, 3> normal_string = {
+ normalElement->Attribute("x"),
+ normalElement->Attribute("y"),
+ normalElement->Attribute("z")
+ };
+ if (nullptr == normal_string[0] || nullptr == normal_string[1] || nullptr == normal_string[2])
return nullptr;
Vector3D normal;
try
{
StringsToNumbers<ScalarType>(3, normal_string, normal);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
ClippingProperty::Pointer cp = ClippingProperty::New(origin, normal);
cp->SetClippingEnabled(enabled);
return cp.GetPointer();
}
protected:
ClippingPropertySerializer() {}
~ClippingPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(ClippingPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkColorPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkColorPropertySerializer.cpp
index cda935b87b..ab3bf11493 100644
--- a/Modules/SceneSerializationBase/src/mitkColorPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkColorPropertySerializer.cpp
@@ -1,84 +1,91 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkColorPropertySerializer_h_included
#define mitkColorPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkColorProperty.h"
#include "mitkStringsToNumbers.h"
#include <mitkLocaleSwitch.h>
+#include <array>
+
+#include <tinyxml2.h>
+
namespace mitk
{
class ColorPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(ColorPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(ColorPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const ColorProperty *prop = dynamic_cast<const ColorProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("color");
+ auto *element = doc.NewElement("color");
Color color = prop->GetValue();
- element->SetAttribute("r", boost::lexical_cast<std::string>(color[0]));
- element->SetAttribute("g", boost::lexical_cast<std::string>(color[1]));
- element->SetAttribute("b", boost::lexical_cast<std::string>(color[2]));
+ element->SetAttribute("r", boost::lexical_cast<std::string>(color[0]).c_str());
+ element->SetAttribute("g", boost::lexical_cast<std::string>(color[1]).c_str());
+ element->SetAttribute("b", boost::lexical_cast<std::string>(color[2]).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
- std::string c_string[3];
- if (element->QueryStringAttribute("r", &c_string[0]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("g", &c_string[1]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("b", &c_string[2]) != TIXML_SUCCESS)
+ std::array<const char*, 3> c_string = {
+ element->Attribute("r"),
+ element->Attribute("g"),
+ element->Attribute("b")
+ };
+
+ if (nullptr == c_string[0] || nullptr == c_string[1] || nullptr == c_string[2])
return nullptr;
+
Color c;
try
{
StringsToNumbers<double>(3, c_string, c);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
return ColorProperty::New(c).GetPointer();
}
protected:
ColorPropertySerializer() {}
~ColorPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(ColorPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkDoublePropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkDoublePropertySerializer.cpp
index b5b2255f66..c1622d4c02 100644
--- a/Modules/SceneSerializationBase/src/mitkDoublePropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkDoublePropertySerializer.cpp
@@ -1,83 +1,86 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkDoublePropertySerializer_h_included
#define mitkDoublePropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
#include <mitkLexicalCast.h>
#include <MitkSceneSerializationBaseExports.h>
#include <mitkLocaleSwitch.h>
+#include <tinyxml2.h>
+
namespace mitk
{
class DoublePropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(DoublePropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(DoublePropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override
{
if (const DoubleProperty *prop = dynamic_cast<const DoubleProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("double");
- element->SetAttribute("value", boost::lexical_cast<std::string>(prop->GetValue()));
+ auto *element = doc.NewElement("double");
+ element->SetAttribute("value", boost::lexical_cast<std::string>(prop->GetValue()).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
- std::string d;
- if (element->QueryStringAttribute("value", &d) == TIXML_SUCCESS)
+ const char* d = element->Attribute("value");
+ if (nullptr != d)
{
try
{
return DoubleProperty::New(boost::lexical_cast<double>(d)).GetPointer();
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
}
else
{
return nullptr;
}
}
protected:
DoublePropertySerializer() {}
~DoublePropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(DoublePropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkEnumerationPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkEnumerationPropertySerializer.cpp
index 6ef0107dc6..c5d0ebde3d 100644
--- a/Modules/SceneSerializationBase/src/mitkEnumerationPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkEnumerationPropertySerializer.cpp
@@ -1,34 +1,35 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkEnumerationPropertySerializer.h"
+#include <tinyxml2.h>
namespace mitk
{
- TiXmlElement *EnumerationPropertySerializer::Serialize()
+ tinyxml2::XMLElement *EnumerationPropertySerializer::Serialize(tinyxml2::XMLDocument &doc)
{
if (const auto *prop = dynamic_cast<const EnumerationProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("enum");
- element->SetAttribute("value", prop->GetValueAsString());
+ auto element = doc.NewElement("enum");
+ element->SetAttribute("value", prop->GetValueAsString().c_str());
return element;
}
else
return nullptr;
}
EnumerationPropertySerializer::EnumerationPropertySerializer() {}
EnumerationPropertySerializer::~EnumerationPropertySerializer() {}
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(EnumerationPropertySerializer);
diff --git a/Modules/SceneSerializationBase/src/mitkEnumerationSubclassesSerializer.cpp b/Modules/SceneSerializationBase/src/mitkEnumerationSubclassesSerializer.cpp
index 518f2d1177..700de1d768 100644
--- a/Modules/SceneSerializationBase/src/mitkEnumerationSubclassesSerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkEnumerationSubclassesSerializer.cpp
@@ -1,72 +1,70 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkEnumerationSubclassesSerializer_h_included
#define mitkEnumerationSubclassesSerializer_h_included
#include "mitkEnumerationPropertySerializer.h"
#include "mitkModalityProperty.h"
#include "mitkPlaneOrientationProperty.h"
#include "mitkPointSetShapeProperty.h"
#include "mitkRenderingModeProperty.h"
#include "mitkVtkInterpolationProperty.h"
#include "mitkVtkRepresentationProperty.h"
#include "mitkVtkResliceInterpolationProperty.h"
#include "mitkVtkScalarModeProperty.h"
#include "mitkVtkVolumeRenderingProperty.h"
-#define MITK_REGISTER_ENUM_SUB_SERIALIZER(classname) \
- \
-namespace mitk \
- \
-{ \
- \
-class classname##Serializer \
- : public EnumerationPropertySerializer\
-{public : \
- \
- mitkClassMacro(classname##Serializer, EnumerationPropertySerializer) itkFactorylessNewMacro(Self) \
- itkCloneMacro(Self) \
- \
- virtual BaseProperty::Pointer Deserialize(TiXmlElement * element) override{if (!element) return nullptr; \
- const char *sa(element->Attribute("value")); \
- \
- std::string s(sa ? sa : ""); \
- classname::Pointer property = classname::New(); \
- property->SetValue(s); \
- \
- return property.GetPointer(); \
- } \
- \
-protected: \
- classname##Serializer() {} \
- virtual ~classname##Serializer() {} \
- \
-} \
- ; \
- \
-} \
- \
+#include <tinyxml2.h>
+
+#define MITK_REGISTER_ENUM_SUB_SERIALIZER(classname) \
+ \
+namespace mitk \
+{ \
+ class classname##Serializer : public EnumerationPropertySerializer \
+ { \
+ public: \
+ mitkClassMacro(classname##Serializer, EnumerationPropertySerializer) \
+ itkFactorylessNewMacro(Self) \
+ itkCloneMacro(Self) \
+ \
+ virtual BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override \
+ { \
+ if (nullptr == element) \
+ return nullptr; \
+ \
+ classname::Pointer property = classname::New(); \
+ property->SetValue(element->Attribute("value")); \
+ \
+ return property.GetPointer(); \
+ } \
+ \
+ protected: \
+ classname##Serializer() {} \
+ virtual ~classname##Serializer() {} \
+ }; \
+} \
+ \
MITK_REGISTER_SERIALIZER(classname##Serializer);
MITK_REGISTER_ENUM_SUB_SERIALIZER(PlaneOrientationProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(VtkInterpolationProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(VtkRepresentationProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(VtkResliceInterpolationProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(VtkScalarModeProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(VtkVolumeRenderingProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(ModalityProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(RenderingModeProperty);
MITK_REGISTER_ENUM_SUB_SERIALIZER(PointSetShapeProperty);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkFloatLookupTablePropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkFloatLookupTablePropertySerializer.cpp
index 935b93e661..29e72ea720 100644
--- a/Modules/SceneSerializationBase/src/mitkFloatLookupTablePropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkFloatLookupTablePropertySerializer.cpp
@@ -1,91 +1,93 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkFloatLookupTablePropertySerializer_h_included
#define mitkFloatLookupTablePropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
#include <mitkLexicalCast.h>
#include <mitkLocaleSwitch.h>
+#include <tinyxml2.h>
namespace mitk
{
class FloatLookupTablePropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(FloatLookupTablePropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(FloatLookupTablePropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override
{
const FloatLookupTableProperty *prop = dynamic_cast<const FloatLookupTableProperty *>(m_Property.GetPointer());
if (prop == nullptr)
return nullptr;
LocaleSwitch localeSwitch("C");
FloatLookupTable lut = prop->GetValue();
// if (lut.IsNull())
// return nullptr; // really?
const FloatLookupTable::LookupTableType &map = lut.GetLookupTable();
- auto element = new TiXmlElement("FloatLookupTableTable");
+ auto *element = doc.NewElement("FloatLookupTableTable");
for (auto it = map.begin(); it != map.end(); ++it)
{
- auto tableEntry = new TiXmlElement("LUTValue");
+ auto *tableEntry = doc.NewElement("LUTValue");
tableEntry->SetAttribute("id", it->first);
- tableEntry->SetAttribute("value", boost::lexical_cast<std::string>(it->second));
- element->LinkEndChild(tableEntry);
+ tableEntry->SetAttribute("value", boost::lexical_cast<std::string>(it->second).c_str());
+ element->InsertEndChild(tableEntry);
}
return element;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
FloatLookupTable lut;
- for (TiXmlElement *child = element->FirstChildElement("LUTValue"); child != nullptr;
+ for (auto *child = element->FirstChildElement("LUTValue"); child != nullptr;
child = child->NextSiblingElement("LUTValue"))
{
int tempID;
- if (child->QueryIntAttribute("id", &tempID) != TIXML_SUCCESS)
+ if (child->QueryIntAttribute("id", &tempID) != tinyxml2::XML_SUCCESS)
return nullptr;
FloatLookupTable::IdentifierType id = static_cast<FloatLookupTable::IdentifierType>(tempID);
- std::string value_string;
- if (child->QueryStringAttribute("value", &value_string) != TIXML_SUCCESS)
+ const char* value_string = child->Attribute("value");
+ if (nullptr == value_string)
return nullptr;
try
{
lut.SetTableValue(id, boost::lexical_cast<float>(value_string));
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
}
return FloatLookupTableProperty::New(lut).GetPointer();
}
protected:
FloatLookupTablePropertySerializer() {}
~FloatLookupTablePropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(FloatLookupTablePropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkFloatPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkFloatPropertySerializer.cpp
index b1aab7b373..3adf5caa0b 100644
--- a/Modules/SceneSerializationBase/src/mitkFloatPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkFloatPropertySerializer.cpp
@@ -1,80 +1,82 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkFloatPropertySerializer_h_included
#define mitkFloatPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
#include "mitkStringsToNumbers.h"
#include <mitkLocaleSwitch.h>
+#include <tinyxml2.h>
namespace mitk
{
class FloatPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(FloatPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(FloatPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const FloatProperty *prop = dynamic_cast<const FloatProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("float");
- element->SetAttribute("value", boost::lexical_cast<std::string>(prop->GetValue()));
+ auto *element = doc.NewElement("float");
+ element->SetAttribute("value", boost::lexical_cast<std::string>(prop->GetValue()).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
- std::string f_string;
- if (element->QueryStringAttribute("value", &f_string) == TIXML_SUCCESS)
+ const char* f_string = element->Attribute("value");
+ if (nullptr != f_string)
{
try
{
return FloatProperty::New(boost::lexical_cast<float>(f_string)).GetPointer();
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
}
else
{
return nullptr;
}
}
protected:
FloatPropertySerializer() {}
~FloatPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(FloatPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkGroupTagPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkGroupTagPropertySerializer.cpp
index bda674c3dc..b9bb5f222d 100644
--- a/Modules/SceneSerializationBase/src/mitkGroupTagPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkGroupTagPropertySerializer.cpp
@@ -1,56 +1,55 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkGroupTagPropertySerializer_h_included
#define mitkGroupTagPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkGroupTagProperty.h"
+#include <tinyxml2.h>
namespace mitk
{
class GroupTagPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(GroupTagPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(GroupTagPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (dynamic_cast<const GroupTagProperty *>(m_Property.GetPointer()) != nullptr)
{
- auto element = new TiXmlElement("GroupTag");
+ auto *element = doc.NewElement("GroupTag");
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *) override
{
- // if (!element)
- // return nullptr;
return GroupTagProperty::New().GetPointer();
}
protected:
GroupTagPropertySerializer() {}
~GroupTagPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(GroupTagPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkIntLookupTablePropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkIntLookupTablePropertySerializer.cpp
index 3b7737b589..c2d2272ea9 100644
--- a/Modules/SceneSerializationBase/src/mitkIntLookupTablePropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkIntLookupTablePropertySerializer.cpp
@@ -1,77 +1,78 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkIntLookupTablePropertySerializer_h_included
#define mitkIntLookupTablePropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkProperties.h"
+#include <tinyxml2.h>
namespace mitk
{
class IntLookupTablePropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(IntLookupTablePropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(IntLookupTablePropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override
{
const IntLookupTableProperty *prop = dynamic_cast<const IntLookupTableProperty *>(m_Property.GetPointer());
if (prop == nullptr)
return nullptr;
IntLookupTable lut = prop->GetValue();
// if (lut.IsNull())
// return nullptr; // really?
const IntLookupTable::LookupTableType &map = lut.GetLookupTable();
- auto element = new TiXmlElement("IntLookupTableTable");
+ auto element = doc.NewElement("IntLookupTableTable");
for (auto it = map.begin(); it != map.end(); ++it)
{
- auto tableEntry = new TiXmlElement("LUTValue");
+ auto tableEntry = doc.NewElement("LUTValue");
tableEntry->SetAttribute("id", it->first);
tableEntry->SetAttribute("value", it->second);
- element->LinkEndChild(tableEntry);
+ element->InsertEndChild(tableEntry);
}
return element;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
IntLookupTable lut;
- for (TiXmlElement *child = element->FirstChildElement("LUTValue"); child != nullptr;
+ for (auto *child = element->FirstChildElement("LUTValue"); child != nullptr;
child = child->NextSiblingElement("LUTValue"))
{
int temp;
- if (child->QueryIntAttribute("id", &temp) == TIXML_WRONG_TYPE)
+ if (child->QueryIntAttribute("id", &temp) != tinyxml2::XML_SUCCESS)
return nullptr; // TODO: can we do a better error handling?
IntLookupTable::IdentifierType id = static_cast<IntLookupTable::IdentifierType>(temp);
- if (child->QueryIntAttribute("value", &temp) == TIXML_WRONG_TYPE)
+ if (child->QueryIntAttribute("value", &temp) != tinyxml2::XML_SUCCESS)
return nullptr; // TODO: can we do a better error handling?
IntLookupTable::ValueType val = static_cast<IntLookupTable::ValueType>(temp);
lut.SetTableValue(id, val);
}
return IntLookupTableProperty::New(lut).GetPointer();
}
protected:
IntLookupTablePropertySerializer() {}
~IntLookupTablePropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(IntLookupTablePropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkIntPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkIntPropertySerializer.cpp
index 5792766f4b..a106b42257 100644
--- a/Modules/SceneSerializationBase/src/mitkIntPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkIntPropertySerializer.cpp
@@ -1,66 +1,67 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkIntPropertySerializer_h_included
#define mitkIntPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkProperties.h"
+#include <tinyxml2.h>
namespace mitk
{
class IntPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(IntPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(IntPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override
{
if (const IntProperty *prop = dynamic_cast<const IntProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("int");
+ auto *element = doc.NewElement("int");
element->SetAttribute("value", prop->GetValue());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
int integer;
- if (element->QueryIntAttribute("value", &integer) == TIXML_SUCCESS)
+ if (element->QueryIntAttribute("value", &integer) == tinyxml2::XML_SUCCESS)
{
return IntProperty::New(integer).GetPointer();
}
else
{
return nullptr;
}
}
protected:
IntPropertySerializer() {}
~IntPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(IntPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkLevelWindowPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkLevelWindowPropertySerializer.cpp
index 82d9274353..aef921409c 100644
--- a/Modules/SceneSerializationBase/src/mitkLevelWindowPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkLevelWindowPropertySerializer.cpp
@@ -1,135 +1,124 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkLevelWindowPropertySerializer_h_included
#define mitkLevelWindowPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkLevelWindowProperty.h"
#include <mitkLexicalCast.h>
#include <mitkLocaleSwitch.h>
+#include <tinyxml2.h>
namespace mitk
{
class LevelWindowPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(LevelWindowPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(LevelWindowPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override
{
if (const LevelWindowProperty *prop = dynamic_cast<const LevelWindowProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("LevelWindow");
+ auto *element = doc.NewElement("LevelWindow");
LevelWindow lw = prop->GetLevelWindow();
- std::string boolString("false");
- if (lw.IsFixed() == true)
- boolString = "true";
- element->SetAttribute("fixed", boolString.c_str());
-
- std::string boolStringFltImage("false");
- if (lw.IsFloatingValues() == true)
- boolStringFltImage = "true";
- element->SetAttribute("isFloatingImage", boolStringFltImage.c_str());
-
- auto child = new TiXmlElement("CurrentSettings");
- element->LinkEndChild(child);
- child->SetAttribute("level", boost::lexical_cast<std::string>(lw.GetLevel()));
- child->SetAttribute("window", boost::lexical_cast<std::string>(lw.GetWindow()));
-
- child = new TiXmlElement("DefaultSettings");
- element->LinkEndChild(child);
- child->SetAttribute("level", boost::lexical_cast<std::string>(lw.GetDefaultLevel()));
- child->SetAttribute("window", boost::lexical_cast<std::string>(lw.GetDefaultWindow()));
-
- child = new TiXmlElement("CurrentRange");
- element->LinkEndChild(child);
- child->SetAttribute("min", boost::lexical_cast<std::string>(lw.GetRangeMin()));
- child->SetAttribute("max", boost::lexical_cast<std::string>(lw.GetRangeMax()));
+ element->SetAttribute("fixed", lw.IsFixed());
+ element->SetAttribute("isFloatingImage", lw.IsFloatingValues());
+
+ auto *child = doc.NewElement("CurrentSettings");
+ element->InsertEndChild(child);
+ child->SetAttribute("level", boost::lexical_cast<std::string>(lw.GetLevel()).c_str());
+ child->SetAttribute("window", boost::lexical_cast<std::string>(lw.GetWindow()).c_str());
+
+ child = doc.NewElement("DefaultSettings");
+ element->InsertEndChild(child);
+ child->SetAttribute("level", boost::lexical_cast<std::string>(lw.GetDefaultLevel()).c_str());
+ child->SetAttribute("window", boost::lexical_cast<std::string>(lw.GetDefaultWindow()).c_str());
+
+ child = doc.NewElement("CurrentRange");
+ element->InsertEndChild(child);
+ child->SetAttribute("min", boost::lexical_cast<std::string>(lw.GetRangeMin()).c_str());
+ child->SetAttribute("max", boost::lexical_cast<std::string>(lw.GetRangeMax()).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
bool isFixed(false);
if (element->Attribute("fixed"))
isFixed = std::string(element->Attribute("fixed")) == "true";
bool isFloatingImage(false);
if (element->Attribute("isFloatingImage"))
isFloatingImage = std::string(element->Attribute("isFloatingImage")) == "true";
- std::string level_string;
- std::string window_string;
- TiXmlElement *child = element->FirstChildElement("CurrentSettings");
- if (child->QueryStringAttribute("level", &level_string) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("window", &window_string) != TIXML_SUCCESS)
+ auto *child = element->FirstChildElement("CurrentSettings");
+ const char* level_string = child->Attribute("level");
+ const char* window_string = child->Attribute("window");
+ if (nullptr == level_string || nullptr == window_string)
return nullptr;
- std::string defaultLevel_string;
- std::string defaultWindow_string;
child = element->FirstChildElement("DefaultSettings");
- if (child->QueryStringAttribute("level", &defaultLevel_string) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("window", &defaultWindow_string) != TIXML_SUCCESS)
+ const char* defaultLevel_string = child->Attribute("level");
+ const char* defaultWindow_string = child->Attribute("window");
+ if (nullptr == defaultLevel_string || nullptr == defaultWindow_string)
return nullptr;
- std::string minRange_string;
- std::string maxRange_string;
child = element->FirstChildElement("CurrentRange");
- if (child->QueryStringAttribute("min", &minRange_string) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("max", &maxRange_string) != TIXML_SUCCESS)
+ const char* minRange_string = child->Attribute("min");
+ const char* maxRange_string = child->Attribute("max");
+ if (nullptr == minRange_string || nullptr == maxRange_string)
return nullptr;
LevelWindow lw;
try
{
lw.SetRangeMinMax(boost::lexical_cast<double>(minRange_string), boost::lexical_cast<double>(maxRange_string));
lw.SetDefaultLevelWindow(boost::lexical_cast<double>(defaultLevel_string),
boost::lexical_cast<double>(defaultWindow_string));
lw.SetLevelWindow(boost::lexical_cast<double>(level_string), boost::lexical_cast<double>(window_string));
lw.SetFixed(isFixed);
lw.SetFloatingValues(isFloatingImage);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
return LevelWindowProperty::New(lw).GetPointer();
}
protected:
LevelWindowPropertySerializer() {}
~LevelWindowPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(LevelWindowPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkLookupTablePropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkLookupTablePropertySerializer.cpp
index e22e63ff9a..3f82689963 100644
--- a/Modules/SceneSerializationBase/src/mitkLookupTablePropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkLookupTablePropertySerializer.cpp
@@ -1,213 +1,227 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkLookupTablePropertySerializer.h"
#include "mitkStringsToNumbers.h"
#include <mitkLocaleSwitch.h>
#include <mitkLookupTableProperty.h>
-TiXmlElement *mitk::LookupTablePropertySerializer::Serialize()
+#include <array>
+
+#include <tinyxml2.h>
+
+tinyxml2::XMLElement *mitk::LookupTablePropertySerializer::Serialize(tinyxml2::XMLDocument& doc)
{
if (const auto *prop = dynamic_cast<const LookupTableProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
LookupTable::Pointer mitkLut = const_cast<LookupTableProperty *>(prop)->GetLookupTable();
if (mitkLut.IsNull())
return nullptr; // really?
vtkLookupTable *lut = mitkLut->GetVtkLookupTable();
if (!lut)
return nullptr;
- auto element = new TiXmlElement("LookupTable");
+ auto *element = doc.NewElement("LookupTable");
double *range;
double *rgba;
- element->SetAttribute("NumberOfColors", lut->GetNumberOfTableValues());
+ element->SetAttribute("NumberOfColors", static_cast<int>(lut->GetNumberOfTableValues()));
element->SetAttribute("Scale", lut->GetScale());
element->SetAttribute("Ramp", lut->GetRamp());
range = lut->GetHueRange();
- auto child = new TiXmlElement("HueRange");
- element->LinkEndChild(child);
- child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]));
- child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]));
+ auto *child = doc.NewElement("HueRange");
+ element->InsertEndChild(child);
+ child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]).c_str());
+ child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]).c_str());
range = lut->GetValueRange();
- child = new TiXmlElement("ValueRange");
- element->LinkEndChild(child);
- child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]));
- child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]));
+ child = doc.NewElement("ValueRange");
+ element->InsertEndChild(child);
+ child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]).c_str());
+ child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]).c_str());
range = lut->GetSaturationRange();
- child = new TiXmlElement("SaturationRange");
- element->LinkEndChild(child);
- child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]));
- child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]));
+ child = doc.NewElement("SaturationRange");
+ element->InsertEndChild(child);
+ child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]).c_str());
+ child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]).c_str());
range = lut->GetAlphaRange();
- child = new TiXmlElement("AlphaRange");
- element->LinkEndChild(child);
- child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]));
- child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]));
+ child = doc.NewElement("AlphaRange");
+ element->InsertEndChild(child);
+ child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]).c_str());
+ child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]).c_str());
range = lut->GetTableRange();
- child = new TiXmlElement("TableRange");
- element->LinkEndChild(child);
- child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]));
- child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]));
+ child = doc.NewElement("TableRange");
+ element->InsertEndChild(child);
+ child->SetAttribute("min", boost::lexical_cast<std::string>(range[0]).c_str());
+ child->SetAttribute("max", boost::lexical_cast<std::string>(range[1]).c_str());
- child = new TiXmlElement("Table");
- element->LinkEndChild(child);
+ child = doc.NewElement("Table");
+ element->InsertEndChild(child);
for (int index = 0; index < lut->GetNumberOfTableValues(); ++index)
{
- auto grandChild = new TiXmlElement("RgbaColor");
+ auto grandChild = doc.NewElement("RgbaColor");
rgba = lut->GetTableValue(index);
- grandChild->SetAttribute("R", boost::lexical_cast<std::string>(rgba[0]));
- grandChild->SetAttribute("G", boost::lexical_cast<std::string>(rgba[1]));
- grandChild->SetAttribute("B", boost::lexical_cast<std::string>(rgba[2]));
- grandChild->SetAttribute("A", boost::lexical_cast<std::string>(rgba[3]));
- child->LinkEndChild(grandChild);
+ grandChild->SetAttribute("R", boost::lexical_cast<std::string>(rgba[0]).c_str());
+ grandChild->SetAttribute("G", boost::lexical_cast<std::string>(rgba[1]).c_str());
+ grandChild->SetAttribute("B", boost::lexical_cast<std::string>(rgba[2]).c_str());
+ grandChild->SetAttribute("A", boost::lexical_cast<std::string>(rgba[3]).c_str());
+ child->InsertEndChild(grandChild);
}
return element;
}
else
return nullptr;
}
-mitk::BaseProperty::Pointer mitk::LookupTablePropertySerializer::Deserialize(TiXmlElement *element)
+mitk::BaseProperty::Pointer mitk::LookupTablePropertySerializer::Deserialize(const tinyxml2::XMLElement *element)
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
double range[2];
double rgba[4];
- std::string double_strings[4];
+ std::array<const char*, 4> double_strings;
vtkSmartPointer<vtkLookupTable> lut = vtkSmartPointer<vtkLookupTable>::New();
int numberOfColors;
int scale;
int ramp; // hope the int values don't change betw. vtk versions...
- if (element->QueryIntAttribute("NumberOfColors", &numberOfColors) == TIXML_SUCCESS)
+ if (element->QueryIntAttribute("NumberOfColors", &numberOfColors) == tinyxml2::XML_SUCCESS)
{
lut->SetNumberOfTableValues(numberOfColors);
}
else
return nullptr;
- if (element->QueryIntAttribute("Scale", &scale) == TIXML_SUCCESS)
+ if (element->QueryIntAttribute("Scale", &scale) == tinyxml2::XML_SUCCESS)
{
lut->SetScale(scale);
}
else
return nullptr;
- if (element->QueryIntAttribute("Ramp", &ramp) == TIXML_SUCCESS)
+ if (element->QueryIntAttribute("Ramp", &ramp) == tinyxml2::XML_SUCCESS)
{
lut->SetRamp(ramp);
}
else
return nullptr;
try
{
- TiXmlElement *child = element->FirstChildElement("HueRange");
+ auto *child = element->FirstChildElement("HueRange");
if (child)
{
- if (child->QueryStringAttribute("min", &double_strings[0]) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("max", &double_strings[1]) != TIXML_SUCCESS)
+ double_strings[0] = child->Attribute("min");
+ double_strings[1] = child->Attribute("max");
+
+ if (nullptr == double_strings[0] || nullptr == double_strings[1])
return nullptr;
+
StringsToNumbers<double>(2, double_strings, range);
lut->SetHueRange(range);
}
child = element->FirstChildElement("ValueRange");
if (child)
{
- if (child->QueryStringAttribute("min", &double_strings[0]) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("max", &double_strings[1]) != TIXML_SUCCESS)
+ double_strings[0] = child->Attribute("min");
+ double_strings[1] = child->Attribute("max");
+
+ if (nullptr == double_strings[0] || nullptr == double_strings[1])
return nullptr;
+
StringsToNumbers<double>(2, double_strings, range);
lut->SetValueRange(range);
}
child = element->FirstChildElement("SaturationRange");
if (child)
{
- if (child->QueryStringAttribute("min", &double_strings[0]) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("max", &double_strings[1]) != TIXML_SUCCESS)
+ double_strings[0] = child->Attribute("min");
+ double_strings[1] = child->Attribute("max");
+
+ if (nullptr == double_strings[0] || nullptr == double_strings[1])
return nullptr;
+
StringsToNumbers<double>(2, double_strings, range);
lut->SetSaturationRange(range);
}
child = element->FirstChildElement("AlphaRange");
if (child)
{
- if (child->QueryStringAttribute("min", &double_strings[0]) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("max", &double_strings[1]) != TIXML_SUCCESS)
+ double_strings[0] = child->Attribute("min");
+ double_strings[1] = child->Attribute("max");
+
+ if (nullptr == double_strings[0] || nullptr == double_strings[1])
return nullptr;
+
StringsToNumbers<double>(2, double_strings, range);
lut->SetAlphaRange(range);
}
child = element->FirstChildElement("TableRange");
if (child)
{
- if (child->QueryStringAttribute("min", &double_strings[0]) != TIXML_SUCCESS)
- return nullptr;
- if (child->QueryStringAttribute("max", &double_strings[1]) != TIXML_SUCCESS)
+ double_strings[0] = child->Attribute("min");
+ double_strings[1] = child->Attribute("max");
+
+ if (nullptr == double_strings[0] || nullptr == double_strings[1])
return nullptr;
+
StringsToNumbers<double>(2, double_strings, range);
lut->SetTableRange(range);
}
child = element->FirstChildElement("Table");
if (child)
{
unsigned int index(0);
- for (TiXmlElement *grandChild = child->FirstChildElement("RgbaColor"); grandChild;
+ for (auto *grandChild = child->FirstChildElement("RgbaColor"); grandChild;
grandChild = grandChild->NextSiblingElement("RgbaColor"))
{
- if (grandChild->QueryStringAttribute("R", &double_strings[0]) != TIXML_SUCCESS)
- return nullptr;
- if (grandChild->QueryStringAttribute("G", &double_strings[1]) != TIXML_SUCCESS)
- return nullptr;
- if (grandChild->QueryStringAttribute("B", &double_strings[2]) != TIXML_SUCCESS)
- return nullptr;
- if (grandChild->QueryStringAttribute("A", &double_strings[3]) != TIXML_SUCCESS)
+ double_strings[0] = grandChild->Attribute("R");
+ double_strings[1] = grandChild->Attribute("G");
+ double_strings[2] = grandChild->Attribute("B");
+ double_strings[3] = grandChild->Attribute("A");
+
+ if (nullptr == double_strings[0] || nullptr == double_strings[1] || nullptr == double_strings[2] || nullptr == double_strings[3])
return nullptr;
+
StringsToNumbers<double>(4, double_strings, rgba);
lut->SetTableValue(index, rgba);
++index;
}
}
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
LookupTable::Pointer mitkLut = LookupTable::New();
mitkLut->SetVtkLookupTable(lut);
return LookupTableProperty::New(mitkLut).GetPointer();
}
diff --git a/Modules/SceneSerializationBase/src/mitkPoint3dPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkPoint3dPropertySerializer.cpp
index e69d344d03..4d29ccf3cd 100644
--- a/Modules/SceneSerializationBase/src/mitkPoint3dPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkPoint3dPropertySerializer.cpp
@@ -1,83 +1,88 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkPoint3dPropertySerializer_h_included
#define mitkPoint3dPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
#include "mitkStringsToNumbers.h"
#include <mitkLocaleSwitch.h>
+#include <array>
+
+#include <tinyxml2.h>
+
namespace mitk
{
class Point3dPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(Point3dPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(Point3dPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const Point3dProperty *prop = dynamic_cast<const Point3dProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("point");
+ auto *element = doc.NewElement("point");
Point3D point = prop->GetValue();
- element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]));
- element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]));
- element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]));
+ element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]).c_str());
+ element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]).c_str());
+ element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
- std::string v_str[3];
- if (element->QueryStringAttribute("x", &v_str[0]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("y", &v_str[1]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("z", &v_str[2]) != TIXML_SUCCESS)
+ std::array<const char*, 3> v_str = {
+ element->Attribute("x"),
+ element->Attribute("y"),
+ element->Attribute("z")
+ };
+ if (nullptr == v_str[0] || nullptr == v_str[1] || nullptr == v_str[2])
return nullptr;
Point3D v;
try
{
StringsToNumbers<double>(3, v_str, v);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
return Point3dProperty::New(v).GetPointer();
}
protected:
Point3dPropertySerializer() {}
~Point3dPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(Point3dPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkPoint3iPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkPoint3iPropertySerializer.cpp
index fc5fb86c6e..8294cf29f7 100644
--- a/Modules/SceneSerializationBase/src/mitkPoint3iPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkPoint3iPropertySerializer.cpp
@@ -1,64 +1,66 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkPoint3iPropertySerializer_h_included
#define mitkPoint3iPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
+#include <tinyxml2.h>
namespace mitk
{
class Point3iPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(Point3iPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(Point3iPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const Point3iProperty *prop = dynamic_cast<const Point3iProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("point");
+ auto *element = doc.NewElement("point");
Point3I point = prop->GetValue();
element->SetAttribute("x", point[0]);
element->SetAttribute("y", point[1]);
element->SetAttribute("z", point[2]);
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
Point3I v;
- if (element->QueryIntAttribute("x", &v[0]) != TIXML_SUCCESS)
+ if (element->QueryIntAttribute("x", &v[0]) != tinyxml2::XML_SUCCESS)
return nullptr;
- if (element->QueryIntAttribute("y", &v[1]) != TIXML_SUCCESS)
+ if (element->QueryIntAttribute("y", &v[1]) != tinyxml2::XML_SUCCESS)
return nullptr;
- if (element->QueryIntAttribute("z", &v[2]) != TIXML_SUCCESS)
+ if (element->QueryIntAttribute("z", &v[2]) != tinyxml2::XML_SUCCESS)
return nullptr;
return Point3iProperty::New(v).GetPointer();
}
protected:
Point3iPropertySerializer() {}
~Point3iPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(Point3iPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkPoint4dPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkPoint4dPropertySerializer.cpp
index 68b59144ba..d35180121e 100644
--- a/Modules/SceneSerializationBase/src/mitkPoint4dPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkPoint4dPropertySerializer.cpp
@@ -1,86 +1,88 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkPoint4dPropertySerializer_h_included
#define mitkPoint4dPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
#include "mitkStringsToNumbers.h"
#include <mitkLocaleSwitch.h>
+#include <array>
+#include <tinyxml2.h>
namespace mitk
{
class Point4dPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(Point4dPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(Point4dPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const Point4dProperty *prop = dynamic_cast<const Point4dProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("point");
+ auto *element = doc.NewElement("point");
Point4D point = prop->GetValue();
- element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]));
- element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]));
- element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]));
- element->SetAttribute("t", boost::lexical_cast<std::string>(point[3]));
+ element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]).c_str());
+ element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]).c_str());
+ element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]).c_str());
+ element->SetAttribute("t", boost::lexical_cast<std::string>(point[3]).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement* element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
- std::string v_str[4];
- if (element->QueryStringAttribute("x", &v_str[0]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("y", &v_str[1]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("z", &v_str[2]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("t", &v_str[3]) != TIXML_SUCCESS)
+ std::array<const char*, 4> v_str = {
+ element->Attribute("x"),
+ element->Attribute("y"),
+ element->Attribute("z"),
+ element->Attribute("t")
+ };
+ if(nullptr == v_str[0] || nullptr == v_str[1] || nullptr == v_str[2] || nullptr == v_str[2])
return nullptr;
Point4D v;
try
{
StringsToNumbers<double>(4, v_str, v);
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
return Point4dProperty::New(v).GetPointer();
}
protected:
Point4dPropertySerializer() {}
~Point4dPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(Point4dPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkPropertyListSerializer.cpp b/Modules/SceneSerializationBase/src/mitkPropertyListSerializer.cpp
index e384cee2ed..171c406681 100644
--- a/Modules/SceneSerializationBase/src/mitkPropertyListSerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkPropertyListSerializer.cpp
@@ -1,171 +1,168 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPropertyListSerializer.h"
#include "mitkBasePropertySerializer.h"
-
-#include <tinyxml.h>
-
#include "mitkStandardFileLocations.h"
#include <itksys/SystemTools.hxx>
+#include <tinyxml2.h>
mitk::PropertyListSerializer::PropertyListSerializer() : m_FilenameHint("unnamed"), m_WorkingDirectory("")
{
}
mitk::PropertyListSerializer::~PropertyListSerializer()
{
}
std::string mitk::PropertyListSerializer::Serialize()
{
m_FailedProperties = PropertyList::New();
if (m_PropertyList.IsNull() || m_PropertyList->IsEmpty())
{
MITK_ERROR << "Not serializing nullptr or empty PropertyList";
return "";
}
// tmpname
static unsigned long count = 1;
unsigned long n = count++;
std::ostringstream name;
for (int i = 0; i < 6; ++i)
{
name << char('a' + (n % 26));
n /= 26;
}
std::string filename;
filename.append(name.str());
std::string fullname(m_WorkingDirectory);
fullname += "/";
fullname += filename;
fullname = itksys::SystemTools::ConvertToOutputPath(fullname.c_str());
// Trim quotes
std::string::size_type length = fullname.length();
if (length >= 2 && fullname[0] == '"' && fullname[length - 1] == '"')
fullname = fullname.substr(1, length - 2);
- TiXmlDocument document;
- auto decl = new TiXmlDeclaration("1.0", "", ""); // TODO what to write here? encoding? etc....
- document.LinkEndChild(decl);
+ tinyxml2::XMLDocument document;
+ document.InsertEndChild(document.NewDeclaration());
- auto version = new TiXmlElement("Version");
+ auto *version = document.NewElement("Version");
version->SetAttribute("Writer", __FILE__);
version->SetAttribute("Revision", "$Revision: 17055 $");
version->SetAttribute("FileVersion", 1);
- document.LinkEndChild(version);
+ document.InsertEndChild(version);
// add XML contents
const PropertyList::PropertyMap *propmap = m_PropertyList->GetMap();
for (auto iter = propmap->begin(); iter != propmap->end(); ++iter)
{
std::string key = iter->first;
const BaseProperty *property = iter->second;
- TiXmlElement *element = SerializeOneProperty(key, property);
+ auto *element = SerializeOneProperty(document, key, property);
if (element)
{
- document.LinkEndChild(element);
+ document.InsertEndChild(element);
// TODO test serializer for error
}
else
{
m_FailedProperties->ReplaceProperty(key, const_cast<BaseProperty *>(property));
}
}
// save XML file
- if (!document.SaveFile(fullname))
+ if (tinyxml2::XML_SUCCESS != document.SaveFile(fullname.c_str()))
{
- MITK_ERROR << "Could not write PropertyList to " << fullname << "\nTinyXML reports '" << document.ErrorDesc()
+ MITK_ERROR << "Could not write PropertyList to " << fullname << "\nTinyXML reports '" << document.ErrorStr()
<< "'";
return "";
}
return filename;
}
-TiXmlElement *mitk::PropertyListSerializer::SerializeOneProperty(const std::string &key, const BaseProperty *property)
+tinyxml2::XMLElement *mitk::PropertyListSerializer::SerializeOneProperty(tinyxml2::XMLDocument &doc, const std::string &key, const BaseProperty *property)
{
- auto keyelement = new TiXmlElement("property");
- keyelement->SetAttribute("key", key);
+ auto *keyelement = doc.NewElement("property");
+ keyelement->SetAttribute("key", key.c_str());
keyelement->SetAttribute("type", property->GetNameOfClass());
// construct name of serializer class
std::string serializername(property->GetNameOfClass());
serializername += "Serializer";
std::list<itk::LightObject::Pointer> allSerializers =
itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str());
if (allSerializers.size() < 1)
{
MITK_ERROR << "No serializer found for " << property->GetNameOfClass() << ". Skipping object";
}
if (allSerializers.size() > 1)
{
MITK_WARN << "Multiple serializers found for " << property->GetNameOfClass() << "Using arbitrarily the first one.";
}
for (auto iter = allSerializers.begin(); iter != allSerializers.end(); ++iter)
{
if (auto *serializer = dynamic_cast<BasePropertySerializer *>(iter->GetPointer()))
{
serializer->SetProperty(property);
try
{
- TiXmlElement *valueelement = serializer->Serialize();
+ auto *valueelement = serializer->Serialize(doc);
if (valueelement)
{
- keyelement->LinkEndChild(valueelement);
+ keyelement->InsertEndChild(valueelement);
}
}
catch (std::exception &e)
{
MITK_ERROR << "Serializer " << serializer->GetNameOfClass() << " failed: " << e.what();
// \TODO: log only if all potential serializers fail?
}
break;
}
else
{
MITK_ERROR << "Found a serializer called '" << (*iter)->GetNameOfClass()
<< "' that does not implement the BasePropertySerializer interface.";
continue;
}
}
if (keyelement->NoChildren())
{
m_FailedProperties->ReplaceProperty(key, const_cast<BaseProperty *>(property));
return nullptr;
}
else
{
return keyelement;
}
}
mitk::PropertyList *mitk::PropertyListSerializer::GetFailedProperties()
{
if (m_FailedProperties.IsNotNull() && !m_FailedProperties->IsEmpty())
{
return m_FailedProperties;
}
else
{
return nullptr;
}
}
diff --git a/Modules/SceneSerializationBase/src/mitkStringLookupTablePropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkStringLookupTablePropertySerializer.cpp
index d8b293b170..c2b8adb17d 100644
--- a/Modules/SceneSerializationBase/src/mitkStringLookupTablePropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkStringLookupTablePropertySerializer.cpp
@@ -1,78 +1,79 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkStringLookupTablePropertySerializer_h_included
#define mitkStringLookupTablePropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkProperties.h"
+#include <tinyxml2.h>
namespace mitk
{
class StringLookupTablePropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(StringLookupTablePropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(StringLookupTablePropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
const StringLookupTableProperty *prop = dynamic_cast<const StringLookupTableProperty *>(m_Property.GetPointer());
if (prop == nullptr)
return nullptr;
StringLookupTable lut = prop->GetValue();
// if (lut.IsNull())
// return nullptr; // really?
const StringLookupTable::LookupTableType &map = lut.GetLookupTable();
- auto element = new TiXmlElement("StringLookupTable");
+ auto *element = doc.NewElement("StringLookupTable");
for (auto it = map.begin(); it != map.end(); ++it)
{
- auto tableEntry = new TiXmlElement("LUTValue");
+ auto *tableEntry = doc.NewElement("LUTValue");
tableEntry->SetAttribute("id", it->first);
- tableEntry->SetAttribute("value", it->second);
- element->LinkEndChild(tableEntry);
+ tableEntry->SetAttribute("value", it->second.c_str());
+ element->InsertEndChild(tableEntry);
}
return element;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
StringLookupTable lut;
- for (TiXmlElement *child = element->FirstChildElement("LUTValue"); child != nullptr;
+ for (auto *child = element->FirstChildElement("LUTValue"); child != nullptr;
child = child->NextSiblingElement("LUTValue"))
{
int temp;
- if (child->QueryIntAttribute("id", &temp) == TIXML_WRONG_TYPE)
+ if (child->QueryIntAttribute("id", &temp) != tinyxml2::XML_SUCCESS)
return nullptr; // TODO: can we do a better error handling?
StringLookupTable::IdentifierType id = static_cast<StringLookupTable::IdentifierType>(temp);
if (child->Attribute("value") == nullptr)
return nullptr; // TODO: can we do a better error handling?
StringLookupTable::ValueType val = child->Attribute("value");
lut.SetTableValue(id, val);
}
return StringLookupTableProperty::New(lut).GetPointer();
}
protected:
StringLookupTablePropertySerializer() {}
~StringLookupTablePropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(StringLookupTablePropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkStringPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkStringPropertySerializer.cpp
index 9144709397..28e053b8cc 100644
--- a/Modules/SceneSerializationBase/src/mitkStringPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkStringPropertySerializer.cpp
@@ -1,58 +1,59 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkStringPropertySerializer_h_included
#define mitkStringPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkStringProperty.h"
+#include <tinyxml2.h>
namespace mitk
{
class StringPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(StringPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(StringPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement *Serialize(tinyxml2::XMLDocument &doc) override
{
if (const StringProperty *prop = dynamic_cast<const StringProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("string");
+ auto *element = doc.NewElement("string");
element->SetAttribute("value", prop->GetValue());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
const char *s(element->Attribute("value"));
return StringProperty::New(std::string(s ? s : "")).GetPointer();
}
protected:
StringPropertySerializer() {}
~StringPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(StringPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkTemporoSpatialStringPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkTemporoSpatialStringPropertySerializer.cpp
index 2d25efcb22..25e2ae1693 100644
--- a/Modules/SceneSerializationBase/src/mitkTemporoSpatialStringPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkTemporoSpatialStringPropertySerializer.cpp
@@ -1,62 +1,63 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkTemporoSpatialStringPropertySerializer_h_included
#define mitkTemporoSpatialStringPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkTemporoSpatialStringProperty.h"
+#include <tinyxml2.h>
namespace mitk
{
class TemporoSpatialStringPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(TemporoSpatialStringPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(TemporoSpatialStringPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const TemporoSpatialStringProperty *prop =
dynamic_cast<const TemporoSpatialStringProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("temporo_spatial_string");
+ auto *element = doc.NewElement("temporo_spatial_string");
std::string content = PropertyPersistenceSerialization::serializeTemporoSpatialStringPropertyToJSON(prop);
- TiXmlText text(content.c_str());
+ auto* text = doc.NewText(content.c_str());
element->InsertEndChild(text);
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
const char *s(element->GetText());
std::string content = s ? s : "";
return PropertyPersistenceDeserialization::deserializeJSONToTemporoSpatialStringProperty(content);
}
protected:
TemporoSpatialStringPropertySerializer() {}
~TemporoSpatialStringPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(TemporoSpatialStringPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkTransferFunctionPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkTransferFunctionPropertySerializer.cpp
index 8b63f9e01a..5b3d9c65ec 100644
--- a/Modules/SceneSerializationBase/src/mitkTransferFunctionPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkTransferFunctionPropertySerializer.cpp
@@ -1,260 +1,249 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkTransferFunctionPropertySerializer.h"
#include <mitkLexicalCast.h>
#include <mitkLocaleSwitch.h>
+#include <tinyxml2.h>
namespace mitk
{
mitk::TransferFunctionPropertySerializer::TransferFunctionPropertySerializer() {}
mitk::TransferFunctionPropertySerializer::~TransferFunctionPropertySerializer() {}
- TiXmlElement *mitk::TransferFunctionPropertySerializer::Serialize()
+ tinyxml2::XMLElement *mitk::TransferFunctionPropertySerializer::Serialize(tinyxml2::XMLDocument &doc)
{
if (const auto *prop =
dynamic_cast<const TransferFunctionProperty *>(mitk::BasePropertySerializer::m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
TransferFunction *transferfunction = prop->GetValue();
if (!transferfunction)
return nullptr;
- auto element = new TiXmlElement("TransferFunction");
+ auto *element = doc.NewElement("TransferFunction");
// serialize scalar opacity function
- auto scalarOpacityPointlist = new TiXmlElement("ScalarOpacity");
+ auto *scalarOpacityPointlist = doc.NewElement("ScalarOpacity");
TransferFunction::ControlPoints scalarOpacityPoints = transferfunction->GetScalarOpacityPoints();
for (auto iter = scalarOpacityPoints.begin(); iter != scalarOpacityPoints.end(); ++iter)
{
- auto pointel = new TiXmlElement("point");
- pointel->SetAttribute("x", boost::lexical_cast<std::string>(iter->first));
- pointel->SetAttribute("y", boost::lexical_cast<std::string>(iter->second));
- scalarOpacityPointlist->LinkEndChild(pointel);
+ auto *pointel = doc.NewElement("point");
+ pointel->SetAttribute("x", boost::lexical_cast<std::string>(iter->first).c_str());
+ pointel->SetAttribute("y", boost::lexical_cast<std::string>(iter->second).c_str());
+ scalarOpacityPointlist->InsertEndChild(pointel);
}
- element->LinkEndChild(scalarOpacityPointlist);
+ element->InsertEndChild(scalarOpacityPointlist);
// serialize gradient opacity function
- auto gradientOpacityPointlist = new TiXmlElement("GradientOpacity");
+ auto *gradientOpacityPointlist = doc.NewElement("GradientOpacity");
TransferFunction::ControlPoints gradientOpacityPoints = transferfunction->GetGradientOpacityPoints();
for (auto iter = gradientOpacityPoints.begin(); iter != gradientOpacityPoints.end(); ++iter)
{
- auto pointel = new TiXmlElement("point");
- pointel->SetAttribute("x", boost::lexical_cast<std::string>(iter->first));
- pointel->SetAttribute("y", boost::lexical_cast<std::string>(iter->second));
- gradientOpacityPointlist->LinkEndChild(pointel);
+ auto *pointel = doc.NewElement("point");
+ pointel->SetAttribute("x", boost::lexical_cast<std::string>(iter->first).c_str());
+ pointel->SetAttribute("y", boost::lexical_cast<std::string>(iter->second).c_str());
+ gradientOpacityPointlist->InsertEndChild(pointel);
}
- element->LinkEndChild(gradientOpacityPointlist);
+ element->InsertEndChild(gradientOpacityPointlist);
// serialize color function
vtkColorTransferFunction *ctf = transferfunction->GetColorTransferFunction();
if (ctf == nullptr)
return nullptr;
- auto pointlist = new TiXmlElement("Color");
+ auto *pointlist = doc.NewElement("Color");
for (int i = 0; i < ctf->GetSize(); i++)
{
double myVal[6];
ctf->GetNodeValue(i, myVal);
- auto pointel = new TiXmlElement("point");
- pointel->SetAttribute("x", boost::lexical_cast<std::string>(myVal[0]));
- pointel->SetAttribute("r", boost::lexical_cast<std::string>(myVal[1]));
- pointel->SetAttribute("g", boost::lexical_cast<std::string>(myVal[2]));
- pointel->SetAttribute("b", boost::lexical_cast<std::string>(myVal[3]));
- pointel->SetAttribute("midpoint", boost::lexical_cast<std::string>(myVal[4]));
- pointel->SetAttribute("sharpness", boost::lexical_cast<std::string>(myVal[5]));
- pointlist->LinkEndChild(pointel);
+ auto *pointel = doc.NewElement("point");
+ pointel->SetAttribute("x", boost::lexical_cast<std::string>(myVal[0]).c_str());
+ pointel->SetAttribute("r", boost::lexical_cast<std::string>(myVal[1]).c_str());
+ pointel->SetAttribute("g", boost::lexical_cast<std::string>(myVal[2]).c_str());
+ pointel->SetAttribute("b", boost::lexical_cast<std::string>(myVal[3]).c_str());
+ pointel->SetAttribute("midpoint", boost::lexical_cast<std::string>(myVal[4]).c_str());
+ pointel->SetAttribute("sharpness", boost::lexical_cast<std::string>(myVal[5]).c_str());
+ pointlist->InsertEndChild(pointel);
}
- element->LinkEndChild(pointlist);
+ element->InsertEndChild(pointlist);
return element;
}
else
return nullptr;
}
bool mitk::TransferFunctionPropertySerializer::SerializeTransferFunction(const char *filename,
TransferFunction::Pointer tf)
{
TransferFunctionPropertySerializer::Pointer tfps = TransferFunctionPropertySerializer::New();
tfps->SetProperty(TransferFunctionProperty::New(tf));
- TiXmlElement *s = tfps->Serialize();
+
+ tinyxml2::XMLDocument doc;
+ auto *s = tfps->Serialize(doc);
if (!s)
{
MITK_ERROR << "cant serialize transfer function";
return false;
}
- TiXmlDocument document;
- auto decl = new TiXmlDeclaration(
- "1.0",
- "UTF-8",
- ""); // TODO what to write here? encoding? standalone would mean that we provide a DTD somewhere...
- document.LinkEndChild(decl);
+ tinyxml2::XMLDocument doc2;
+ doc2.InsertEndChild(doc2.NewDeclaration());
- auto version = new TiXmlElement("Version");
+ auto *version = doc2.NewElement("Version");
version->SetAttribute("TransferfunctionVersion", 1);
- document.LinkEndChild(version);
- document.LinkEndChild(s);
+ doc2.InsertEndChild(version);
+ doc2.InsertEndChild(s->DeepClone(&doc2));
- if (!document.SaveFile(filename))
+ if (tinyxml2::XML_SUCCESS != doc2.SaveFile(filename))
{
- MITK_ERROR << "Could not write scene to " << filename << "\nTinyXML reports '" << document.ErrorDesc() << "'";
+ MITK_ERROR << "Could not write scene to " << filename << "\nTinyXML reports '" << doc2.ErrorStr() << "'";
return false;
}
return true;
}
- BaseProperty::Pointer mitk::TransferFunctionPropertySerializer::Deserialize(TiXmlElement *element)
+ BaseProperty::Pointer mitk::TransferFunctionPropertySerializer::Deserialize(const tinyxml2::XMLElement *element)
{
if (!element)
return nullptr;
mitk::LocaleSwitch localeSwitch("C");
TransferFunction::Pointer tf = TransferFunction::New();
// deserialize scalar opacity function
- TiXmlElement *scalarOpacityPointlist = element->FirstChildElement("ScalarOpacity");
+ auto *scalarOpacityPointlist = element->FirstChildElement("ScalarOpacity");
if (scalarOpacityPointlist == nullptr)
{
return nullptr;
}
tf->ClearScalarOpacityPoints();
try
{
- for (TiXmlElement *pointElement = scalarOpacityPointlist->FirstChildElement("point"); pointElement != nullptr;
+ for (auto *pointElement = scalarOpacityPointlist->FirstChildElement("point"); pointElement != nullptr;
pointElement = pointElement->NextSiblingElement("point"))
{
- std::string x;
- std::string y;
- if (pointElement->QueryStringAttribute("x", &x) != TIXML_SUCCESS)
- return nullptr;
- if (pointElement->QueryStringAttribute("y", &y) != TIXML_SUCCESS)
+ const char* x = pointElement->Attribute("x");
+ const char* y = pointElement->Attribute("y");
+ if (nullptr == x || nullptr == y)
return nullptr;
tf->AddScalarOpacityPoint(boost::lexical_cast<double>(x), boost::lexical_cast<double>(y));
}
- TiXmlElement *gradientOpacityPointlist = element->FirstChildElement("GradientOpacity");
+ auto *gradientOpacityPointlist = element->FirstChildElement("GradientOpacity");
if (gradientOpacityPointlist == nullptr)
{
return nullptr;
}
tf->ClearGradientOpacityPoints();
- for (TiXmlElement *pointElement = gradientOpacityPointlist->FirstChildElement("point"); pointElement != nullptr;
+ for (auto *pointElement = gradientOpacityPointlist->FirstChildElement("point"); pointElement != nullptr;
pointElement = pointElement->NextSiblingElement("point"))
{
- std::string x;
- std::string y;
- if (pointElement->QueryStringAttribute("x", &x) != TIXML_SUCCESS)
- return nullptr;
- if (pointElement->QueryStringAttribute("y", &y) != TIXML_SUCCESS)
+ const char* x = pointElement->Attribute("x");
+ const char* y = pointElement->Attribute("y");
+ if (nullptr == x || nullptr == y)
return nullptr;
tf->AddGradientOpacityPoint(boost::lexical_cast<double>(x), boost::lexical_cast<double>(y));
}
- TiXmlElement *rgbPointlist = element->FirstChildElement("Color");
+ auto *rgbPointlist = element->FirstChildElement("Color");
if (rgbPointlist == nullptr)
{
return nullptr;
}
vtkColorTransferFunction *ctf = tf->GetColorTransferFunction();
if (ctf == nullptr)
{
return nullptr;
}
ctf->RemoveAllPoints();
- for (TiXmlElement *pointElement = rgbPointlist->FirstChildElement("point"); pointElement != nullptr;
+ for (auto *pointElement = rgbPointlist->FirstChildElement("point"); pointElement != nullptr;
pointElement = pointElement->NextSiblingElement("point"))
{
- std::string x;
- std::string r, g, b, midpoint, sharpness;
- if (pointElement->QueryStringAttribute("x", &x) != TIXML_SUCCESS)
- return nullptr;
- if (pointElement->QueryStringAttribute("r", &r) != TIXML_SUCCESS)
- return nullptr;
- if (pointElement->QueryStringAttribute("g", &g) != TIXML_SUCCESS)
- return nullptr;
- if (pointElement->QueryStringAttribute("b", &b) != TIXML_SUCCESS)
- return nullptr;
- if (pointElement->QueryStringAttribute("midpoint", &midpoint) != TIXML_SUCCESS)
- return nullptr;
- if (pointElement->QueryStringAttribute("sharpness", &sharpness) != TIXML_SUCCESS)
+ const char* x = pointElement->Attribute("x");
+ const char* r = pointElement->Attribute("r");
+ const char* g = pointElement->Attribute("g");
+ const char* b = pointElement->Attribute("b");
+ const char* midpoint = pointElement->Attribute("midpoint");
+ const char* sharpness = pointElement->Attribute("sharpness");
+ if (nullptr == x || nullptr == r || nullptr == g || nullptr == b || nullptr == midpoint || nullptr == sharpness)
return nullptr;
ctf->AddRGBPoint(boost::lexical_cast<double>(x),
boost::lexical_cast<double>(r),
boost::lexical_cast<double>(g),
boost::lexical_cast<double>(b),
boost::lexical_cast<double>(midpoint),
boost::lexical_cast<double>(sharpness));
}
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
return TransferFunctionProperty::New(tf).GetPointer();
}
mitk::TransferFunction::Pointer mitk::TransferFunctionPropertySerializer::DeserializeTransferFunction(
const char *filePath)
{
- TiXmlDocument document(filePath);
+ tinyxml2::XMLDocument document;
- if (!document.LoadFile())
+ if (tinyxml2::XML_SUCCESS != document.LoadFile(filePath))
{
- MITK_ERROR << "Could not open/read/parse " << filePath << "\nTinyXML reports: " << document.ErrorDesc()
+ MITK_ERROR << "Could not open/read/parse " << filePath << "\nTinyXML reports: " << document.ErrorStr()
<< std::endl;
return nullptr;
}
// find version node --> note version in some variable
int fileVersion = 1;
- TiXmlElement *versionObject = document.FirstChildElement("Version");
+ auto *versionObject = document.FirstChildElement("Version");
if (versionObject)
{
- if (versionObject->QueryIntAttribute("TransferfunctionVersion", &fileVersion) != TIXML_SUCCESS)
+ if (versionObject->QueryIntAttribute("TransferfunctionVersion", &fileVersion) != tinyxml2::XML_SUCCESS)
{
MITK_WARN << "Transferfunction file " << filePath
<< " does not contain version information! Trying version 1 format.";
}
}
- TiXmlElement *input = document.FirstChildElement("TransferFunction");
+ auto *input = document.FirstChildElement("TransferFunction");
TransferFunctionPropertySerializer::Pointer tfpd = TransferFunctionPropertySerializer::New();
BaseProperty::Pointer bp = tfpd->Deserialize(input);
TransferFunctionProperty::Pointer tfp = dynamic_cast<TransferFunctionProperty *>(bp.GetPointer());
if (tfp.IsNotNull())
{
TransferFunction::Pointer tf = tfp->GetValue();
return tf;
}
MITK_WARN << "Can't deserialize transfer function";
return nullptr;
}
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(TransferFunctionPropertySerializer);
diff --git a/Modules/SceneSerializationBase/src/mitkUIntPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkUIntPropertySerializer.cpp
index d6695bf813..3efaca23c7 100644
--- a/Modules/SceneSerializationBase/src/mitkUIntPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkUIntPropertySerializer.cpp
@@ -1,66 +1,67 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkUIntPropertySerializer_h_included
#define mitkUIntPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkProperties.h"
+#include <tinyxml2.h>
namespace mitk
{
class UIntPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(UIntPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(UIntPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const UIntProperty *prop = dynamic_cast<const UIntProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("unsigned");
+ auto *element = doc.NewElement("unsigned");
element->SetAttribute("value", static_cast<unsigned int>(prop->GetValue()));
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
unsigned int integer;
- if (element->QueryUnsignedAttribute("value", &integer) == TIXML_SUCCESS)
+ if (element->QueryUnsignedAttribute("value", &integer) == tinyxml2::XML_SUCCESS)
{
return UIntProperty::New(integer).GetPointer();
}
else
{
return nullptr;
}
}
protected:
UIntPropertySerializer() {}
~UIntPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(UIntPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkUShortPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkUShortPropertySerializer.cpp
index 5d58407616..8aa03d622e 100644
--- a/Modules/SceneSerializationBase/src/mitkUShortPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkUShortPropertySerializer.cpp
@@ -1,66 +1,67 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkUShortPropertySerializer_h_included
#define mitkUShortPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
-
#include "mitkProperties.h"
+#include <tinyxml2.h>
namespace mitk
{
class UShortPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(UShortPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(UShortPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const UShortProperty *prop = dynamic_cast<const UShortProperty *>(m_Property.GetPointer()))
{
- auto element = new TiXmlElement("unsigned");
+ auto *element = doc.NewElement("unsigned");
element->SetAttribute("value", static_cast<unsigned short>(prop->GetValue()));
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
unsigned int value;
- if (element->QueryUnsignedAttribute("value", &value) == TIXML_SUCCESS)
+ if (element->QueryUnsignedAttribute("value", &value) == tinyxml2::XML_SUCCESS)
{
return UShortProperty::New(static_cast<unsigned short>(value)).GetPointer();
}
else
{
return nullptr;
}
}
protected:
UShortPropertySerializer() {}
~UShortPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(UShortPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/src/mitkVector3DPropertySerializer.cpp b/Modules/SceneSerializationBase/src/mitkVector3DPropertySerializer.cpp
index 8861398cd3..e961a00a96 100644
--- a/Modules/SceneSerializationBase/src/mitkVector3DPropertySerializer.cpp
+++ b/Modules/SceneSerializationBase/src/mitkVector3DPropertySerializer.cpp
@@ -1,84 +1,89 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkVector3DPropertySerializer_h_included
#define mitkVector3DPropertySerializer_h_included
#include "mitkBasePropertySerializer.h"
#include "mitkProperties.h"
#include "mitkStringsToNumbers.h"
#include <mitkLocaleSwitch.h>
+#include <array>
+
+#include <tinyxml2.h>
+
namespace mitk
{
class Vector3DPropertySerializer : public BasePropertySerializer
{
public:
- mitkClassMacro(Vector3DPropertySerializer, BasePropertySerializer);
- itkFactorylessNewMacro(Self) itkCloneMacro(Self)
+ mitkClassMacro(Vector3DPropertySerializer, BasePropertySerializer)
+ itkFactorylessNewMacro(Self)
+ itkCloneMacro(Self)
- TiXmlElement *Serialize() override
+ tinyxml2::XMLElement* Serialize(tinyxml2::XMLDocument& doc) override
{
if (const Vector3DProperty *prop = dynamic_cast<const Vector3DProperty *>(m_Property.GetPointer()))
{
LocaleSwitch localeSwitch("C");
- auto element = new TiXmlElement("vector");
+ auto *element = doc.NewElement("vector");
Vector3D point = prop->GetValue();
- element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]));
- element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]));
- element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]));
+ element->SetAttribute("x", boost::lexical_cast<std::string>(point[0]).c_str());
+ element->SetAttribute("y", boost::lexical_cast<std::string>(point[1]).c_str());
+ element->SetAttribute("z", boost::lexical_cast<std::string>(point[2]).c_str());
return element;
}
else
return nullptr;
}
- BaseProperty::Pointer Deserialize(TiXmlElement *element) override
+ BaseProperty::Pointer Deserialize(const tinyxml2::XMLElement *element) override
{
if (!element)
return nullptr;
LocaleSwitch localeSwitch("C");
- std::string v_str[3];
- if (element->QueryStringAttribute("x", &v_str[0]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("y", &v_str[1]) != TIXML_SUCCESS)
- return nullptr;
- if (element->QueryStringAttribute("z", &v_str[2]) != TIXML_SUCCESS)
+ std::array<const char*, 3> v_str = {
+ element->Attribute("x"),
+ element->Attribute("y"),
+ element->Attribute("z")
+ };
+ if (nullptr == v_str[0] || nullptr == v_str[1] || nullptr == v_str[2])
return nullptr;
Vector3D v;
try
{
StringsToNumbers<double>(3, v_str, v);
}
catch (boost::bad_lexical_cast &e)
{
- MITK_ERROR << "Could not parse string '" << v_str << "'as number: " << e.what();
+ MITK_ERROR << "Could not parse strings as numbers: " << e.what();
return nullptr;
}
return Vector3DProperty::New(v).GetPointer();
}
protected:
Vector3DPropertySerializer() {}
~Vector3DPropertySerializer() override {}
};
} // namespace
// important to put this into the GLOBAL namespace (because it starts with 'namespace mitk')
MITK_REGISTER_SERIALIZER(Vector3DPropertySerializer);
#endif
diff --git a/Modules/SceneSerializationBase/test/mitkPropertySerializationTest.cpp b/Modules/SceneSerializationBase/test/mitkPropertySerializationTest.cpp
index c6cfe3b656..df7caa32f5 100644
--- a/Modules/SceneSerializationBase/test/mitkPropertySerializationTest.cpp
+++ b/Modules/SceneSerializationBase/test/mitkPropertySerializationTest.cpp
@@ -1,199 +1,202 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkTestingMacros.h"
#include "mitkCoreObjectFactory.h"
#include "mitkBaseProperty.h"
#include "mitkProperties.h"
#include <mitkAnnotationProperty.h>
#include <mitkClippingProperty.h>
#include <mitkColorProperty.h>
#include <mitkEnumerationProperty.h>
#include <mitkModalityProperty.h>
#include <mitkGroupTagProperty.h>
#include <mitkLevelWindowProperty.h>
#include <mitkLookupTableProperty.h>
#include <mitkPlaneOrientationProperty.h>
#include <mitkStringProperty.h>
#include <mitkTransferFunctionProperty.h>
#include <mitkVtkInterpolationProperty.h>
#include <mitkVtkRepresentationProperty.h>
#include <mitkVtkResliceInterpolationProperty.h>
#include <mitkVtkScalarModeProperty.h>
#include <mitkVtkVolumeRenderingProperty.h>
#include "mitkBasePropertySerializer.h"
#include "mitkPropertyList.h"
#include "mitkPropertyListSerializer.h"
#include <mitkImage.h>
#include <mitkPointSet.h>
#include <mitkSurface.h>
#include <mitkVtkWidgetRendering.h>
+#include <tinyxml2.h>
+
void TestAllProperties(const mitk::PropertyList *propList);
/**Documentation
* \brief Test for all PropertySerializer classes.
*
*/
int mitkPropertySerializationTest(int /* argc */, char * /*argv*/ [])
{
MITK_TEST_BEGIN("PropertySerializationTest");
mitk::PropertyListSerializer::Pointer serializer =
mitk::PropertyListSerializer::New(); // make sure something from the lib is actually used (registration of
// serializers)
/* build list of properties that will be serialized and deserialized */
mitk::PropertyList::Pointer propList = mitk::PropertyList::New();
propList->SetProperty("booltrue", mitk::BoolProperty::New(true));
propList->SetProperty("boolfalse", mitk::BoolProperty::New(false));
propList->SetProperty("int", mitk::IntProperty::New(-32));
propList->SetProperty("float", mitk::FloatProperty::New(-31.337));
propList->SetProperty("double", mitk::DoubleProperty::New(-31.337));
propList->SetProperty("string", mitk::StringProperty::New("Hello MITK"));
mitk::Point3D p3d;
mitk::FillVector3D(p3d, 1.0, 2.2, -3.3);
propList->SetProperty("p3d", mitk::Point3dProperty::New(p3d));
mitk::Point3I p3i;
mitk::FillVector3D(p3i, 1, 2, -3);
propList->SetProperty("p3i", mitk::Point3iProperty::New(p3i));
mitk::Point4D p4d;
mitk::FillVector4D(p4d, 1.5, 2.6, -3.7, 4.44);
propList->SetProperty("p4d", mitk::Point4dProperty::New(p4d));
mitk::Vector3D v3d;
mitk::FillVector3D(v3d, 1.0, 2.2, -3.3);
propList->SetProperty("v3d", mitk::Vector3DProperty::New(v3d));
propList->SetProperty("annotation", mitk::AnnotationProperty::New("My Annotation", p3d));
propList->SetProperty("clipping", mitk::ClippingProperty::New(p3d, v3d));
propList->SetProperty("color", mitk::ColorProperty::New(1.0, 0.2, 0.2));
propList->SetProperty("modality", mitk::ModalityProperty::New("Color Doppler"));
propList->SetProperty("PlaneOrientationProperty",
mitk::PlaneOrientationProperty::New("Arrows in positive direction"));
propList->SetProperty("VtkInterpolationProperty", mitk::VtkInterpolationProperty::New("Gouraud"));
propList->SetProperty("VtkRepresentationProperty", mitk::VtkRepresentationProperty::New("Surface"));
propList->SetProperty("VtkResliceInterpolationProperty", mitk::VtkResliceInterpolationProperty::New("Cubic"));
propList->SetProperty("VtkScalarModeProperty", mitk::VtkScalarModeProperty::New("PointFieldData"));
propList->SetProperty("VtkVolumeRenderingProperty", mitk::VtkVolumeRenderingProperty::New("COMPOSITE"));
mitk::BoolLookupTable blt;
blt.SetTableValue(0, true);
blt.SetTableValue(1, false);
blt.SetTableValue(2, true);
propList->SetProperty("BoolLookupTableProperty", mitk::BoolLookupTableProperty::New(blt));
mitk::FloatLookupTable flt;
flt.SetTableValue(0, 3.1);
flt.SetTableValue(1, 3.3);
flt.SetTableValue(2, 7.0);
propList->SetProperty("FloatLookupTableProperty", mitk::FloatLookupTableProperty::New(flt));
mitk::IntLookupTable ilt;
ilt.SetTableValue(0, 3);
ilt.SetTableValue(1, 2);
ilt.SetTableValue(2, 11);
propList->SetProperty("IntLookupTableProperty", mitk::IntLookupTableProperty::New(ilt));
mitk::StringLookupTable slt;
slt.SetTableValue(0, "Hello");
slt.SetTableValue(1, "MITK");
slt.SetTableValue(2, "world");
propList->SetProperty("StringLookupTableProperty", mitk::StringLookupTableProperty::New(slt));
propList->SetProperty("GroupTagProperty", mitk::GroupTagProperty::New());
propList->SetProperty("LevelWindowProperty", mitk::LevelWindowProperty::New(mitk::LevelWindow(100.0, 50.0)));
mitk::LookupTable::Pointer lt = mitk::LookupTable::New();
lt->ChangeOpacityForAll(0.25);
lt->ChangeOpacity(17, 0.88);
propList->SetProperty("LookupTableProperty", mitk::LookupTableProperty::New(lt));
propList->SetProperty("StringProperty", mitk::StringProperty::New("Oh why, gruel world"));
MITK_TEST_CONDITION_REQUIRED(propList->GetMap()->size() > 0, "Initialize PropertyList");
TestAllProperties(propList);
/* test default property lists of basedata objects */
// activate the following tests after MaterialProperty is deleted
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(mitk::PointSet::New());
TestAllProperties(node->GetPropertyList());
node->SetData(mitk::Image::New());
TestAllProperties(node->GetPropertyList());
node->SetData(mitk::Surface::New());
TestAllProperties(node->GetPropertyList());
node->SetData(mitk::VtkWidgetRendering::New());
TestAllProperties(node->GetPropertyList());
MITK_TEST_END();
}
void TestAllProperties(const mitk::PropertyList *propList)
{
assert(propList);
/* try to serialize each property in the list, then deserialize again and check for equality */
for (auto it = propList->GetMap()->begin();
it != propList->GetMap()->end();
++it)
{
const mitk::BaseProperty *prop = it->second;
// construct name of serializer class
std::string serializername = std::string(prop->GetNameOfClass()) + "Serializer";
std::list<itk::LightObject::Pointer> allSerializers =
itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str());
MITK_TEST_CONDITION(allSerializers.size() > 0, std::string("Creating serializers for ") + serializername);
if (allSerializers.size() == 0)
{
MITK_TEST_OUTPUT(<< "serialization not possible, skipping " << prop->GetNameOfClass());
continue;
}
if (allSerializers.size() > 1)
{
MITK_TEST_OUTPUT(<< "Warning: " << allSerializers.size() << " serializers found for " << prop->GetNameOfClass()
<< "testing only the first one.");
}
auto *serializer =
dynamic_cast<mitk::BasePropertySerializer *>(allSerializers.begin()->GetPointer());
MITK_TEST_CONDITION(serializer != nullptr, serializername + std::string(" is valid"));
if (serializer != nullptr)
{
serializer->SetProperty(prop);
- TiXmlElement *valueelement = nullptr;
+ tinyxml2::XMLDocument doc;
+ tinyxml2::XMLElement *valueelement = nullptr;
try
{
- valueelement = serializer->Serialize();
+ valueelement = serializer->Serialize(doc);
}
catch (...)
{
}
MITK_TEST_CONDITION(valueelement != nullptr, std::string("Serialize property with ") + serializername);
if (valueelement == nullptr)
{
MITK_TEST_OUTPUT(<< "serialization failed, skipping deserialization");
continue;
}
mitk::BaseProperty::Pointer deserializedProp = serializer->Deserialize(valueelement);
MITK_TEST_CONDITION(deserializedProp.IsNotNull(), "serializer created valid property");
if (deserializedProp.IsNotNull())
{
MITK_TEST_CONDITION(*(deserializedProp.GetPointer()) == *prop,
"deserialized property equals initial property for type " << prop->GetNameOfClass());
}
}
else
{
MITK_TEST_OUTPUT(<< "created serializer object is of class "
<< allSerializers.begin()->GetPointer()->GetNameOfClass())
}
} // for all properties
}
diff --git a/Modules/SceneSerializationBase/test/mitkVectorPropertySerializerTest.cpp b/Modules/SceneSerializationBase/test/mitkVectorPropertySerializerTest.cpp
index b8c3556e0f..ffbee130f4 100644
--- a/Modules/SceneSerializationBase/test/mitkVectorPropertySerializerTest.cpp
+++ b/Modules/SceneSerializationBase/test/mitkVectorPropertySerializerTest.cpp
@@ -1,141 +1,144 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkTestFixture.h"
#include "mitkTestingMacros.h"
#include "mitkBasePropertySerializer.h"
#include "mitkVectorProperty.h"
#include <mitkLexicalCast.h>
#include <limits>
#include <cmath>
#include "mitkEqual.h"
+#include <tinyxml2.h>
+
/**
\brief Test for VectorPropertySerializer.
Creates simple std::vector instances, puts them
into a VectorProperty of appropriate type, then
asks a serializer to serialize them into XML.
Test expects that there is a deserializer somewhere
in the system (i.e. registered with the ITK object
factory. The test further expects that this
deserializer is able to create a VectorProperty
from XML and that this VectorProperty equals the
input of serialization.
*/
class mitkVectorPropertySerializerTestSuite : public mitk::TestFixture
{
CPPUNIT_TEST_SUITE(mitkVectorPropertySerializerTestSuite);
MITK_TEST(TestSerialize<int>);
MITK_TEST(TestSerialize<double>);
MITK_TEST(TestSerializeIntTypedef);
MITK_TEST(TestSerializeDoubleTypedef);
CPPUNIT_TEST_SUITE_END();
public:
void setUp() override {}
void tearDown() override {}
template <typename DATATYPE>
typename mitk::VectorProperty<DATATYPE>::Pointer MakeExampleProperty()
{
typename mitk::VectorProperty<DATATYPE>::Pointer vectorProperty = mitk::VectorProperty<DATATYPE>::New();
std::vector<DATATYPE> data;
data.push_back(static_cast<DATATYPE>(-918273674.6172838));
data.push_back(0);
data.push_back(static_cast<DATATYPE>(+6172838.918273674));
data.push_back(sqrt(2));
if (std::numeric_limits<DATATYPE>::has_infinity)
{
data.push_back(std::numeric_limits<DATATYPE>::infinity());
data.push_back(-std::numeric_limits<DATATYPE>::infinity());
}
// do NOT test NaN: cannot be == to itself, so cannot be tested like the others
// NaN is covered in a different test (FloatToStringTest at the time of writing this)
// data.push_back( std::numeric_limits<DATATYPE>::quiet_NaN() );
vectorProperty->SetValue(data);
return vectorProperty;
}
mitk::BaseProperty::Pointer TestSerialize(mitk::BaseProperty *property)
{
std::string serializername = std::string(property->GetNameOfClass()) + "Serializer";
std::list<itk::LightObject::Pointer> allSerializers =
itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str());
CPPUNIT_ASSERT_EQUAL(size_t(1), allSerializers.size());
auto *serializer =
dynamic_cast<mitk::BasePropertySerializer *>(allSerializers.begin()->GetPointer());
CPPUNIT_ASSERT(serializer != nullptr);
if (!serializer)
return nullptr;
serializer->SetProperty(property);
- TiXmlElement *serialization(nullptr);
+ tinyxml2::XMLDocument doc;
+ tinyxml2::XMLElement *serialization(nullptr);
try
{
- serialization = serializer->Serialize();
+ serialization = serializer->Serialize(doc);
}
catch (...)
{
}
CPPUNIT_ASSERT(serialization != nullptr);
if (!serialization)
return nullptr;
mitk::BaseProperty::Pointer restoredProperty = serializer->Deserialize(serialization);
CPPUNIT_ASSERT(restoredProperty.IsNotNull());
return restoredProperty;
}
template <typename DATATYPE>
void TestSerialize()
{
auto property = MakeExampleProperty<DATATYPE>();
mitk::BaseProperty::Pointer restored_property = TestSerialize(property);
typename mitk::VectorProperty<DATATYPE>::Pointer restored_vector_property =
dynamic_cast<mitk::VectorProperty<DATATYPE> *>(restored_property.GetPointer());
CPPUNIT_ASSERT(restored_vector_property.IsNotNull());
auto orig_vector = property->GetValue();
auto restored_vector = restored_vector_property->GetValue();
CPPUNIT_ASSERT_EQUAL(orig_vector.size(), restored_vector.size());
for (unsigned int i = 0; i < orig_vector.size(); ++i)
{
// compare using Equal, i.e. with tolerance of mitk::eps
CPPUNIT_ASSERT_MESSAGE(std::string("Verifying element ") + boost::lexical_cast<std::string>(i),
mitk::Equal(orig_vector[i], restored_vector[i]));
}
}
void TestSerializeIntTypedef()
{
mitk::IntVectorProperty::Pointer intVectorProperty = MakeExampleProperty<int>().GetPointer();
TestSerialize(intVectorProperty.GetPointer());
}
void TestSerializeDoubleTypedef()
{
mitk::DoubleVectorProperty::Pointer doubleVectorProperty = MakeExampleProperty<double>().GetPointer();
TestSerialize(doubleVectorProperty.GetPointer());
}
}; // class
MITK_TEST_SUITE_REGISTRATION(mitkVectorPropertySerializer)
diff --git a/Modules/Segmentation/CMakeLists.txt b/Modules/Segmentation/CMakeLists.txt
index 1528dd107f..b73d0ba055 100644
--- a/Modules/Segmentation/CMakeLists.txt
+++ b/Modules/Segmentation/CMakeLists.txt
@@ -1,9 +1,9 @@
-MITK_CREATE_MODULE(
+mitk_create_module(
INCLUDE_DIRS Algorithms Controllers DataManagement Interactions Rendering SegmentationUtilities/BooleanOperations SegmentationUtilities/MorphologicalOperations
DEPENDS MitkAlgorithmsExt MitkIpSegmentation MitkIpFunc MitkSurfaceInterpolation MitkGraphAlgorithms MitkContourModel MitkMultilabel
PACKAGE_DEPENDS
- PUBLIC ITK|ITKBinaryMathematicalMorphology+ITKLabelVoting+ITKRegionGrowing+ITKFastMarching+ITKAnisotropicSmoothing+ITKWatersheds
- PRIVATE VTK|ImagingGeneral
+ PUBLIC ITK|QuadEdgeMesh
+ PRIVATE ITK|LabelMap+Watersheds VTK|ImagingGeneral
)
add_subdirectory(Testing)
diff --git a/Modules/Segmentation/Interactions/mitkContourTool.cpp b/Modules/Segmentation/Interactions/mitkContourTool.cpp
index 7c16912f7b..3cc6e941fe 100644
--- a/Modules/Segmentation/Interactions/mitkContourTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkContourTool.cpp
@@ -1,197 +1,180 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkContourTool.h"
#include "mitkAbstractTransformGeometry.h"
#include "mitkOverwriteDirectedPlaneImageFilter.h"
#include "mitkOverwriteSliceImageFilter.h"
#include "mitkToolManager.h"
#include "mitkBaseRenderer.h"
#include "mitkRenderingManager.h"
-//#include "mitkProperties.h"
-//#include "mitkPlanarCircle.h"
-#include "mitkLabelSetImage.h"
#include "mitkInteractionEvent.h"
#include "mitkStateMachineAction.h"
mitk::ContourTool::ContourTool(int paintingPixelValue)
: FeedbackContourTool("PressMoveReleaseWithCTRLInversion"),
- m_PaintingPixelValue(paintingPixelValue),
- m_CurrentLabelID(1)
+ m_PaintingPixelValue(paintingPixelValue)
{
}
mitk::ContourTool::~ContourTool()
{
}
void mitk::ContourTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Move", OnMouseMoved);
CONNECT_FUNCTION("Release", OnMouseReleased);
CONNECT_FUNCTION("InvertLogic", OnInvertLogic);
}
void mitk::ContourTool::Activated()
{
Superclass::Activated();
}
void mitk::ContourTool::Deactivated()
{
Superclass::Deactivated();
}
/**
Just show the contour, insert the first point.
*/
void mitk::ContourTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
int timestep = positionEvent->GetSender()->GetTimeStep();
ContourModel *contour = FeedbackContourTool::GetFeedbackContour();
// Clear feedback contour
contour->Initialize();
// expand time bounds because our contour was initialized
contour->Expand(timestep + 1);
// draw as a closed contour
contour->SetClosed(true, timestep);
// add first mouse position
mitk::Point3D point = positionEvent->GetPositionInWorld();
contour->AddVertex(point, timestep);
FeedbackContourTool::SetFeedbackContourVisible(true);
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
/**
Insert the point to the feedback contour.
*/
void mitk::ContourTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
int timestep = positionEvent->GetSender()->GetTimeStep();
ContourModel *contour = FeedbackContourTool::GetFeedbackContour();
mitk::Point3D point = positionEvent->GetPositionInWorld();
contour->AddVertex(point, timestep);
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
/**
Close the contour, project it to the image slice and fill it in 2D.
*/
void mitk::ContourTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
// const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
- auto *image = dynamic_cast<Image *>(workingNode->GetData());
+ auto workingImage = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
- if (!image || !planeGeometry)
+ if (!workingImage || !planeGeometry)
return;
- // Check if it is a multilabel-image
- // If yes, get the new drawing color from it.
- // Otherwise nothing happens.
- auto *labelSetImage = dynamic_cast<LabelSetImage *>(image);
- if (labelSetImage)
- {
- mitk::Label *label = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer());
- m_CurrentLabelID = label->GetValue();
- }
- else
- {
- m_CurrentLabelID = 1;
- }
-
const auto *abstractTransformGeometry(
dynamic_cast<const AbstractTransformGeometry *>(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
- if (!image || abstractTransformGeometry)
+ if (!workingImage || abstractTransformGeometry)
return;
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
- Image::Pointer slice = SegTool2D::GetAffectedImageSliceAs2DImage(positionEvent, image);
+ Image::Pointer slice = SegTool2D::GetAffectedImageSliceAs2DImage(positionEvent, workingImage);
if (slice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
ContourModel *feedbackContour = FeedbackContourTool::GetFeedbackContour();
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice(
slice, feedbackContour, true, false); // true: actually no idea why this is neccessary, but it works :-(
if (projectedContour.IsNull())
return;
int timestep = positionEvent->GetSender()->GetTimeStep();
+ int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage);
// m_PaintingPixelValue only decides whether to paint or erase
mitk::ContourModelUtils::FillContourInSlice(
- projectedContour, timestep, slice, image, (m_PaintingPixelValue * m_CurrentLabelID));
+ projectedContour, timestep, slice, workingImage, m_PaintingPixelValue * activePixelValue);
// this->WriteBackSegmentationResult(positionEvent, slice);
SegTool2D::WriteBackSegmentationResult(positionEvent, slice);
// 4. Make sure the result is drawn again --> is visible then.
assert(positionEvent->GetSender()->GetRenderWindow());
}
/**
Called when the CTRL key is pressed. Will change the painting pixel value from 0 to 1 or from 1 to 0.
*/
void mitk::ContourTool::OnInvertLogic(StateMachineAction *, InteractionEvent *)
{
// Inversion only for 0 and 1 as painting values
if (m_PaintingPixelValue == 1)
{
m_PaintingPixelValue = 0;
FeedbackContourTool::SetFeedbackContourColor(1.0, 0.0, 0.0);
}
else if (m_PaintingPixelValue == 0)
{
m_PaintingPixelValue = 1;
FeedbackContourTool::SetFeedbackContourColorDefault();
}
}
diff --git a/Modules/Segmentation/Interactions/mitkContourTool.h b/Modules/Segmentation/Interactions/mitkContourTool.h
index 88b0317a83..23e7d7a79c 100644
--- a/Modules/Segmentation/Interactions/mitkContourTool.h
+++ b/Modules/Segmentation/Interactions/mitkContourTool.h
@@ -1,72 +1,71 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkContourTool_h_Included
#define mitkContourTool_h_Included
#include "mitkCommon.h"
#include "mitkFeedbackContourTool.h"
#include <MitkSegmentationExports.h>
namespace mitk
{
class Image;
class StateMachineAction;
class InteractionEvent;
/**
\brief Simple contour filling tool.
\sa FeedbackContourTool
\sa ExtractImageFilter
\sa OverwriteSliceImageFilter
\ingroup Interaction
\ingroup ToolManagerEtAl
Fills a visible contour (from FeedbackContourTool) during mouse dragging. When the mouse button
is released, ContourTool tries to extract a slice from the working image and fill in
the (filled) contour as a binary image.
The painting "color" is defined by m_PaintingPixelValue, which is set in the constructor
(by sub-classes) or during some event (e.g. in OnInvertLogic - when CTRL is pressed).
\warning Only to be instantiated by mitk::ToolManager.
$Author$
*/
class MITKSEGMENTATION_EXPORT ContourTool : public FeedbackContourTool
{
public:
mitkClassMacro(ContourTool, FeedbackContourTool);
protected:
ContourTool(int paintingPixelValue = 1); // purposely hidden
~ContourTool() override;
void Activated() override;
void Deactivated() override;
virtual void OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent);
virtual void OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent);
virtual void OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent);
virtual void OnInvertLogic(StateMachineAction *, InteractionEvent *interactionEvent);
void ConnectActionsAndFunctions() override;
int m_PaintingPixelValue;
- int m_CurrentLabelID;
};
} // namespace
#endif
diff --git a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp
index 8dcf41b457..0e928ed279 100644
--- a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp
+++ b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp
@@ -1,207 +1,204 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkCorrectorTool2D.h"
#include "mitkCorrectorAlgorithm.h"
#include "mitkAbstractTransformGeometry.h"
#include "mitkBaseRenderer.h"
#include "mitkImageReadAccessor.h"
#include "mitkLabelSetImage.h"
#include "mitkRenderingManager.h"
#include "mitkToolManager.h"
#include "mitkCorrectorTool2D.xpm"
#include "mitkLabelSetImage.h"
// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, CorrectorTool2D, "Correction tool");
}
mitk::CorrectorTool2D::CorrectorTool2D(int paintingPixelValue)
: FeedbackContourTool("PressMoveRelease"), m_PaintingPixelValue(paintingPixelValue)
{
GetFeedbackContour()->SetClosed(false); // don't close the contour to a polygon
}
mitk::CorrectorTool2D::~CorrectorTool2D()
{
}
void mitk::CorrectorTool2D::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Move", OnMouseMoved);
CONNECT_FUNCTION("Release", OnMouseReleased);
}
const char **mitk::CorrectorTool2D::GetXPM() const
{
return mitkCorrectorTool2D_xpm;
}
us::ModuleResource mitk::CorrectorTool2D::GetIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("Correction_48x48.png");
return resource;
}
us::ModuleResource mitk::CorrectorTool2D::GetCursorIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("Correction_Cursor_32x32.png");
return resource;
}
const char *mitk::CorrectorTool2D::GetName() const
{
return "Correction";
}
void mitk::CorrectorTool2D::Activated()
{
Superclass::Activated();
}
void mitk::CorrectorTool2D::Deactivated()
{
Superclass::Deactivated();
}
void mitk::CorrectorTool2D::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
int timestep = positionEvent->GetSender()->GetTimeStep();
ContourModel *contour = FeedbackContourTool::GetFeedbackContour();
contour->Initialize();
contour->Expand(timestep + 1);
contour->SetClosed(false, timestep);
mitk::Point3D point = positionEvent->GetPositionInWorld();
contour->AddVertex(point, timestep);
FeedbackContourTool::SetFeedbackContourVisible(true);
}
void mitk::CorrectorTool2D::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
int timestep = positionEvent->GetSender()->GetTimeStep();
ContourModel *contour = FeedbackContourTool::GetFeedbackContour();
mitk::Point3D point = positionEvent->GetPositionInWorld();
contour->AddVertex(point, timestep);
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::CorrectorTool2D::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
// const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
- auto *image = dynamic_cast<Image *>(workingNode->GetData());
+ auto *workingImage = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
- if (!image || !planeGeometry)
+ if (!workingImage || !planeGeometry)
return;
const auto *abstractTransformGeometry(
dynamic_cast<const AbstractTransformGeometry *>(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
- if (!image || abstractTransformGeometry)
+ if (!workingImage || abstractTransformGeometry)
return;
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
- m_WorkingSlice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image);
+ m_WorkingSlice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, workingImage);
if (m_WorkingSlice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
int timestep = positionEvent->GetSender()->GetTimeStep();
mitk::ContourModel::Pointer singleTimestepContour = mitk::ContourModel::New();
auto it = FeedbackContourTool::GetFeedbackContour()->Begin(timestep);
auto end = FeedbackContourTool::GetFeedbackContour()->End(timestep);
while (it != end)
{
singleTimestepContour->AddVertex((*it)->Coordinates);
it++;
}
CorrectorAlgorithm::Pointer algorithm = CorrectorAlgorithm::New();
algorithm->SetInput(m_WorkingSlice);
algorithm->SetContour(singleTimestepContour);
- mitk::LabelSetImage::Pointer labelSetImage = dynamic_cast<LabelSetImage *>(workingNode->GetData());
- int workingColorId(1);
- if (labelSetImage.IsNotNull())
- {
- workingColorId = labelSetImage->GetActiveLabel()->GetValue();
- algorithm->SetFillColor(workingColorId);
- }
+ int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage);
+ algorithm->SetFillColor(activePixelValue);
+
try
{
algorithm->UpdateLargestPossibleRegion();
}
catch (std::exception &e)
{
MITK_ERROR << "Caught exception '" << e.what() << "'" << std::endl;
}
mitk::Image::Pointer resultSlice = mitk::Image::New();
resultSlice->Initialize(algorithm->GetOutput());
- if (labelSetImage.IsNotNull())
+ auto* labelSetImage = dynamic_cast<LabelSetImage*>(workingImage);
+ if (nullptr != labelSetImage)
{
- mitk::Image::Pointer erg1 = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image);
- SegTool2D::WritePreviewOnWorkingImage(erg1, algorithm->GetOutput(), image, workingColorId, 0);
+ mitk::Image::Pointer erg1 = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, workingImage);
+ SegTool2D::WritePreviewOnWorkingImage(erg1, algorithm->GetOutput(), workingImage, activePixelValue, 0);
SegTool2D::WriteBackSegmentationResult(positionEvent, erg1);
}
else
{
mitk::ImageReadAccessor imAccess(algorithm->GetOutput());
resultSlice->SetVolume(imAccess.GetData());
this->WriteBackSegmentationResult(positionEvent, resultSlice);
}
}
diff --git a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp b/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp
index 48a1301bf6..8ada9faf2b 100644
--- a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp
+++ b/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp
@@ -1,334 +1,334 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkFastMarchingTool3D.h"
#include "mitkToolManager.h"
#include "mitkBaseRenderer.h"
#include "mitkInteractionConst.h"
#include "mitkRenderingManager.h"
#include "mitkImageAccessByItk.h"
// itk filter
#include "itkBinaryThresholdImageFilter.h"
#include "itkCurvatureAnisotropicDiffusionImageFilter.h"
#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h"
#include "itkSigmoidImageFilter.h"
// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, FastMarchingTool3D, "FastMarching3D tool");
}
mitk::FastMarchingTool3D::FastMarchingTool3D()
: AutoSegmentationWithPreviewTool(),
m_LowerThreshold(0),
m_UpperThreshold(200),
m_StoppingValue(100),
m_Sigma(1.0),
m_Alpha(-0.5),
m_Beta(3.0),
m_PointSetAddObserverTag(0),
m_PointSetRemoveObserverTag(0)
{
}
mitk::FastMarchingTool3D::~FastMarchingTool3D()
{
}
bool mitk::FastMarchingTool3D::CanHandle(const BaseData* referenceData, const BaseData* workingData) const
{
if(!Superclass::CanHandle(referenceData, workingData))
return false;
if (referenceData == nullptr)
return false;
auto *image = dynamic_cast<const Image *>(referenceData);
if (image == nullptr)
return false;
if (image->GetDimension() < 3)
return false;
return true;
}
const char **mitk::FastMarchingTool3D::GetXPM() const
{
return nullptr; // mitkFastMarchingTool3D_xpm;
}
us::ModuleResource mitk::FastMarchingTool3D::GetIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("FastMarching_48x48.png");
return resource;
}
const char *mitk::FastMarchingTool3D::GetName() const
{
return "Fast Marching 3D";
}
void mitk::FastMarchingTool3D::SetUpperThreshold(double value)
{
m_UpperThreshold = value / 10.0;
}
void mitk::FastMarchingTool3D::SetLowerThreshold(double value)
{
m_LowerThreshold = value / 10.0;
}
void mitk::FastMarchingTool3D::SetBeta(double value)
{
if (m_Beta != value)
{
m_Beta = value;
}
}
void mitk::FastMarchingTool3D::SetSigma(double value)
{
if (m_Sigma != value)
{
if (value > 0.0)
{
m_Sigma = value;
}
}
}
void mitk::FastMarchingTool3D::SetAlpha(double value)
{
if (m_Alpha != value)
{
m_Alpha = value;
}
}
void mitk::FastMarchingTool3D::SetStoppingValue(double value)
{
if (m_StoppingValue != value)
{
m_StoppingValue = value;
}
}
void mitk::FastMarchingTool3D::Activated()
{
Superclass::Activated();
m_SeedsAsPointSet = mitk::PointSet::New();
m_SeedsAsPointSetNode = mitk::DataNode::New();
m_SeedsAsPointSetNode->SetData(m_SeedsAsPointSet);
m_SeedsAsPointSetNode->SetName("3D_FastMarching_PointSet");
m_SeedsAsPointSetNode->SetBoolProperty("helper object", true);
m_SeedsAsPointSetNode->SetColor(0.0, 1.0, 0.0);
m_SeedsAsPointSetNode->SetVisibility(true);
// Create PointSetData Interactor
m_SeedPointInteractor = mitk::PointSetDataInteractor::New();
// Load the according state machine for regular point set interaction
m_SeedPointInteractor->LoadStateMachine("PointSet.xml");
// Set the configuration file that defines the triggers for the transitions
m_SeedPointInteractor->SetEventConfig("PointSetConfig.xml");
// set the DataNode (which already is added to the DataStorage
m_SeedPointInteractor->SetDataNode(m_SeedsAsPointSetNode);
m_ToolManager->GetDataStorage()->Add(m_SeedsAsPointSetNode, m_ToolManager->GetWorkingData(0));
m_SeedContainer = NodeContainer::New();
m_SeedContainer->Initialize();
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::Pointer pointAddedCommand =
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::New();
pointAddedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnAddPoint);
m_PointSetAddObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetAddEvent(), pointAddedCommand);
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::Pointer pointRemovedCommand =
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::New();
pointRemovedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnDelete);
m_PointSetRemoveObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetRemoveEvent(), pointRemovedCommand);
}
void mitk::FastMarchingTool3D::Deactivated()
{
this->ClearSeeds();
// Deactivate Interaction
m_SeedPointInteractor->SetDataNode(nullptr);
m_ToolManager->GetDataStorage()->Remove(m_SeedsAsPointSetNode);
m_SeedsAsPointSetNode = nullptr;
m_SeedsAsPointSet->RemoveObserver(m_PointSetAddObserverTag);
m_SeedsAsPointSet->RemoveObserver(m_PointSetRemoveObserverTag);
m_SeedsAsPointSet = nullptr;
Superclass::Deactivated();
}
void mitk::FastMarchingTool3D::OnAddPoint()
{
// Add a new seed point for FastMarching algorithm
mitk::Point3D clickInIndex;
this->GetReferenceData()->GetGeometry()->WorldToIndex(m_SeedsAsPointSet->GetPoint(m_SeedsAsPointSet->GetSize() - 1),
clickInIndex);
itk::Index<3> seedPosition;
seedPosition[0] = clickInIndex[0];
seedPosition[1] = clickInIndex[1];
seedPosition[2] = clickInIndex[2];
NodeType node;
const double seedValue = 0.0;
node.SetValue(seedValue);
node.SetIndex(seedPosition);
this->m_SeedContainer->InsertElement(this->m_SeedContainer->Size(), node);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
this->UpdatePreview();
}
void mitk::FastMarchingTool3D::OnDelete()
{
// delete last seed point
if (!(this->m_SeedContainer->empty()))
{
// delete last element of seeds container
this->m_SeedContainer->pop_back();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
this->UpdatePreview();
}
}
void mitk::FastMarchingTool3D::ClearSeeds()
{
// clear seeds for FastMarching as well as the PointSet for visualization
if (this->m_SeedContainer.IsNotNull())
this->m_SeedContainer->Initialize();
if (this->m_SeedsAsPointSet.IsNotNull())
{
// remove observers from current pointset
m_SeedsAsPointSet->RemoveObserver(m_PointSetAddObserverTag);
m_SeedsAsPointSet->RemoveObserver(m_PointSetRemoveObserverTag);
// renew pointset
this->m_SeedsAsPointSet = mitk::PointSet::New();
this->m_SeedsAsPointSetNode->SetData(this->m_SeedsAsPointSet);
m_SeedsAsPointSetNode->SetName("Seeds_Preview");
m_SeedsAsPointSetNode->SetBoolProperty("helper object", true);
m_SeedsAsPointSetNode->SetColor(0.0, 1.0, 0.0);
m_SeedsAsPointSetNode->SetVisibility(true);
// add callback function for adding and removing points
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::Pointer pointAddedCommand =
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::New();
pointAddedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnAddPoint);
m_PointSetAddObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetAddEvent(), pointAddedCommand);
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::Pointer pointRemovedCommand =
itk::SimpleMemberCommand<mitk::FastMarchingTool3D>::New();
pointRemovedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnDelete);
m_PointSetRemoveObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetRemoveEvent(), pointRemovedCommand);
}
}
template <typename TPixel, unsigned int VImageDimension>
void mitk::FastMarchingTool3D::DoITKFastMarching(const itk::Image<TPixel, VImageDimension>* inputImage,
mitk::Image* segmentation, unsigned int timeStep)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
/* typedefs for itk pipeline */
typedef mitk::Tool::DefaultSegmentationDataType OutputPixelType;
typedef itk::Image<OutputPixelType, VImageDimension> OutputImageType;
typedef itk::CurvatureAnisotropicDiffusionImageFilter<InputImageType, InternalImageType> SmoothingFilterType;
typedef itk::GradientMagnitudeRecursiveGaussianImageFilter<InternalImageType, InternalImageType> GradientFilterType;
typedef itk::SigmoidImageFilter<InternalImageType, InternalImageType> SigmoidFilterType;
typedef itk::BinaryThresholdImageFilter<InternalImageType, OutputImageType> ThresholdingFilterType;
auto smoothFilter = SmoothingFilterType::New();
smoothFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
smoothFilter->SetTimeStep(0.05);
smoothFilter->SetNumberOfIterations(2);
smoothFilter->SetConductanceParameter(9.0);
auto gradientMagnitudeFilter = GradientFilterType::New();
gradientMagnitudeFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
gradientMagnitudeFilter->SetSigma(m_Sigma);
auto sigmoidFilter = SigmoidFilterType::New();
sigmoidFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
sigmoidFilter->SetAlpha(m_Alpha);
sigmoidFilter->SetBeta(m_Beta);
sigmoidFilter->SetOutputMinimum(0.0);
sigmoidFilter->SetOutputMaximum(1.0);
auto fastMarchingFilter = FastMarchingFilterType::New();
fastMarchingFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
fastMarchingFilter->SetStoppingValue(m_StoppingValue);
fastMarchingFilter->SetTrialPoints(m_SeedContainer);
auto thresholdFilter = ThresholdingFilterType::New();
thresholdFilter->SetLowerThreshold(m_LowerThreshold);
thresholdFilter->SetUpperThreshold(m_UpperThreshold);
thresholdFilter->SetOutsideValue(0);
thresholdFilter->SetInsideValue(1.0);
// set up pipeline
smoothFilter->SetInput(inputImage);
gradientMagnitudeFilter->SetInput(smoothFilter->GetOutput());
sigmoidFilter->SetInput(gradientMagnitudeFilter->GetOutput());
fastMarchingFilter->SetInput(sigmoidFilter->GetOutput());
thresholdFilter->SetInput(fastMarchingFilter->GetOutput());
thresholdFilter->Update();
segmentation->SetVolume((void*)(thresholdFilter->GetOutput()->GetPixelContainer()->GetBufferPointer()), timeStep);
}
void mitk::FastMarchingTool3D::UpdatePrepare()
{
// remove interaction with poinset while updating
if (m_SeedPointInteractor.IsNotNull())
m_SeedPointInteractor->SetDataNode(nullptr);
}
void mitk::FastMarchingTool3D::UpdateCleanUp()
{
// add interaction with poinset again
if (m_SeedPointInteractor.IsNotNull())
m_SeedPointInteractor->SetDataNode(m_SeedsAsPointSetNode);
}
void mitk::FastMarchingTool3D::DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep)
{
- if (nullptr != inputAtTimeStep && nullptr != previewImage && m_SeedContainer.IsNotNull() && !m_SeedContainer->empty())
+ if (nullptr != inputAtTimeStep && nullptr != previewImage && m_SeedContainer.IsNotNull())
{
AccessFixedDimensionByItk_n(inputAtTimeStep, DoITKFastMarching, 3, (previewImage, timeStep));
}
}
diff --git a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp
index 4dca280975..a75e5bd1ce 100644
--- a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp
+++ b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp
@@ -1,591 +1,593 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include <mitkContourModelUtils.h>
#include <mitkLiveWireTool2D.h>
#include <mitkLiveWireTool2D.xpm>
#include <mitkToolManager.h>
#include <usGetModuleContext.h>
#include <usModuleResource.h>
#include <type_traits>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, LiveWireTool2D, "LiveWire tool");
}
mitk::LiveWireTool2D::LiveWireTool2D()
: SegTool2D("LiveWireTool"), m_CreateAndUseDynamicCosts(false)
{
}
mitk::LiveWireTool2D::~LiveWireTool2D()
{
this->ClearSegmentation();
}
void mitk::LiveWireTool2D::RemoveHelperObjects()
{
auto dataStorage = m_ToolManager->GetDataStorage();
if (nullptr == dataStorage)
return;
for (const auto &editingContour : m_EditingContours)
dataStorage->Remove(editingContour.first);
for (const auto &workingContour : m_WorkingContours)
dataStorage->Remove(workingContour.first);
if (m_EditingContourNode.IsNotNull())
dataStorage->Remove(m_EditingContourNode);
if (m_LiveWireContourNode.IsNotNull())
dataStorage->Remove(m_LiveWireContourNode);
if (m_ContourNode.IsNotNull())
dataStorage->Remove(m_ContourNode);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::LiveWireTool2D::ReleaseHelperObjects()
{
this->RemoveHelperObjects();
m_EditingContours.clear();
m_WorkingContours.clear();
m_EditingContourNode = nullptr;
m_EditingContour = nullptr;
m_LiveWireContourNode = nullptr;
m_LiveWireContour = nullptr;
m_ContourNode = nullptr;
m_Contour = nullptr;
}
void mitk::LiveWireTool2D::ReleaseInteractors()
{
this->EnableContourLiveWireInteraction(false);
m_LiveWireInteractors.clear();
}
void mitk::LiveWireTool2D::ConnectActionsAndFunctions()
{
CONNECT_CONDITION("CheckContourClosed", OnCheckPoint);
CONNECT_FUNCTION("InitObject", OnInitLiveWire);
CONNECT_FUNCTION("AddPoint", OnAddPoint);
CONNECT_FUNCTION("CtrlAddPoint", OnAddPoint);
CONNECT_FUNCTION("MovePoint", OnMouseMoveNoDynamicCosts);
CONNECT_FUNCTION("FinishContour", OnFinish);
CONNECT_FUNCTION("DeletePoint", OnLastSegmentDelete);
CONNECT_FUNCTION("CtrlMovePoint", OnMouseMoved);
}
const char **mitk::LiveWireTool2D::GetXPM() const
{
return mitkLiveWireTool2D_xpm;
}
us::ModuleResource mitk::LiveWireTool2D::GetIconResource() const
{
return us::GetModuleContext()->GetModule()->GetResource("LiveWire_48x48.png");
}
us::ModuleResource mitk::LiveWireTool2D::GetCursorIconResource() const
{
return us::GetModuleContext()->GetModule()->GetResource("LiveWire_Cursor_32x32.png");
}
const char *mitk::LiveWireTool2D::GetName() const
{
return "Live Wire";
}
void mitk::LiveWireTool2D::Activated()
{
Superclass::Activated();
this->ResetToStartState();
this->EnableContourLiveWireInteraction(true);
}
void mitk::LiveWireTool2D::Deactivated()
{
this->ConfirmSegmentation();
Superclass::Deactivated();
}
void mitk::LiveWireTool2D::EnableContourLiveWireInteraction(bool on)
{
for (const auto &interactor : m_LiveWireInteractors)
interactor->EnableInteraction(on);
}
void mitk::LiveWireTool2D::ConfirmSegmentation()
{
auto referenceNode = m_ToolManager->GetReferenceData(0);
auto workingNode = m_ToolManager->GetWorkingData(0);
if (nullptr == referenceNode || nullptr == workingNode)
return;
auto referenceImage = dynamic_cast<Image *>(referenceNode->GetData());
auto workingImage = dynamic_cast<Image *>(workingNode->GetData());
if (nullptr == referenceImage || nullptr == workingImage)
return;
std::vector<SliceInformation> sliceInfos;
sliceInfos.reserve(m_WorkingContours.size());
for (const auto &workingContour : m_WorkingContours)
{
auto contour = dynamic_cast<ContourModel *>(workingContour.first->GetData());
if (nullptr == contour)
continue;
const auto numberOfTimeSteps = contour->GetTimeSteps();
for (std::remove_const_t<decltype(numberOfTimeSteps)> t = 0; t < numberOfTimeSteps; ++t)
{
if (contour->IsEmptyTimeStep(t))
continue;
TimePointType referenceImageTimePoint = referenceImage->GetTimeGeometry()->TimeStepToTimePoint(t);
TimeStepType workingImageTimeStep = workingImage->GetTimeGeometry()->TimePointToTimeStep(referenceImageTimePoint);
auto workingSlice = this->GetAffectedImageSliceAs2DImage(workingContour.second, workingImage, workingImageTimeStep);
auto projectedContour = ContourModelUtils::ProjectContourTo2DSlice(workingSlice, contour, true, false);
+ int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage);
- ContourModelUtils::FillContourInSlice(projectedContour, referenceImageTimePoint, workingSlice, workingImage, 1);
+ ContourModelUtils::FillContourInSlice(
+ projectedContour, referenceImageTimePoint, workingSlice, workingImage, activePixelValue);
sliceInfos.emplace_back(workingSlice, workingContour.second, referenceImageTimePoint);
this->WriteSliceToVolume(sliceInfos.back());
}
}
this->WriteBackSegmentationResult(sliceInfos, false);
this->ClearSegmentation();
}
void mitk::LiveWireTool2D::ClearSegmentation()
{
this->ReleaseHelperObjects();
this->ReleaseInteractors();
this->ResetToStartState();
}
bool mitk::LiveWireTool2D::IsPositionEventInsideImageRegion(mitk::InteractionPositionEvent *positionEvent,
mitk::BaseData *data)
{
bool isPositionEventInsideImageRegion = nullptr != data && data->GetGeometry()->IsInside(positionEvent->GetPositionInWorld());
if (!isPositionEventInsideImageRegion)
MITK_WARN("LiveWireTool2D") << "PositionEvent is outside ImageRegion!";
return isPositionEventInsideImageRegion;
}
void mitk::LiveWireTool2D::OnInitLiveWire(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (nullptr == positionEvent)
return;
auto workingDataNode = m_ToolManager->GetWorkingData(0);
if (!IsPositionEventInsideImageRegion(positionEvent, workingDataNode->GetData()))
{
this->ResetToStartState();
return;
}
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
auto t = positionEvent->GetSender()->GetTimeStep();
m_Contour = mitk::ContourModel::New();
m_Contour->Expand(t + 1);
m_ContourNode = mitk::DataNode::New();
m_ContourNode->SetData(m_Contour);
m_ContourNode->SetName("working contour node");
m_ContourNode->SetProperty("layer", IntProperty::New(100));
m_ContourNode->AddProperty("fixedLayer", BoolProperty::New(true));
m_ContourNode->SetProperty("helper object", mitk::BoolProperty::New(true));
m_ContourNode->AddProperty("contour.color", ColorProperty::New(1.0f, 1.0f, 0.0f), nullptr, true);
m_ContourNode->AddProperty("contour.points.color", ColorProperty::New(1.0f, 0.0f, 0.1f), nullptr, true);
m_ContourNode->AddProperty("contour.controlpoints.show", BoolProperty::New(true), nullptr, true);
m_LiveWireContour = mitk::ContourModel::New();
m_LiveWireContour->Expand(t + 1);
m_LiveWireContourNode = mitk::DataNode::New();
m_LiveWireContourNode->SetData(m_LiveWireContour);
m_LiveWireContourNode->SetName("active livewire node");
m_LiveWireContourNode->SetProperty("layer", IntProperty::New(101));
m_LiveWireContourNode->AddProperty("fixedLayer", BoolProperty::New(true));
m_LiveWireContourNode->SetProperty("helper object", mitk::BoolProperty::New(true));
m_LiveWireContourNode->AddProperty("contour.color", ColorProperty::New(0.1f, 1.0f, 0.1f), nullptr, true);
m_LiveWireContourNode->AddProperty("contour.width", mitk::FloatProperty::New(4.0f), nullptr, true);
m_EditingContour = mitk::ContourModel::New();
m_EditingContour->Expand(t + 1);
m_EditingContourNode = mitk::DataNode::New();
m_EditingContourNode->SetData(m_EditingContour);
m_EditingContourNode->SetName("editing node");
m_EditingContourNode->SetProperty("layer", IntProperty::New(102));
m_EditingContourNode->AddProperty("fixedLayer", BoolProperty::New(true));
m_EditingContourNode->SetProperty("helper object", mitk::BoolProperty::New(true));
m_EditingContourNode->AddProperty("contour.color", ColorProperty::New(0.1f, 1.0f, 0.1f), nullptr, true);
m_EditingContourNode->AddProperty("contour.points.color", ColorProperty::New(0.0f, 0.0f, 1.0f), nullptr, true);
m_EditingContourNode->AddProperty("contour.width", mitk::FloatProperty::New(4.0f), nullptr, true);
auto dataStorage = m_ToolManager->GetDataStorage();
dataStorage->Add(m_ContourNode, workingDataNode);
dataStorage->Add(m_LiveWireContourNode, workingDataNode);
dataStorage->Add(m_EditingContourNode, workingDataNode);
// Set current slice as input for ImageToLiveWireContourFilter
m_WorkingSlice = this->GetAffectedReferenceSlice(positionEvent);
auto origin = m_WorkingSlice->GetSlicedGeometry()->GetOrigin();
m_WorkingSlice->GetSlicedGeometry()->WorldToIndex(origin, origin);
m_WorkingSlice->GetSlicedGeometry()->IndexToWorld(origin, origin);
m_WorkingSlice->GetSlicedGeometry()->SetOrigin(origin);
m_LiveWireFilter = ImageLiveWireContourModelFilter::New();
m_LiveWireFilter->SetInput(m_WorkingSlice);
// Map click to pixel coordinates
auto click = positionEvent->GetPositionInWorld();
itk::Index<3> idx;
m_WorkingSlice->GetGeometry()->WorldToIndex(click, idx);
// Get the pixel with the highest gradient in a 7x7 region
itk::Index<3> indexWithHighestGradient;
AccessFixedDimensionByItk_2(m_WorkingSlice, FindHighestGradientMagnitudeByITK, 2, idx, indexWithHighestGradient);
click[0] = indexWithHighestGradient[0];
click[1] = indexWithHighestGradient[1];
click[2] = indexWithHighestGradient[2];
m_WorkingSlice->GetGeometry()->IndexToWorld(click, click);
// Set initial start point
m_Contour->AddVertex(click, true, t);
m_LiveWireFilter->SetStartPoint(click);
// Remember PlaneGeometry to determine if events were triggered in the same plane
m_PlaneGeometry = interactionEvent->GetSender()->GetCurrentWorldPlaneGeometry();
m_CreateAndUseDynamicCosts = true;
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::LiveWireTool2D::OnAddPoint(StateMachineAction *, InteractionEvent *interactionEvent)
{
// Complete LiveWire interaction for the last segment. Add current LiveWire contour to
// the finished contour and reset to start a new segment and computation.
auto positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (nullptr == positionEvent)
return;
if (m_PlaneGeometry.IsNotNull())
{
// Check if the point is in the correct slice
if (m_PlaneGeometry->DistanceFromPlane(positionEvent->GetPositionInWorld()) > mitk::sqrteps)
return;
}
auto t = static_cast<int>(positionEvent->GetSender()->GetTimeStep());
// Add repulsive points to avoid getting the same path again
std::for_each(m_LiveWireContour->IteratorBegin(), m_LiveWireContour->IteratorEnd(), [this](ContourElement::VertexType *vertex) {
ImageLiveWireContourModelFilter::InternalImageType::IndexType idx;
this->m_WorkingSlice->GetGeometry()->WorldToIndex(vertex->Coordinates, idx);
this->m_LiveWireFilter->AddRepulsivePoint(idx);
});
// Remove duplicate first vertex, it's already contained in m_Contour
m_LiveWireContour->RemoveVertexAt(0, t);
// Set last point as control point
m_LiveWireContour->SetControlVertexAt(m_LiveWireContour->GetNumberOfVertices(t) - 1, t);
// Merge contours
m_Contour->Concatenate(m_LiveWireContour, t);
// Clear the LiveWire contour and reset the corresponding DataNode
m_LiveWireContour->Clear(t);
// Set new start point
m_LiveWireFilter->SetStartPoint(positionEvent->GetPositionInWorld());
if (m_CreateAndUseDynamicCosts)
{
// Use dynamic cost map for next update
m_LiveWireFilter->CreateDynamicCostMap(m_Contour);
m_LiveWireFilter->SetUseDynamicCostMap(true);
}
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::LiveWireTool2D::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
// Compute LiveWire segment from last control point to current mouse position
auto positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (nullptr == positionEvent)
return;
auto t = positionEvent->GetSender()->GetTimeStep();
m_LiveWireFilter->SetEndPoint(positionEvent->GetPositionInWorld());
m_LiveWireFilter->SetTimeStep(t);
m_LiveWireFilter->Update();
m_LiveWireContour = this->m_LiveWireFilter->GetOutput();
m_LiveWireContourNode->SetData(this->m_LiveWireContour);
RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::LiveWireTool2D::OnMouseMoveNoDynamicCosts(StateMachineAction *, InteractionEvent *interactionEvent)
{
m_LiveWireFilter->SetUseDynamicCostMap(false);
this->OnMouseMoved(nullptr, interactionEvent);
m_LiveWireFilter->SetUseDynamicCostMap(true);
}
bool mitk::LiveWireTool2D::OnCheckPoint(const InteractionEvent *interactionEvent)
{
// Check double click on first control point to finish the LiveWire tool
auto positionEvent = dynamic_cast<const mitk::InteractionPositionEvent *>(interactionEvent);
if (nullptr == positionEvent)
return false;
auto t = static_cast<int>(positionEvent->GetSender()->GetTimeStep());
mitk::Point3D click = positionEvent->GetPositionInWorld();
mitk::Point3D first = this->m_Contour->GetVertexAt(0, t)->Coordinates;
return first.EuclideanDistanceTo(click) < 4.5;
}
void mitk::LiveWireTool2D::OnFinish(StateMachineAction *, InteractionEvent *interactionEvent)
{
// Finish LiveWire tool interaction
auto positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (nullptr == positionEvent)
return;
// Have to do that here so that the m_LastEventSender is set correctly
mitk::SegTool2D::AddContourmarker();
auto t = static_cast<int>(positionEvent->GetSender()->GetTimeStep());
// Remove last control point added by double click
m_Contour->RemoveVertexAt(m_Contour->GetNumberOfVertices(t) - 1, t);
// Save contour and corresponding plane geometry to list
this->m_WorkingContours.emplace_back(std::make_pair(m_ContourNode, positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()->Clone()));
this->m_EditingContours.emplace_back(std::make_pair(m_EditingContourNode, positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()->Clone()));
m_LiveWireFilter->SetUseDynamicCostMap(false);
this->FinishTool();
}
void mitk::LiveWireTool2D::FinishTool()
{
auto numberOfTimesteps = static_cast<int>(m_Contour->GetTimeGeometry()->CountTimeSteps());
for (int i = 0; i <= numberOfTimesteps; ++i)
m_Contour->Close(i);
m_ToolManager->GetDataStorage()->Remove(m_LiveWireContourNode);
m_LiveWireContourNode = nullptr;
m_LiveWireContour = nullptr;
m_ContourInteractor = mitk::ContourModelLiveWireInteractor::New();
m_ContourInteractor->SetDataNode(m_ContourNode);
m_ContourInteractor->LoadStateMachine("ContourModelModificationInteractor.xml", us::GetModuleContext()->GetModule());
m_ContourInteractor->SetEventConfig("ContourModelModificationConfig.xml", us::GetModuleContext()->GetModule());
m_ContourInteractor->SetWorkingImage(this->m_WorkingSlice);
m_ContourInteractor->SetEditingContourModelNode(this->m_EditingContourNode);
m_ContourNode->SetDataInteractor(m_ContourInteractor.GetPointer());
this->m_LiveWireInteractors.push_back(m_ContourInteractor);
}
void mitk::LiveWireTool2D::OnLastSegmentDelete(StateMachineAction *, InteractionEvent *interactionEvent)
{
int t = static_cast<int>(interactionEvent->GetSender()->GetTimeStep());
// If last point of current contour will be removed go to start state and remove nodes
if (m_Contour->GetNumberOfVertices(t) <= 1)
{
auto dataStorage = m_ToolManager->GetDataStorage();
dataStorage->Remove(m_LiveWireContourNode);
dataStorage->Remove(m_ContourNode);
dataStorage->Remove(m_EditingContourNode);
m_LiveWireContour = mitk::ContourModel::New();
m_LiveWireContourNode->SetData(m_LiveWireContour);
m_Contour = mitk::ContourModel::New();
m_ContourNode->SetData(m_Contour);
this->ResetToStartState();
}
else // Remove last segment from contour and reset LiveWire contour
{
m_LiveWireContour = mitk::ContourModel::New();
m_LiveWireContourNode->SetData(m_LiveWireContour);
auto newContour = mitk::ContourModel::New();
newContour->Expand(m_Contour->GetTimeSteps());
auto begin = m_Contour->IteratorBegin();
// Iterate from last point to next active point
auto newLast = m_Contour->IteratorBegin() + (m_Contour->GetNumberOfVertices() - 1);
// Go at least one down
if (newLast != begin)
--newLast;
// Search next active control point
while (newLast != begin && !((*newLast)->IsControlPoint))
--newLast;
// Set position of start point for LiveWire filter to coordinates of the new last point
m_LiveWireFilter->SetStartPoint((*newLast)->Coordinates);
auto it = m_Contour->IteratorBegin();
// Fll new Contour
while (it <= newLast)
{
newContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, t);
++it;
}
newContour->SetClosed(m_Contour->IsClosed());
m_ContourNode->SetData(newContour);
m_Contour = newContour;
mitk::RenderingManager::GetInstance()->RequestUpdate(interactionEvent->GetSender()->GetRenderWindow());
}
}
template <typename TPixel, unsigned int VImageDimension>
void mitk::LiveWireTool2D::FindHighestGradientMagnitudeByITK(itk::Image<TPixel, VImageDimension> *inputImage,
itk::Index<3> &index,
itk::Index<3> &returnIndex)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef typename InputImageType::IndexType IndexType;
const auto MAX_X = inputImage->GetLargestPossibleRegion().GetSize()[0];
const auto MAX_Y = inputImage->GetLargestPossibleRegion().GetSize()[1];
returnIndex[0] = index[0];
returnIndex[1] = index[1];
returnIndex[2] = 0.0;
double gradientMagnitude = 0.0;
double maxGradientMagnitude = 0.0;
// The size and thus the region of 7x7 is only used to calculate the gradient magnitude in that region,
// not for searching the maximum value.
// Maximum value in each direction for size
typename InputImageType::SizeType size;
size[0] = 7;
size[1] = 7;
// Minimum value in each direction for startRegion
IndexType startRegion;
startRegion[0] = index[0] - 3;
startRegion[1] = index[1] - 3;
if (startRegion[0] < 0)
startRegion[0] = 0;
if (startRegion[1] < 0)
startRegion[1] = 0;
if (MAX_X - index[0] < 7)
startRegion[0] = MAX_X - 7;
if (MAX_Y - index[1] < 7)
startRegion[1] = MAX_Y - 7;
index[0] = startRegion[0] + 3;
index[1] = startRegion[1] + 3;
typename InputImageType::RegionType region;
region.SetSize(size);
region.SetIndex(startRegion);
typedef typename itk::GradientMagnitudeImageFilter<InputImageType, InputImageType> GradientMagnitudeFilterType;
typename GradientMagnitudeFilterType::Pointer gradientFilter = GradientMagnitudeFilterType::New();
gradientFilter->SetInput(inputImage);
gradientFilter->GetOutput()->SetRequestedRegion(region);
gradientFilter->Update();
typename InputImageType::Pointer gradientMagnitudeImage;
gradientMagnitudeImage = gradientFilter->GetOutput();
IndexType currentIndex;
currentIndex[0] = 0;
currentIndex[1] = 0;
// Search max (approximate) gradient magnitude
for (int x = -1; x <= 1; ++x)
{
currentIndex[0] = index[0] + x;
for (int y = -1; y <= 1; ++y)
{
currentIndex[1] = index[1] + y;
gradientMagnitude = gradientMagnitudeImage->GetPixel(currentIndex);
// Check for new max
if (maxGradientMagnitude < gradientMagnitude)
{
maxGradientMagnitude = gradientMagnitude;
returnIndex[0] = currentIndex[0];
returnIndex[1] = currentIndex[1];
returnIndex[2] = 0.0;
}
}
currentIndex[1] = index[1];
}
}
diff --git a/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp
index 1cb67b63d1..de9837ba8d 100644
--- a/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp
@@ -1,594 +1,587 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkPaintbrushTool.h"
#include "ipSegmentation.h"
#include "mitkAbstractTransformGeometry.h"
#include "mitkBaseRenderer.h"
#include "mitkImageDataItem.h"
#include "mitkOverwriteSliceImageFilter.h"
#include "mitkToolManager.h"
#include "mitkContourModelUtils.h"
-#include "mitkLabelSetImage.h"
#include "mitkLevelWindowProperty.h"
int mitk::PaintbrushTool::m_Size = 1;
mitk::PaintbrushTool::PaintbrushTool(int paintingPixelValue)
: FeedbackContourTool("PressMoveReleaseWithCTRLInversionAllMouseMoves"),
m_PaintingPixelValue(paintingPixelValue),
m_LastContourSize(0) // other than initial mitk::PaintbrushTool::m_Size (around l. 28)
{
m_MasterContour = ContourModel::New();
m_MasterContour->Initialize();
m_CurrentPlane = nullptr;
m_WorkingNode = DataNode::New();
m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1)));
m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true));
}
mitk::PaintbrushTool::~PaintbrushTool()
{
}
void mitk::PaintbrushTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Move", OnPrimaryButtonPressedMoved);
CONNECT_FUNCTION("MouseMove", OnMouseMoved);
CONNECT_FUNCTION("Release", OnMouseReleased);
CONNECT_FUNCTION("InvertLogic", OnInvertLogic);
}
void mitk::PaintbrushTool::Activated()
{
Superclass::Activated();
FeedbackContourTool::SetFeedbackContourVisible(true);
SizeChanged.Send(m_Size);
m_ToolManager->WorkingDataChanged +=
mitk::MessageDelegate<mitk::PaintbrushTool>(this, &mitk::PaintbrushTool::OnToolManagerWorkingDataModified);
}
void mitk::PaintbrushTool::Deactivated()
{
FeedbackContourTool::SetFeedbackContourVisible(false);
if (m_ToolManager->GetDataStorage()->Exists(m_WorkingNode))
m_ToolManager->GetDataStorage()->Remove(m_WorkingNode);
m_WorkingSlice = nullptr;
m_CurrentPlane = nullptr;
m_ToolManager->WorkingDataChanged -=
mitk::MessageDelegate<mitk::PaintbrushTool>(this, &mitk::PaintbrushTool::OnToolManagerWorkingDataModified);
Superclass::Deactivated();
}
void mitk::PaintbrushTool::SetSize(int value)
{
m_Size = value;
}
mitk::Point2D mitk::PaintbrushTool::upperLeft(mitk::Point2D p)
{
p[0] -= 0.5;
p[1] += 0.5;
return p;
}
void mitk::PaintbrushTool::UpdateContour(const InteractionPositionEvent *positionEvent)
{
// MITK_INFO<<"Update...";
// examine stateEvent and create a contour that matches the pixel mask that we are going to draw
// mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
// const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent)
return;
// Get Spacing of current Slice
// mitk::Vector3D vSpacing = m_WorkingSlice->GetSlicedGeometry()->GetPlaneGeometry(0)->GetSpacing();
//
// Draw a contour in Square according to selected brush size
//
int radius = (m_Size) / 2;
float fradius = static_cast<float>(m_Size) / 2.0f;
ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
// estimate center point of the brush ( relative to the pixel the mouse points on )
// -- left upper corner for even sizes,
// -- midpoint for uneven sizes
mitk::Point2D centerCorrection;
centerCorrection.Fill(0);
// even --> correction of [+0.5, +0.5]
bool evenSize = ((m_Size % 2) == 0);
if (evenSize)
{
centerCorrection[0] += 0.5;
centerCorrection[1] += 0.5;
}
// we will compute the control points for the upper left quarter part of a circle contour
std::vector<mitk::Point2D> quarterCycleUpperRight;
std::vector<mitk::Point2D> quarterCycleLowerRight;
std::vector<mitk::Point2D> quarterCycleLowerLeft;
std::vector<mitk::Point2D> quarterCycleUpperLeft;
mitk::Point2D curPoint;
bool curPointIsInside = true;
curPoint[0] = 0;
curPoint[1] = radius;
quarterCycleUpperRight.push_back(upperLeft(curPoint));
// to estimate if a pixel is inside the circle, we need to compare against the 'outer radius'
// i.e. the distance from the midpoint [0,0] to the border of the pixel [0,radius]
// const float outer_radius = static_cast<float>(radius) + 0.5;
while (curPoint[1] > 0)
{
// Move right until pixel is outside circle
float curPointX_squared = 0.0f;
float curPointY_squared = (curPoint[1] - centerCorrection[1]) * (curPoint[1] - centerCorrection[1]);
while (curPointIsInside)
{
// increment posX and chec
curPoint[0]++;
curPointX_squared = (curPoint[0] - centerCorrection[0]) * (curPoint[0] - centerCorrection[0]);
const float len = sqrt(curPointX_squared + curPointY_squared);
if (len > fradius)
{
// found first Pixel in this horizontal line, that is outside the circle
curPointIsInside = false;
}
}
quarterCycleUpperRight.push_back(upperLeft(curPoint));
// Move down until pixel is inside circle
while (!curPointIsInside)
{
// increment posX and chec
curPoint[1]--;
curPointY_squared = (curPoint[1] - centerCorrection[1]) * (curPoint[1] - centerCorrection[1]);
const float len = sqrt(curPointX_squared + curPointY_squared);
if (len <= fradius)
{
// found first Pixel in this horizontal line, that is outside the circle
curPointIsInside = true;
quarterCycleUpperRight.push_back(upperLeft(curPoint));
}
// Quarter cycle is full, when curPoint y position is 0
if (curPoint[1] <= 0)
break;
}
}
// QuarterCycle is full! Now copy quarter cycle to other quarters.
if (!evenSize)
{
std::vector<mitk::Point2D>::const_iterator it = quarterCycleUpperRight.begin();
while (it != quarterCycleUpperRight.end())
{
mitk::Point2D p;
p = *it;
// the contour points in the lower right corner have same position but with negative y values
p[1] *= -1;
quarterCycleLowerRight.push_back(p);
// the contour points in the lower left corner have same position
// but with both x,y negative
p[0] *= -1;
quarterCycleLowerLeft.push_back(p);
// the contour points in the upper left corner have same position
// but with x negative
p[1] *= -1;
quarterCycleUpperLeft.push_back(p);
it++;
}
}
else
{
std::vector<mitk::Point2D>::const_iterator it = quarterCycleUpperRight.begin();
while (it != quarterCycleUpperRight.end())
{
mitk::Point2D p, q;
p = *it;
q = p;
// the contour points in the lower right corner have same position but with negative y values
q[1] *= -1;
// correct for moved offset if size even = the midpoint is not the midpoint of the current pixel
// but its upper rigt corner
q[1] += 1;
quarterCycleLowerRight.push_back(q);
q = p;
// the contour points in the lower left corner have same position
// but with both x,y negative
q[1] = -1.0f * q[1] + 1;
q[0] = -1.0f * q[0] + 1;
quarterCycleLowerLeft.push_back(q);
// the contour points in the upper left corner have same position
// but with x negative
q = p;
q[0] *= -1;
q[0] += 1;
quarterCycleUpperLeft.push_back(q);
it++;
}
}
// fill contour with poins in right ordering, starting with the upperRight block
mitk::Point3D tempPoint;
for (unsigned int i = 0; i < quarterCycleUpperRight.size(); i++)
{
tempPoint[0] = quarterCycleUpperRight[i][0];
tempPoint[1] = quarterCycleUpperRight[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
// the lower right has to be parsed in reverse order
for (int i = quarterCycleLowerRight.size() - 1; i >= 0; i--)
{
tempPoint[0] = quarterCycleLowerRight[i][0];
tempPoint[1] = quarterCycleLowerRight[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
for (unsigned int i = 0; i < quarterCycleLowerLeft.size(); i++)
{
tempPoint[0] = quarterCycleLowerLeft[i][0];
tempPoint[1] = quarterCycleLowerLeft[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
// the upper left also has to be parsed in reverse order
for (int i = quarterCycleUpperLeft.size() - 1; i >= 0; i--)
{
tempPoint[0] = quarterCycleUpperLeft[i][0];
tempPoint[1] = quarterCycleUpperLeft[i][1];
tempPoint[2] = 0;
contourInImageIndexCoordinates->AddVertex(tempPoint);
}
m_MasterContour = contourInImageIndexCoordinates;
}
/**
Just show the contour, get one point as the central point and add surrounding points to the contour.
*/
void mitk::PaintbrushTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
if (m_WorkingSlice.IsNull())
return;
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_WorkingSlice->GetGeometry()->WorldToIndex(positionEvent->GetPositionInWorld(), m_LastPosition);
// create new working node
// a fresh node is needed to only display the actual drawing process for
// the undo function
if (m_ToolManager->GetDataStorage()->Exists(m_WorkingNode))
m_ToolManager->GetDataStorage()->Remove(m_WorkingNode);
m_WorkingSlice = nullptr;
m_CurrentPlane = nullptr;
m_WorkingNode = DataNode::New();
m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1)));
m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true));
this->m_WorkingNode->SetVisibility(true);
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
m_MasterContour->SetClosed(true);
this->MouseMoved(interactionEvent, true);
}
void mitk::PaintbrushTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
MouseMoved(interactionEvent, false);
}
void mitk::PaintbrushTool::OnPrimaryButtonPressedMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
MouseMoved(interactionEvent, true);
}
/**
Insert the point to the feedback contour,finish to build the contour and at the same time the painting function
*/
void mitk::PaintbrushTool::MouseMoved(mitk::InteractionEvent *interactionEvent, bool leftMouseButtonPressed)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
CheckIfCurrentSliceHasChanged(positionEvent);
if (m_LastContourSize != m_Size)
{
UpdateContour(positionEvent);
m_LastContourSize = m_Size;
}
Point3D worldCoordinates = positionEvent->GetPositionInWorld();
Point3D indexCoordinates;
m_WorkingSlice->GetGeometry()->WorldToIndex(worldCoordinates, indexCoordinates);
// round to nearest voxel center (abort if this hasn't changed)
if (m_Size % 2 == 0) // even
{
indexCoordinates[0] = std::round(indexCoordinates[0]);
indexCoordinates[1] = std::round(indexCoordinates[1]);
}
else // odd
{
indexCoordinates[0] = std::round(indexCoordinates[0]);
indexCoordinates[1] = std::round(indexCoordinates[1]);
}
static Point3D lastPos; // uninitialized: if somebody finds out how this can be initialized in a one-liner, tell me
if (fabs(indexCoordinates[0] - lastPos[0]) > mitk::eps || fabs(indexCoordinates[1] - lastPos[1]) > mitk::eps ||
fabs(indexCoordinates[2] - lastPos[2]) > mitk::eps || leftMouseButtonPressed)
{
lastPos = indexCoordinates;
}
else
{
return;
}
int t = positionEvent->GetSender()->GetTimeStep();
auto contour = ContourModel::New();
contour->SetClosed(true);
auto it = m_MasterContour->Begin();
auto end = m_MasterContour->End();
while (it != end)
{
auto point = (*it)->Coordinates;
point[0] += indexCoordinates[0];
point[1] += indexCoordinates[1];
contour->AddVertex(point);
++it;
}
if (leftMouseButtonPressed)
{
const double dist = indexCoordinates.EuclideanDistanceTo(m_LastPosition);
const double radius = static_cast<double>(m_Size) / 2.0;
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
- Image::Pointer image = dynamic_cast<Image *>(workingNode->GetData());
- auto *labelImage = dynamic_cast<LabelSetImage *>(image.GetPointer());
-
- int activeColor = 1;
- if (labelImage)
- {
- activeColor = labelImage->GetActiveLabel(labelImage->GetActiveLayer())->GetValue();
- }
+ auto workingImage = dynamic_cast<Image*>(workingNode->GetData());
+ int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage);
// m_PaintingPixelValue only decides whether to paint or erase
mitk::ContourModelUtils::FillContourInSlice(
- contour, m_WorkingSlice, image, m_PaintingPixelValue * activeColor);
+ contour, m_WorkingSlice, workingImage, m_PaintingPixelValue * activePixelValue);
m_WorkingNode->SetData(m_WorkingSlice);
m_WorkingNode->Modified();
// if points are >= radius away draw rectangle to fill empty holes
// in between the 2 points
if (dist > radius)
{
const mitk::Point3D ¤tPos = indexCoordinates;
mitk::Point3D direction;
mitk::Point3D vertex;
mitk::Point3D normal;
direction[0] = indexCoordinates[0] - m_LastPosition[0];
direction[1] = indexCoordinates[1] - m_LastPosition[1];
direction[2] = indexCoordinates[2] - m_LastPosition[2];
direction[0] = direction.GetVnlVector().normalize()[0];
direction[1] = direction.GetVnlVector().normalize()[1];
direction[2] = direction.GetVnlVector().normalize()[2];
// 90 degrees rotation of direction
normal[0] = -1.0 * direction[1];
normal[1] = direction[0];
contour->Clear();
// upper left corner
vertex[0] = m_LastPosition[0] + (normal[0] * radius);
vertex[1] = m_LastPosition[1] + (normal[1] * radius);
contour->AddVertex(vertex);
// upper right corner
vertex[0] = currentPos[0] + (normal[0] * radius);
vertex[1] = currentPos[1] + (normal[1] * radius);
contour->AddVertex(vertex);
// lower right corner
vertex[0] = currentPos[0] - (normal[0] * radius);
vertex[1] = currentPos[1] - (normal[1] * radius);
contour->AddVertex(vertex);
// lower left corner
vertex[0] = m_LastPosition[0] - (normal[0] * radius);
vertex[1] = m_LastPosition[1] - (normal[1] * radius);
contour->AddVertex(vertex);
- mitk::ContourModelUtils::FillContourInSlice(contour, m_WorkingSlice, image, m_PaintingPixelValue * activeColor);
+ mitk::ContourModelUtils::FillContourInSlice(contour, m_WorkingSlice, workingImage, m_PaintingPixelValue * activePixelValue);
m_WorkingNode->SetData(m_WorkingSlice);
m_WorkingNode->Modified();
}
}
else
{
// switched from different renderwindow
// no activate hover highlighting. Otherwise undo / redo wont work
this->m_WorkingNode->SetVisibility(false);
}
m_LastPosition = indexCoordinates;
// visualize contour
ContourModel::Pointer displayContour = FeedbackContourTool::GetFeedbackContour();
displayContour->Clear();
ContourModel::Pointer tmp =
FeedbackContourTool::BackProjectContourFrom2DSlice(m_WorkingSlice->GetGeometry(), contour);
// copy transformed contour into display contour
it = tmp->Begin();
end = tmp->End();
while (it != end)
{
Point3D point = (*it)->Coordinates;
displayContour->AddVertex(point, t);
it++;
}
m_FeedbackContourNode->GetData()->Modified();
assert(positionEvent->GetSender()->GetRenderWindow());
RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::PaintbrushTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
// When mouse is released write segmentationresult back into image
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice->Clone());
// deactivate visibility of helper node
m_WorkingNode->SetVisibility(false);
RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
/**
Called when the CTRL key is pressed. Will change the painting pixel value from 0 to 1 or from 1 to 0.
*/
void mitk::PaintbrushTool::OnInvertLogic(StateMachineAction *, InteractionEvent *)
{
// Inversion only for 0 and 1 as painting values
if (m_PaintingPixelValue == 1)
{
m_PaintingPixelValue = 0;
FeedbackContourTool::SetFeedbackContourColor(1.0, 0.0, 0.0);
}
else if (m_PaintingPixelValue == 0)
{
m_PaintingPixelValue = 1;
FeedbackContourTool::SetFeedbackContourColorDefault();
}
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::PaintbrushTool::CheckIfCurrentSliceHasChanged(const InteractionPositionEvent *event)
{
const PlaneGeometry *planeGeometry((event->GetSender()->GetCurrentWorldPlaneGeometry()));
const auto *abstractTransformGeometry(
dynamic_cast<const AbstractTransformGeometry *>(event->GetSender()->GetCurrentWorldPlaneGeometry()));
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
Image::Pointer image = dynamic_cast<Image *>(workingNode->GetData());
if (!image || !planeGeometry || abstractTransformGeometry)
return;
if (m_CurrentPlane.IsNull() || m_WorkingSlice.IsNull())
{
m_CurrentPlane = planeGeometry;
m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone();
m_WorkingNode->ReplaceProperty("color", workingNode->GetProperty("color"));
m_WorkingNode->SetData(m_WorkingSlice);
}
else
{
bool isSameSlice(false);
isSameSlice = mitk::MatrixEqualElementWise(planeGeometry->GetIndexToWorldTransform()->GetMatrix(),
m_CurrentPlane->GetIndexToWorldTransform()->GetMatrix());
isSameSlice = mitk::Equal(planeGeometry->GetIndexToWorldTransform()->GetOffset(),
m_CurrentPlane->GetIndexToWorldTransform()->GetOffset());
if (!isSameSlice)
{
m_ToolManager->GetDataStorage()->Remove(m_WorkingNode);
m_CurrentPlane = nullptr;
m_WorkingSlice = nullptr;
m_WorkingNode = nullptr;
m_CurrentPlane = planeGeometry;
m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone();
m_WorkingNode = mitk::DataNode::New();
m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1)));
m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true));
m_WorkingNode->SetData(m_WorkingSlice);
// So that the paintbrush contour vanished in the previous render window
RenderingManager::GetInstance()->RequestUpdateAll();
}
}
if (!m_ToolManager->GetDataStorage()->Exists(m_WorkingNode))
{
m_WorkingNode->SetProperty("outline binary", mitk::BoolProperty::New(true));
m_WorkingNode->SetProperty("color", workingNode->GetProperty("color"));
m_WorkingNode->SetProperty("name", mitk::StringProperty::New("Paintbrush_Node"));
m_WorkingNode->SetProperty("helper object", mitk::BoolProperty::New(true));
m_WorkingNode->SetProperty("opacity", mitk::FloatProperty::New(0.8));
m_WorkingNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false));
m_WorkingNode->SetVisibility(
false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3")));
m_ToolManager->GetDataStorage()->Add(m_WorkingNode);
}
}
void mitk::PaintbrushTool::OnToolManagerWorkingDataModified()
{
// Here we simply set the current working slice to null. The next time the mouse is moved
// within a renderwindow a new slice will be extracted from the new working data
m_WorkingSlice = nullptr;
}
diff --git a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp
index 988d50cc5c..7a46716569 100644
--- a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp
@@ -1,664 +1,650 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkRegionGrowingTool.h"
#include "mitkApplicationCursor.h"
#include "mitkBaseRenderer.h"
#include "mitkImageDataItem.h"
#include "mitkImageToContourModelFilter.h"
#include "mitkOverwriteSliceImageFilter.h"
#include "mitkRegionGrowingTool.xpm"
#include "mitkRenderingManager.h"
#include "mitkToolManager.h"
#include "mitkExtractDirectedPlaneImageFilterNew.h"
#include "mitkLabelSetImage.h"
#include "mitkOverwriteDirectedPlaneImageFilter.h"
// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
// ITK
#include "mitkITKImageImport.h"
#include "mitkImageAccessByItk.h"
#include <itkConnectedComponentImageFilter.h>
#include <itkConnectedThresholdImageFilter.h>
#include <itkImageRegionIteratorWithIndex.h>
#include <itkNeighborhoodIterator.h>
#include <itkImageDuplicator.h>
#include <limits>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, RegionGrowingTool, "Region growing tool");
}
#define ROUND(a) ((a) > 0 ? (int)((a) + 0.5) : -(int)(0.5 - (a)))
mitk::RegionGrowingTool::RegionGrowingTool()
: FeedbackContourTool("PressMoveRelease"),
m_SeedValue(0),
m_ScreenYDifference(0),
m_ScreenXDifference(0),
m_MouseDistanceScaleFactor(0.5),
m_PaintingPixelValue(0),
m_FillFeedbackContour(true),
m_ConnectedComponentValue(1)
{
}
mitk::RegionGrowingTool::~RegionGrowingTool()
{
}
void mitk::RegionGrowingTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Move", OnMouseMoved);
CONNECT_FUNCTION("Release", OnMouseReleased);
}
const char **mitk::RegionGrowingTool::GetXPM() const
{
return mitkRegionGrowingTool_xpm;
}
us::ModuleResource mitk::RegionGrowingTool::GetIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("RegionGrowing_48x48.png");
return resource;
}
us::ModuleResource mitk::RegionGrowingTool::GetCursorIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("RegionGrowing_Cursor_32x32.png");
return resource;
}
const char *mitk::RegionGrowingTool::GetName() const
{
return "Region Growing";
}
void mitk::RegionGrowingTool::Activated()
{
Superclass::Activated();
}
void mitk::RegionGrowingTool::Deactivated()
{
Superclass::Deactivated();
}
// Get the average pixel value of square/cube with radius=neighborhood around index
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::GetNeighborhoodAverage(const itk::Image<TPixel, imageDimension> *itkImage,
const itk::Index<imageDimension>& index,
ScalarType *result,
unsigned int neighborhood)
{
// maybe assert that image dimension is only 2 or 3?
auto neighborhoodInt = (int)neighborhood;
TPixel averageValue(0);
unsigned int numberOfPixels = (2 * neighborhood + 1) * (2 * neighborhood + 1);
if (imageDimension == 3)
{
numberOfPixels *= (2 * neighborhood + 1);
}
MITK_DEBUG << "Getting neighborhood of " << numberOfPixels << " pixels around " << index;
itk::Index<imageDimension> currentIndex;
for (int i = (0 - neighborhoodInt); i <= neighborhoodInt; ++i)
{
currentIndex[0] = index[0] + i;
for (int j = (0 - neighborhoodInt); j <= neighborhoodInt; ++j)
{
currentIndex[1] = index[1] + j;
if (imageDimension == 3)
{
for (int k = (0 - neighborhoodInt); k <= neighborhoodInt; ++k)
{
currentIndex[2] = index[2] + k;
if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex))
{
averageValue += itkImage->GetPixel(currentIndex);
}
else
{
numberOfPixels -= 1;
}
}
}
else
{
if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex))
{
averageValue += itkImage->GetPixel(currentIndex);
}
else
{
numberOfPixels -= 1;
}
}
}
}
*result = (ScalarType)averageValue;
*result /= numberOfPixels;
}
// Check whether index lies inside a segmentation
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::IsInsideSegmentation(const itk::Image<TPixel, imageDimension> *itkImage,
const itk::Index<imageDimension>& index,
bool *result)
{
if (itkImage->GetPixel(index) > 0)
{
*result = true;
}
else
{
*result = false;
}
}
// Do the region growing (i.e. call an ITK filter that does it)
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::StartRegionGrowing(const itk::Image<TPixel, imageDimension> *inputImage,
const itk::Index<imageDimension>& seedIndex,
const std::array<ScalarType, 2>& thresholds,
mitk::Image::Pointer &outputImage)
{
MITK_DEBUG << "Starting region growing at index " << seedIndex << " with lower threshold " << thresholds[0]
<< " and upper threshold " << thresholds[1];
typedef itk::Image<TPixel, imageDimension> InputImageType;
typedef itk::Image<DefaultSegmentationDataType, imageDimension> OutputImageType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> RegionGrowingFilterType;
typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// perform region growing in desired segmented region
regionGrower->SetInput(inputImage);
regionGrower->SetSeed(seedIndex);
regionGrower->SetLower(thresholds[0]);
regionGrower->SetUpper(thresholds[1]);
try
{
regionGrower->Update();
}
catch (...)
{
return; // Should we do something?
}
typename OutputImageType::Pointer resultImage = regionGrower->GetOutput();
// Smooth result: Every pixel is replaced by the majority of the neighborhood
typedef itk::NeighborhoodIterator<OutputImageType> NeighborhoodIteratorType;
typedef itk::ImageRegionIterator<OutputImageType> ImageIteratorType;
typename NeighborhoodIteratorType::RadiusType radius;
radius.Fill(2); // for now, maybe make this something the user can adjust in the preferences?
typedef itk::ImageDuplicator< OutputImageType > DuplicatorType;
typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage(resultImage);
duplicator->Update();
typename OutputImageType::Pointer resultDup = duplicator->GetOutput();
NeighborhoodIteratorType neighborhoodIterator(radius, resultDup, resultDup->GetRequestedRegion());
ImageIteratorType imageIterator(resultImage, resultImage->GetRequestedRegion());
for (neighborhoodIterator.GoToBegin(), imageIterator.GoToBegin(); !neighborhoodIterator.IsAtEnd();
++neighborhoodIterator, ++imageIterator)
{
DefaultSegmentationDataType voteYes(0);
DefaultSegmentationDataType voteNo(0);
for (unsigned int i = 0; i < neighborhoodIterator.Size(); ++i)
{
if (neighborhoodIterator.GetPixel(i) > 0)
{
voteYes += 1;
}
else
{
voteNo += 1;
}
}
if (voteYes > voteNo)
{
imageIterator.Set(1);
}
else
{
imageIterator.Set(0);
}
}
if (resultImage.IsNull())
{
MITK_DEBUG << "Region growing result is empty.";
}
// Can potentially have multiple regions, use connected component image filter to label disjunct regions
typedef itk::ConnectedComponentImageFilter<OutputImageType, OutputImageType> ConnectedComponentImageFilterType;
typename ConnectedComponentImageFilterType::Pointer connectedComponentFilter =
ConnectedComponentImageFilterType::New();
connectedComponentFilter->SetInput(resultImage);
connectedComponentFilter->Update();
typename OutputImageType::Pointer resultImageCC = connectedComponentFilter->GetOutput();
m_ConnectedComponentValue = resultImageCC->GetPixel(seedIndex);
outputImage = mitk::GrabItkImageMemory(resultImageCC);
}
template <typename TPixel, unsigned int imageDimension>
void mitk::RegionGrowingTool::CalculateInitialThresholds(const itk::Image<TPixel, imageDimension>*)
{
LevelWindow levelWindow;
m_ToolManager->GetReferenceData(0)->GetLevelWindow(levelWindow);
m_ThresholdExtrema[0] = static_cast<ScalarType>(std::numeric_limits<TPixel>::lowest());
m_ThresholdExtrema[1] = static_cast<ScalarType>(std::numeric_limits<TPixel>::max());
const ScalarType lowerWindowBound = std::max(m_ThresholdExtrema[0], levelWindow.GetLowerWindowBound());
const ScalarType upperWindowBound = std::min(m_ThresholdExtrema[1], levelWindow.GetUpperWindowBound());
if (m_SeedValue < lowerWindowBound)
{
m_InitialThresholds = { m_ThresholdExtrema[0], lowerWindowBound };
}
else if (m_SeedValue > upperWindowBound)
{
m_InitialThresholds = { upperWindowBound, m_ThresholdExtrema[1] };
}
else
{
const ScalarType range = 0.1 * (upperWindowBound - lowerWindowBound); // 10% of the visible window
m_InitialThresholds[0] = std::min(std::max(lowerWindowBound, m_SeedValue - 0.5 * range), upperWindowBound - range);
m_InitialThresholds[1] = m_InitialThresholds[0] + range;
}
}
void mitk::RegionGrowingTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
- MITK_DEBUG << "OnMousePressed";
-
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
m_LastScreenPosition = positionEvent->GetPointerPositionOnScreen();
// ReferenceSlice is from the underlying image, WorkingSlice from the active segmentation (can be empty)
m_ReferenceSlice = FeedbackContourTool::GetAffectedReferenceSlice(positionEvent);
m_WorkingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent);
if (m_WorkingSlice.IsNotNull()) // can't do anything without a working slice (i.e. a possibly empty segmentation)
{
- MITK_DEBUG << "OnMousePressed: got working slice";
-
// 2. Determine if the user clicked inside or outside of the segmentation/working slice (i.e. the whole volume)
mitk::BaseGeometry::Pointer workingSliceGeometry;
workingSliceGeometry = m_WorkingSlice->GetGeometry();
workingSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), m_SeedPoint);
itk::Index<2> indexInWorkingSlice2D;
indexInWorkingSlice2D[0] = m_SeedPoint[0];
indexInWorkingSlice2D[1] = m_SeedPoint[1];
if (workingSliceGeometry->IsIndexInside(m_SeedPoint))
{
MITK_DEBUG << "OnMousePressed: point " << positionEvent->GetPositionInWorld() << " (index coordinates "
<< m_SeedPoint << ") is inside working slice";
// 3. determine the pixel value under the last click to determine what to do
bool inside(true);
AccessFixedDimensionByItk_2(m_WorkingSlice, IsInsideSegmentation, 2, indexInWorkingSlice2D, &inside);
m_PaintingPixelValue = inside ? 0 : 1;
if (inside)
{
MITK_DEBUG << "Clicked inside segmentation";
// For now, we're doing nothing when the user clicks inside the segmentation. Behaviour can be implemented via
// OnMousePressedInside()
// When you do, be sure to remove the m_PaintingPixelValue check in OnMouseMoved() and OnMouseReleased()
return;
}
else
{
MITK_DEBUG << "Clicked outside of segmentation";
OnMousePressedOutside(nullptr, interactionEvent);
}
}
}
}
// Use this to implement a behaviour for when the user clicks inside a segmentation (for example remove something)
// Old IpPic code is kept as comment for reference
void mitk::RegionGrowingTool::OnMousePressedInside()
{
// mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent
// );
// //const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent()); // checked in
// OnMousePressed
// // 3.1.1. Create a skeletonization of the segmentation and try to find a nice cut
// // apply the skeletonization-and-cut algorithm
// // generate contour to remove
// // set m_ReferenceSlice = nullptr so nothing will happen during mouse move
// // remember to fill the contour with 0 in mouserelease
// mitkIpPicDescriptor* segmentationHistory = ipMITKSegmentationCreateGrowerHistory( workingPicSlice,
// m_LastWorkingSeed, nullptr ); // free again
// if (segmentationHistory)
// {
// tCutResult cutContour = ipMITKSegmentationGetCutPoints( workingPicSlice, segmentationHistory,
// initialWorkingOffset ); // tCutResult is a ipSegmentation type
// mitkIpPicFree( segmentationHistory );
// if (cutContour.cutIt)
// {
// int timestep = positionEvent->GetSender()->GetTimeStep();
// // 3.1.2 copy point from float* to mitk::Contour
// ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New();
// contourInImageIndexCoordinates->Expand(timestep + 1);
// contourInImageIndexCoordinates->SetClosed(true, timestep);
// Point3D newPoint;
// for (int index = 0; index < cutContour.deleteSize; ++index)
// {
// newPoint[0] = cutContour.deleteCurve[ 2 * index + 0 ] - 0.5;//correction is needed because the
// output of the algorithm is center based
// newPoint[1] = cutContour.deleteCurve[ 2 * index + 1 ] - 0.5;//and we want our contour displayed
// corner based.
// newPoint[2] = 0.0;
// contourInImageIndexCoordinates->AddVertex( newPoint, timestep );
// }
// free(cutContour.traceline);
// free(cutContour.deleteCurve); // perhaps visualize this for fun?
// free(cutContour.onGradient);
// ContourModel::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice(
// m_WorkingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for
// ipSegmentation correction
// FeedbackContourTool::SetFeedbackContour( contourInWorldCoordinates );
// FeedbackContourTool::SetFeedbackContourVisible(true);
// mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
// m_FillFeedbackContour = true;
// }
// else
// {
// m_FillFeedbackContour = false;
// }
// }
// else
// {
// m_FillFeedbackContour = false;
// }
// m_ReferenceSlice = nullptr;
// return true;
}
void mitk::RegionGrowingTool::OnMousePressedOutside(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (positionEvent)
{
// Get geometry and indices
mitk::BaseGeometry::Pointer workingSliceGeometry;
workingSliceGeometry = m_WorkingSlice->GetGeometry();
itk::Index<2> indexInWorkingSlice2D;
indexInWorkingSlice2D[0] = m_SeedPoint[0];
indexInWorkingSlice2D[1] = m_SeedPoint[1];
mitk::BaseGeometry::Pointer referenceSliceGeometry;
referenceSliceGeometry =
m_ReferenceSlice->GetGeometry();
itk::Index<3> indexInReferenceSlice;
itk::Index<2> indexInReferenceSlice2D;
referenceSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), indexInReferenceSlice);
indexInReferenceSlice2D[0] = indexInReferenceSlice[0];
indexInReferenceSlice2D[1] = indexInReferenceSlice[1];
// Get seed neighborhood
ScalarType averageValue(0);
AccessFixedDimensionByItk_3(m_ReferenceSlice, GetNeighborhoodAverage, 2, indexInReferenceSlice2D, &averageValue, 1);
m_SeedValue = averageValue;
MITK_DEBUG << "Seed value is " << m_SeedValue;
// Calculate initial thresholds
AccessFixedDimensionByItk(m_ReferenceSlice, CalculateInitialThresholds, 2);
m_Thresholds[0] = m_InitialThresholds[0];
m_Thresholds[1] = m_InitialThresholds[1];
// Perform region growing
mitk::Image::Pointer resultImage = mitk::Image::New();
AccessFixedDimensionByItk_3(
m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage);
resultImage->SetGeometry(workingSliceGeometry);
// Extract contour
if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1)
{
float isoOffset = 0.33;
mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New();
contourExtractor->SetInput(resultImage);
contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset);
contourExtractor->Update();
ContourModel::Pointer resultContour = ContourModel::New();
resultContour = contourExtractor->GetOutput();
// Show contour
if (resultContour.IsNotNull())
{
ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice(
workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour));
// this is not a beautiful solution, just one that works, check T22412 for details
auto t = positionEvent->GetSender()->GetTimeStep();
FeedbackContourTool::SetFeedbackContour(0 != t
? ContourModelUtils::MoveZerothContourTimeStep(resultContourWorld, t)
: resultContourWorld);
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(m_LastEventSender->GetRenderWindow());
}
}
}
}
void mitk::RegionGrowingTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent)
{
// Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0,
// i.e. when the user clicked inside the segmentation
if (m_PaintingPixelValue == 0)
{
return;
}
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (m_ReferenceSlice.IsNotNull() && positionEvent)
{
// Get geometry and indices
mitk::BaseGeometry::Pointer workingSliceGeometry;
workingSliceGeometry = m_WorkingSlice->GetGeometry();
itk::Index<2> indexInWorkingSlice2D;
indexInWorkingSlice2D[0] = m_SeedPoint[0];
indexInWorkingSlice2D[1] = m_SeedPoint[1];
m_ScreenYDifference += positionEvent->GetPointerPositionOnScreen()[1] - m_LastScreenPosition[1];
m_ScreenXDifference += positionEvent->GetPointerPositionOnScreen()[0] - m_LastScreenPosition[0];
m_LastScreenPosition = positionEvent->GetPointerPositionOnScreen();
// Moving the mouse up and down adjusts the width of the threshold window,
// moving it left and right shifts the threshold window
m_Thresholds[0] = std::min(m_SeedValue, m_InitialThresholds[0] - (m_ScreenYDifference - m_ScreenXDifference) * m_MouseDistanceScaleFactor);
m_Thresholds[1] = std::max(m_SeedValue, m_InitialThresholds[1] + (m_ScreenYDifference + m_ScreenXDifference) * m_MouseDistanceScaleFactor);
// Do not exceed the pixel type extrema of the reference slice, though
m_Thresholds[0] = std::max(m_ThresholdExtrema[0], m_Thresholds[0]);
m_Thresholds[1] = std::min(m_ThresholdExtrema[1], m_Thresholds[1]);
// Perform region growing again and show the result
mitk::Image::Pointer resultImage = mitk::Image::New();
AccessFixedDimensionByItk_3(
m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage);
resultImage->SetGeometry(workingSliceGeometry);
// Update the contour
if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1)
{
float isoOffset = 0.33;
mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New();
contourExtractor->SetInput(resultImage);
contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset);
contourExtractor->Update();
ContourModel::Pointer resultContour = ContourModel::New();
resultContour = contourExtractor->GetOutput();
// Show contour
if (resultContour.IsNotNull())
{
ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice(
workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour));
// this is not a beautiful solution, just one that works, check T22412 for details
int timestep = positionEvent->GetSender()->GetTimeStep();
if (0 != timestep)
{
int size = resultContourWorld->GetNumberOfVertices(0);
auto resultContourTimeWorld = mitk::ContourModel::New();
resultContourTimeWorld->Expand(timestep + 1);
for (int loop = 0; loop < size; ++loop)
{
resultContourTimeWorld->AddVertex(resultContourWorld->GetVertexAt(loop, 0), timestep);
}
FeedbackContourTool::SetFeedbackContour(resultContourTimeWorld);
}
else
{
FeedbackContourTool::SetFeedbackContour(resultContourWorld);
}
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->ForceImmediateUpdate(positionEvent->GetSender()->GetRenderWindow());
}
}
}
}
void mitk::RegionGrowingTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
// Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0,
// i.e. when the user clicked inside the segmentation
if (m_PaintingPixelValue == 0)
{
return;
}
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (m_WorkingSlice.IsNotNull() && m_FillFeedbackContour && positionEvent)
{
// Project contour into working slice
ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour());
ContourModel::Pointer projectedContour;
// this is not a beautiful solution, just one that works, check T22412 for details
int timestep = positionEvent->GetSender()->GetTimeStep();
if (0 != timestep)
{
int size = feedbackContour->GetNumberOfVertices(timestep);
auto feedbackContourTime = mitk::ContourModel::New();
feedbackContourTime->Expand(timestep + 1);
for (int loop = 0; loop < size; ++loop)
{
feedbackContourTime->AddVertex(feedbackContour->GetVertexAt(loop, timestep), 0);
}
projectedContour =
FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, feedbackContourTime, false, false);
}
else
{
projectedContour =
FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, feedbackContour, false, false);
}
// If there is a projected contour, fill it
if (projectedContour.IsNotNull())
{
- // Get working data to pass to following method so we don't overwrite locked labels in a LabelSetImage
mitk::DataNode *workingNode(m_ToolManager->GetWorkingData(0));
- mitk::LabelSetImage *labelImage = workingNode != nullptr
- ? dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData())
- : nullptr;
-
- MITK_DEBUG << "Filling Segmentation";
-
- if (labelImage != nullptr)
+ if (nullptr == workingNode)
{
- // m_PaintingPixelValue only decides whether to paint or not
- // For LabelSetImages we want to paint with the active label value
- auto activeLabel = labelImage->GetActiveLabel(labelImage->GetActiveLayer())->GetValue();
- mitk::ContourModelUtils::FillContourInSlice(projectedContour,
- 0,
- m_WorkingSlice,
- labelImage,
- m_PaintingPixelValue * activeLabel);
+ return;
}
- else
+
+ auto workingImage = dynamic_cast<Image*>(workingNode->GetData());
+ if (nullptr == workingImage)
{
- mitk::ContourModelUtils::FillContourInSlice(projectedContour,
- 0,
- m_WorkingSlice,
- m_WorkingSlice,
- m_PaintingPixelValue);
+ return;
}
+
+ // m_PaintingPixelValue only decides whether to paint or erase
+ int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage);
+ mitk::ContourModelUtils::FillContourInSlice(
+ projectedContour, 0, m_WorkingSlice, workingImage, m_PaintingPixelValue * activePixelValue);
+
this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice);
FeedbackContourTool::SetFeedbackContourVisible(false);
}
m_ScreenYDifference = 0;
m_ScreenXDifference = 0;
}
}
diff --git a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp
index 4029a52fa9..bf0bbfe459 100644
--- a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp
+++ b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp
@@ -1,181 +1,176 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkSetRegionTool.h"
#include "mitkToolManager.h"
#include "mitkBaseRenderer.h"
#include "mitkImageDataItem.h"
#include "mitkLabelSetImage.h"
#include <mitkITKImageImport.h>
#include <mitkImagePixelReadAccessor.h>
#include <mitkImageToContourModelFilter.h>
#include <itkBinaryFillholeImageFilter.h>
#include <itkConnectedThresholdImageFilter.h>
mitk::SetRegionTool::SetRegionTool(int paintingPixelValue)
: FeedbackContourTool("PressMoveRelease"), m_PaintingPixelValue(paintingPixelValue)
{
}
mitk::SetRegionTool::~SetRegionTool()
{
}
void mitk::SetRegionTool::ConnectActionsAndFunctions()
{
CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed);
CONNECT_FUNCTION("Release", OnMouseReleased);
CONNECT_FUNCTION("Move", OnMouseMoved);
}
void mitk::SetRegionTool::Activated()
{
Superclass::Activated();
}
void mitk::SetRegionTool::Deactivated()
{
Superclass::Deactivated();
}
void mitk::SetRegionTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
m_LastEventSender = positionEvent->GetSender();
m_LastEventSlice = m_LastEventSender->GetSlice();
// 1. Get the working image
Image::Pointer workingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent);
if (workingSlice.IsNull())
return; // can't do anything without the segmentation
// if click was outside the image, don't continue
const BaseGeometry *sliceGeometry = workingSlice->GetGeometry();
itk::Index<3> projectedPointIn2D;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), projectedPointIn2D);
if (!sliceGeometry->IsIndexInside(projectedPointIn2D))
{
MITK_WARN << "Point outside of segmentation slice." << std::endl;
return; // can't use that as a seed point
}
typedef itk::Image<DefaultSegmentationDataType, 2> InputImageType;
typedef InputImageType::IndexType IndexType;
typedef itk::ConnectedThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
// convert world coordinates to image indices
IndexType seedIndex;
sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), seedIndex);
// perform region growing in desired segmented region
InputImageType::Pointer itkImage = InputImageType::New();
CastToItkImage(workingSlice, itkImage);
regionGrower->SetInput(itkImage);
regionGrower->AddSeed(seedIndex);
InputImageType::PixelType bound = itkImage->GetPixel(seedIndex);
regionGrower->SetLower(bound);
regionGrower->SetUpper(bound);
regionGrower->SetReplaceValue(1);
itk::BinaryFillholeImageFilter<InputImageType>::Pointer fillHolesFilter =
itk::BinaryFillholeImageFilter<InputImageType>::New();
fillHolesFilter->SetInput(regionGrower->GetOutput());
fillHolesFilter->SetForegroundValue(1);
// Store result and preview
mitk::Image::Pointer resultImage = mitk::GrabItkImageMemory(fillHolesFilter->GetOutput());
resultImage->SetGeometry(workingSlice->GetGeometry());
// Get the current working color
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
mitk::ImageToContourModelFilter::Pointer contourextractor = mitk::ImageToContourModelFilter::New();
contourextractor->SetInput(resultImage);
contourextractor->Update();
mitk::ContourModel::Pointer awesomeContour = contourextractor->GetOutput();
auto t = positionEvent->GetSender()->GetTimeStep();
FeedbackContourTool::SetFeedbackContour(0 != t
? ContourModelUtils::MoveZerothContourTimeStep(awesomeContour, t)
: awesomeContour);
FeedbackContourTool::SetFeedbackContourVisible(true);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
}
void mitk::SetRegionTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
auto *image = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (!image || !planeGeometry)
return;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image);
if (slice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour());
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice(
slice, feedbackContour, false, false); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull())
return;
- auto *labelImage = dynamic_cast<LabelSetImage *>(image);
- int activeColor = 1;
- if (labelImage != nullptr)
- {
- activeColor = labelImage->GetActiveLabel()->GetValue();
- }
+ int activePixelValue = ContourModelUtils::GetActivePixelValue(image);
mitk::ContourModelUtils::FillContourInSlice(
- projectedContour, timeStep, slice, image, m_PaintingPixelValue * activeColor);
+ projectedContour, timeStep, slice, image, m_PaintingPixelValue * activePixelValue);
this->WriteBackSegmentationResult(positionEvent, slice);
}
void mitk::SetRegionTool::OnMouseMoved(mitk::StateMachineAction *, mitk::InteractionEvent *)
{
}
diff --git a/Modules/ToFHardware/CMakeLists.txt b/Modules/ToFHardware/CMakeLists.txt
index 3c591fa061..f6f70f68c1 100644
--- a/Modules/ToFHardware/CMakeLists.txt
+++ b/Modules/ToFHardware/CMakeLists.txt
@@ -1,32 +1,32 @@
#Define the platform string
mitkMacroGetPMDPlatformString(_PLATFORM_STRING)
MITK_CREATE_MODULE(
DEPENDS MitkOpenCVVideoSupport MitkIGTBase MitkCameraCalibration MitkIpPic
- PACKAGE_DEPENDS ITK|ITKIONRRD
+ PACKAGE_DEPENDS PRIVATE ITK|IONRRD
ADDITIONAL_LIBS ${ADDITIONAL_LIBS}
)
# set(tofHardware_srcs )
# usFunctionEmbedResources(tofHardware_srcs
# LIBRARY_NAME mitkToFHardware
# ROOT_DIR ${MITK_DATA_DIR}/ToF-Data/CalibrationFiles
# FILES Default_Parameters.xml Kinect_IR_camera.xml Kinect_RGB_camera.xml Mesa-SR4000_Camera.xml PMDCamBoard_camera.xml PMDCamCube2_camera.xml PMDCamCube3_camera.xml
# )
add_subdirectory(Testing)
add_subdirectory(Kinect)
add_subdirectory(KinectV2)
add_subdirectory(PMD)
add_subdirectory(MesaSR4000)
# Install external libraries which are not directly linked to a MITK module
include(${CMAKE_CURRENT_SOURCE_DIR}/mitkToFHardwareInstallRules.cmake)
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/mitkToFHardwareInstallRules.cmake
${PROJECT_BINARY_DIR}/mitkToFHardwareInstallRules.cmake COPYONLY)
CONFIGURE_FILE(mitkToFConfig.h.in ${PROJECT_BINARY_DIR}/mitkToFConfig.h @ONLY)
#foreach(tofhardwaresubfolder_dir ${tofhardwaresubfolder_dirs})
# add_subdirectory(${tofhardwaresubfolder_dirs})
#endforeach()
diff --git a/Modules/ToFHardware/mitkAbstractToFDeviceFactory.cpp b/Modules/ToFHardware/mitkAbstractToFDeviceFactory.cpp
index 383feb2ae0..1106656ccb 100644
--- a/Modules/ToFHardware/mitkAbstractToFDeviceFactory.cpp
+++ b/Modules/ToFHardware/mitkAbstractToFDeviceFactory.cpp
@@ -1,82 +1,83 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkAbstractToFDeviceFactory.h"
#include <mitkCameraIntrinsics.h>
#include <mitkCameraIntrinsicsProperty.h>
//Microservices
#include <usModuleContext.h>
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleResource.h>
#include <usModuleResourceStream.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
mitk::ToFCameraDevice::Pointer mitk::AbstractToFDeviceFactory::ConnectToFDevice()
{
ToFCameraDevice::Pointer device = CreateToFCameraDevice();
mitk::CameraIntrinsics::Pointer cameraIntrinsics = GetCameraIntrinsics();
device->SetProperty("CameraIntrinsics", mitk::CameraIntrinsicsProperty::New(cameraIntrinsics));
m_Devices.push_back(device);
us::ModuleContext* context = us::GetModuleContext();
us::ServiceProperties deviceProps;
deviceProps["ToFDeviceName"] = GetCurrentDeviceName();
m_DeviceRegistrations.insert(std::make_pair(device.GetPointer(), context->RegisterService(device.GetPointer(),deviceProps)));
return device;
}
void mitk::AbstractToFDeviceFactory::DisconnectToFDevice(const ToFCameraDevice::Pointer& device)
{
std::map<ToFCameraDevice*,us::ServiceRegistration<ToFCameraDevice> >::iterator i = m_DeviceRegistrations.find(device.GetPointer());
if (i == m_DeviceRegistrations.end()) return;
i->second.Unregister();
m_DeviceRegistrations.erase(i);
m_Devices.erase(std::remove(m_Devices.begin(), m_Devices.end(), device), m_Devices.end());
}
size_t mitk::AbstractToFDeviceFactory::GetNumberOfDevices()
{
return m_Devices.size();
}
mitk::CameraIntrinsics::Pointer mitk::AbstractToFDeviceFactory::GetCameraIntrinsics()
{
us::ModuleResource resource = GetIntrinsicsResource();
if (! resource.IsValid())
{
MITK_WARN << "Could not load resource '" << resource.GetName() << "'. CameraIntrinsics are invalid!";
}
// Create ResourceStream from Resource
us::ModuleResourceStream resStream(resource);
+ std::string resString(std::istreambuf_iterator<char>(resStream), {});
// Parse XML
- TiXmlDocument xmlDocument;
- resStream >> xmlDocument;
+ tinyxml2::XMLDocument xmlDocument;
+ xmlDocument.Parse(resString.c_str());
//Retrieve Child Element and convert to CamerIntrinsics
- TiXmlElement* element = xmlDocument.FirstChildElement();
+ auto* element = xmlDocument.FirstChildElement();
mitk::CameraIntrinsics::Pointer intrinsics = mitk::CameraIntrinsics::New();
intrinsics->FromXML(element);
return intrinsics;
}
us::ModuleResource mitk::AbstractToFDeviceFactory::GetIntrinsicsResource()
{
us::Module* module = us::GetModuleContext()->GetModule();
return module->GetResource("CalibrationFiles/Default_Parameters.xml");
MITK_WARN << "Loaded Default CameraIntrinsics. Overwrite AbstractToFDeviceFactory::GetIntrinsicsResource() if you want to define your own.";
}
diff --git a/Modules/ToFProcessing/Testing/CMakeLists.txt b/Modules/ToFProcessing/Testing/CMakeLists.txt
index 5c76b6f021..237d89c83a 100644
--- a/Modules/ToFProcessing/Testing/CMakeLists.txt
+++ b/Modules/ToFProcessing/Testing/CMakeLists.txt
@@ -1,12 +1,10 @@
MITK_CREATE_MODULE_TESTS()
if(TARGET ${TESTDRIVER})
- mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK|ITKThresholding)
-
mitkAddCustomModuleTest(mitkKinectReconstructionTest_LegoPhantom mitkKinectReconstructionTest
${MITK_DATA_DIR}/ToF-Data/CalibrationFiles/Kinect_RGB_camera.xml #camera intrinsics
${MITK_DATA_DIR}/ToF-Data/Kinect_Lego_Phantom_DistanceImage.nrrd #kinect distance image
)
#mitkAddCustomModuleTest(mitkToFImageDownsamplingFilterTest_20 mitkToFImageDownsamplingFilterTest PMDCamCube2_MF0_IT0_20Images_DistanceImage.pic)
#mitkAddCustomModuleTest(mitkToFImageDownsamplingFilterTest_1 mitkToFImageDownsamplingFilterTest PMDCamCube2_MF0_IT0_1Images_DistanceImage.pic)
endif()
diff --git a/Modules/TubeGraph/CMakeLists.txt b/Modules/TubeGraph/CMakeLists.txt
index 1d4949980d..13e719c1a9 100644
--- a/Modules/TubeGraph/CMakeLists.txt
+++ b/Modules/TubeGraph/CMakeLists.txt
@@ -1,19 +1,6 @@
-set(disable_module 0)
-if(GCC_VERSION VERSION_GREATER 0 AND
- GCC_VERSION VERSION_LESS 4.7)
- # The Boost Graph library at least up to version 1.57 does not
- # compile with gcc < 4.7 and -std=c++0x, see
- # http://stackoverflow.com/questions/25395805/compile-error-with-boost-graph-1-56-0-and-g-4-6-4
- set(disable_module 1)
-endif()
-
-if(NOT disable_module)
-
MITK_CREATE_MODULE(
INCLUDE_DIRS PRIVATE src/Algorithms src/DataStructure src/Interactions src/Rendering src/IO
DEPENDS MitkSceneSerializationBase
)
#add_subdirectory(test)
-
-endif()
diff --git a/Modules/TubeGraph/include/mitkTubeGraphIO.h b/Modules/TubeGraph/include/mitkTubeGraphIO.h
index b4a0b0afea..35f4bcaa95 100644
--- a/Modules/TubeGraph/include/mitkTubeGraphIO.h
+++ b/Modules/TubeGraph/include/mitkTubeGraphIO.h
@@ -1,71 +1,69 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef _MITK_TUBE_GRAPH_IO_H_
#define _MITK_TUBE_GRAPH_IO_H_
#include <mitkAbstractFileIO.h>
#include <mitkCustomMimeType.h>
#include <mitkIOMimeTypes.h>
#include "mitkTubeGraph.h"
-class TiXmlElement;
-
namespace mitk
{
/**
* @brief reader and writer for xml representations of mitk::TubeGraph
*
* @ingroup IO
*/
class TubeGraphIO : public mitk::AbstractFileIO
{
public:
TubeGraphIO();
// -------------- AbstractFileReader -------------
using AbstractFileReader::Read;
ConfidenceLevel GetReaderConfidenceLevel() const override;
// -------------- AbstractFileWriter -------------
void Write() override;
ConfidenceLevel GetWriterConfidenceLevel() const override;
static CustomMimeType TUBEGRAPH_MIMETYPE() // tsf
{
CustomMimeType mimeType(TUBEGRAPH_MIMETYPE_NAME());
mimeType.AddExtension("tsf");
mimeType.SetCategory("Graphs");
mimeType.SetComment("MITK Tube Graph Structure File");
return mimeType;
}
static std::string TUBEGRAPH_MIMETYPE_NAME()
{
static std::string name = mitk::IOMimeTypes::DEFAULT_BASE_NAME() + ".graphs.tubular-sructure";
return name;
}
protected:
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
private:
TubeGraphIO *IOClone() const override;
TubeGraphIO(const TubeGraphIO &other);
const BoundingBox::Pointer ComputeBoundingBox(TubeGraph::Pointer graph) const;
};
}
#endif //_MITK_SURFACE_VTK_IO_H_
diff --git a/Modules/TubeGraph/src/IO/mitkTubeGraphIO.cpp b/Modules/TubeGraph/src/IO/mitkTubeGraphIO.cpp
index 9d764365d5..9edfb8e2d9 100644
--- a/Modules/TubeGraph/src/IO/mitkTubeGraphIO.cpp
+++ b/Modules/TubeGraph/src/IO/mitkTubeGraphIO.cpp
@@ -1,593 +1,580 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkTubeGraphIO.h"
#include "mitkCircularProfileTubeElement.h"
#include "mitkTubeGraphDefinitions.h"
#include "mitkTubeGraphProperty.h"
#include <mitkIOMimeTypes.h>
-#include <tinyxml.h>
+#include <tinyxml2.h>
#include <vtkMatrix4x4.h>
#include <itksys/SystemTools.hxx>
namespace mitk
{
TubeGraphIO::TubeGraphIO(const TubeGraphIO &other) : AbstractFileIO(other) {}
TubeGraphIO::TubeGraphIO()
: AbstractFileIO(
mitk::TubeGraph::GetStaticNameOfClass(), mitk::TubeGraphIO::TUBEGRAPH_MIMETYPE(), "Tube Graph Structure File")
{
this->RegisterService();
}
std::vector<BaseData::Pointer> TubeGraphIO::DoRead()
{
std::locale::global(std::locale("C"));
std::vector<itk::SmartPointer<mitk::BaseData>> result;
InputStream stream(this);
+ std::string string(std::istreambuf_iterator<char>(stream), {});
+ tinyxml2::XMLDocument doc;
- TiXmlDocument doc;
- stream >> doc;
- if (!doc.Error())
+ if (tinyxml2::XML_SUCCESS == doc.Parse(string.c_str()))
{
TubeGraph::Pointer newTubeGraph = TubeGraph::New();
- TiXmlHandle hDoc(&doc);
- TiXmlElement *pElem;
- TiXmlHandle hRoot(nullptr);
-
- pElem = hDoc.FirstChildElement().Element();
-
- // save this for later
- hRoot = TiXmlHandle(pElem);
-
- pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_GEOMETRY).Element();
+ tinyxml2::XMLHandle hDoc(&doc);
+ tinyxml2::XMLHandle hRoot = hDoc.FirstChildElement();
+ tinyxml2::XMLElement *pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_GEOMETRY.c_str()).ToElement();
// read geometry
mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
geometry->Initialize();
// read origin
mitk::Point3D origin;
double temp = 0;
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_ORIGIN_X, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_X.c_str(), &temp);
origin[0] = temp;
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Y, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Y.c_str(), &temp);
origin[1] = temp;
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Z, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Z.c_str(), &temp);
origin[2] = temp;
geometry->SetOrigin(origin);
// read spacing
Vector3D spacing;
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_SPACING_X, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_SPACING_X.c_str(), &temp);
spacing.SetElement(0, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_SPACING_Y, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_SPACING_Y.c_str(), &temp);
spacing.SetElement(1, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_SPACING_Z, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_SPACING_Z.c_str(), &temp);
spacing.SetElement(2, temp);
geometry->SetSpacing(spacing);
// read transform
vtkMatrix4x4 *m = vtkMatrix4x4::New();
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_XX, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XX.c_str(), &temp);
m->SetElement(0, 0, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_XY, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XY.c_str(), &temp);
m->SetElement(1, 0, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_XZ, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XZ.c_str(), &temp);
m->SetElement(2, 0, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_YX, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YX.c_str(), &temp);
m->SetElement(0, 1, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_YY, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YY.c_str(), &temp);
m->SetElement(1, 1, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_YZ, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YZ.c_str(), &temp);
m->SetElement(2, 1, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZX, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZX.c_str(), &temp);
m->SetElement(0, 2, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZY, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZY.c_str(), &temp);
m->SetElement(1, 2, temp);
- pElem->Attribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZZ, &temp);
+ pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZZ.c_str(), &temp);
m->SetElement(2, 2, temp);
m->SetElement(0, 3, origin[0]);
m->SetElement(1, 3, origin[1]);
m->SetElement(2, 3, origin[2]);
m->SetElement(3, 3, 1);
geometry->SetIndexToWorldTransformByVtkMatrix(m);
geometry->SetImageGeometry(false);
// read tube graph
// read vertices
- pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_VERTICES).Element();
+ pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_VERTICES.c_str()).ToElement();
if (pElem != nullptr)
{
// walk through the vertices
- for (TiXmlElement *vertexElement = pElem->FirstChildElement(); vertexElement != nullptr; vertexElement = vertexElement->NextSiblingElement())
+ for (auto *vertexElement = pElem->FirstChildElement(); vertexElement != nullptr; vertexElement = vertexElement->NextSiblingElement())
{
int vertexID(0);
mitk::Point3D coordinate;
coordinate.Fill(0.0);
double diameter(0);
- vertexElement->Attribute(mitk::TubeGraphDefinitions::XML_VERTEX_ID, &vertexID);
+ vertexElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_VERTEX_ID.c_str(), &vertexID);
- TiXmlElement *tubeElement = vertexElement->FirstChildElement();
+ auto *tubeElement = vertexElement->FirstChildElement();
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X, &temp);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(), &temp);
coordinate[0] = temp;
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y, &temp);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(), &temp);
coordinate[1] = temp;
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z, &temp);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(), &temp);
coordinate[2] = temp;
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER, &diameter);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(), &diameter);
mitk::TubeGraphVertex vertexData;
auto *newElement = new mitk::CircularProfileTubeElement(coordinate, diameter);
vertexData.SetTubeElement(newElement);
mitk::TubeGraph::VertexDescriptorType newVertex = newTubeGraph->AddVertex(vertexData);
if (static_cast<int>(newVertex) != vertexID)
{
MITK_ERROR << "Aborting tube graph creation, different vertex ids.";
return result;
;
}
}
}
// read edges
- pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_EDGES).Element();
+ pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_EDGES.c_str()).ToElement();
if (pElem != nullptr)
{
// walk through the edges
auto edgeElement = pElem->FirstChildElement();
for ( ; edgeElement != nullptr; edgeElement = edgeElement->NextSiblingElement())
{
int edgeID(0), edgeSourceID(0), edgeTargetID(0);
mitk::Point3D coordinate;
double diameter(0);
- edgeElement->Attribute(mitk::TubeGraphDefinitions::XML_EDGE_ID, &edgeID);
- edgeElement->Attribute(mitk::TubeGraphDefinitions::XML_EDGE_SOURCE_ID, &edgeSourceID);
- edgeElement->Attribute(mitk::TubeGraphDefinitions::XML_EDGE_TARGET_ID, &edgeTargetID);
+ edgeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_EDGE_ID.c_str(), &edgeID);
+ edgeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_EDGE_SOURCE_ID.c_str(), &edgeSourceID);
+ edgeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_EDGE_TARGET_ID.c_str(), &edgeTargetID);
mitk::TubeGraphEdge edgeData;
- for (TiXmlElement *tubeElement = edgeElement->FirstChildElement(mitk::TubeGraphDefinitions::XML_ELEMENT); tubeElement != nullptr; tubeElement = tubeElement->NextSiblingElement())
+ for (auto *tubeElement = edgeElement->FirstChildElement(mitk::TubeGraphDefinitions::XML_ELEMENT.c_str()); tubeElement != nullptr; tubeElement = tubeElement->NextSiblingElement())
{
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X, &temp);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(), &temp);
coordinate[0] = temp;
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y, &temp);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(), &temp);
coordinate[1] = temp;
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z, &temp);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(), &temp);
coordinate[2] = temp;
- tubeElement->Attribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER, &diameter);
+ tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(), &diameter);
auto *newElement = new mitk::CircularProfileTubeElement(coordinate, diameter);
edgeData.AddTubeElement(newElement);
}
try
{
newTubeGraph->AddEdge(edgeSourceID, edgeTargetID, edgeData);
}
catch (const std::runtime_error &error)
{
MITK_ERROR << error.what();
return result;
}
}
}
// Compute bounding box
BoundingBox::Pointer bb = this->ComputeBoundingBox(newTubeGraph);
geometry->SetBounds(bb->GetBounds());
MITK_INFO << "Tube Graph read";
MITK_INFO << "Edge numb:" << newTubeGraph->GetNumberOfEdges()
<< " Vertices: " << newTubeGraph->GetNumberOfVertices();
MITK_INFO << "Reading tube graph property";
mitk::TubeGraphProperty::Pointer newProperty = mitk::TubeGraphProperty::New();
// read label groups
- pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_LABELGROUPS).Element();
+ pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_LABELGROUPS.c_str()).ToElement();
if (pElem != nullptr)
{
// walk through the label groups
- for (TiXmlElement *labelGroupElement = pElem->FirstChildElement(); labelGroupElement != nullptr; labelGroupElement = labelGroupElement->NextSiblingElement())
+ for (auto *labelGroupElement = pElem->FirstChildElement(); labelGroupElement != nullptr; labelGroupElement = labelGroupElement->NextSiblingElement())
{
auto *newLabelGroup = new mitk::TubeGraphProperty::LabelGroup();
const char *labelGroupName;
labelGroupName =
labelGroupElement->Attribute((char *)mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME.c_str());
if (labelGroupName)
newLabelGroup->labelGroupName = labelGroupName;
- for (TiXmlElement *labelElement = labelGroupElement->FirstChildElement(mitk::TubeGraphDefinitions::XML_LABEL); labelElement != nullptr; labelElement = labelElement->NextSiblingElement())
+ for (auto *labelElement = labelGroupElement->FirstChildElement(mitk::TubeGraphDefinitions::XML_LABEL.c_str()); labelElement != nullptr; labelElement = labelElement->NextSiblingElement())
{
auto *newLabel = new mitk::TubeGraphProperty::LabelGroup::Label();
const char *labelName;
bool isVisible = true;
Color color;
labelName = labelElement->Attribute((char *)mitk::TubeGraphDefinitions::XML_LABEL_NAME.c_str());
if (labelName)
newLabel->labelName = labelName;
- labelElement->Attribute(mitk::TubeGraphDefinitions::XML_LABEL_VISIBILITY, &temp);
+ labelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_LABEL_VISIBILITY.c_str(), &temp);
if (temp == 0)
isVisible = false;
else
isVisible = true;
- labelElement->Attribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_R, &temp);
+ labelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_R.c_str(), &temp);
color[0] = temp;
- labelElement->Attribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_G, &temp);
+ labelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_G.c_str(), &temp);
color[1] = temp;
- labelElement->Attribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_B, &temp);
+ labelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_B.c_str(), &temp);
color[2] = temp;
newLabel->isVisible = isVisible;
newLabel->labelColor = color;
newLabelGroup->labels.push_back(newLabel);
}
newProperty->AddLabelGroup(newLabelGroup, newProperty->GetLabelGroups().size());
}
}
// read attributations
- pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_ATTRIBUTIONS).Element();
+ pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_ATTRIBUTIONS.c_str()).ToElement();
if (pElem != nullptr)
{
std::map<TubeGraphProperty::TubeToLabelGroupType, std::string> tubeToLabelsMap;
- for (TiXmlElement *tubeToLabelElement = pElem->FirstChildElement(); tubeToLabelElement != nullptr; tubeToLabelElement = tubeToLabelElement->NextSiblingElement())
+ for (auto *tubeToLabelElement = pElem->FirstChildElement(); tubeToLabelElement != nullptr; tubeToLabelElement = tubeToLabelElement->NextSiblingElement())
{
TubeGraph::TubeDescriptorType tube;
auto *labelGroup = new mitk::TubeGraphProperty::LabelGroup();
auto *label = new mitk::TubeGraphProperty::LabelGroup::Label();
- tubeToLabelElement->Attribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1, &temp);
+ tubeToLabelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1.c_str(), &temp);
tube.first = temp;
- tubeToLabelElement->Attribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2, &temp);
+ tubeToLabelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2.c_str(), &temp);
tube.second = temp;
const char *labelGroupName =
- tubeToLabelElement->Attribute((char *)mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME.c_str());
+ tubeToLabelElement->Attribute(mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME.c_str());
if (labelGroupName)
labelGroup = newProperty->GetLabelGroupByName(labelGroupName);
const char *labelName =
- tubeToLabelElement->Attribute((char *)mitk::TubeGraphDefinitions::XML_LABEL_NAME.c_str());
+ tubeToLabelElement->Attribute(mitk::TubeGraphDefinitions::XML_LABEL_NAME.c_str());
if (labelName)
label = newProperty->GetLabelByName(labelGroup, labelName);
if (tube != TubeGraph::ErrorId && labelGroup != nullptr && label != nullptr)
{
TubeGraphProperty::TubeToLabelGroupType tubeToLabelGroup(tube, labelGroupName);
tubeToLabelsMap.insert(
std::pair<TubeGraphProperty::TubeToLabelGroupType, std::string>(tubeToLabelGroup, labelName));
}
}
if (tubeToLabelsMap.size() > 0)
newProperty->SetTubesToLabels(tubeToLabelsMap);
}
// read annotations
- pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_ANNOTATIONS).Element();
+ pElem = hRoot.FirstChildElement(mitk::TubeGraphDefinitions::XML_ANNOTATIONS.c_str()).ToElement();
if (pElem != nullptr)
{
- for (TiXmlElement *annotationElement = pElem->FirstChildElement(); annotationElement != nullptr; annotationElement = annotationElement->NextSiblingElement())
+ for (auto *annotationElement = pElem->FirstChildElement(); annotationElement != nullptr; annotationElement = annotationElement->NextSiblingElement())
{
auto *annotation = new mitk::TubeGraphProperty::Annotation();
- std::string annotationName;
- std::string annotationDescription;
TubeGraph::TubeDescriptorType tube;
- annotationName =
- annotationElement->Attribute((char *)mitk::TubeGraphDefinitions::XML_ANNOTATION_NAME.c_str());
- annotation->name = annotationName;
+ const char *annotationName =
+ annotationElement->Attribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_NAME.c_str());
+ annotation->name = nullptr != annotationName ? annotationName : "";
- annotationDescription =
- annotationElement->Attribute((char *)mitk::TubeGraphDefinitions::XML_ANNOTATION_DESCRIPTION.c_str());
- annotation->description = annotationDescription;
+ const char *annotationDescription =
+ annotationElement->Attribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_DESCRIPTION.c_str());
+ annotation->description = nullptr != annotationDescription ? annotationDescription : "";
- annotationElement->Attribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1, &temp);
+ annotationElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1.c_str(), &temp);
tube.first = temp;
- annotationElement->Attribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2, &temp);
+ annotationElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2.c_str(), &temp);
tube.second = temp;
if (tube != TubeGraph::ErrorId)
{
annotation->tube = tube;
newProperty->AddAnnotation(annotation);
}
}
}
MITK_INFO << "Tube Graph Property read";
newTubeGraph->SetGeometry(geometry);
newTubeGraph->SetProperty("Tube Graph.Visualization Information", newProperty);
result.push_back(newTubeGraph.GetPointer());
}
-
else
{
- mitkThrow() << "Parsing error at line " << doc.ErrorRow() << ", col " << doc.ErrorCol() << ": "
- << doc.ErrorDesc();
+ mitkThrow() << "Parsing error at line " << doc.ErrorLineNum() << ": " << doc.ErrorStr();
}
return result;
}
AbstractFileIO::ConfidenceLevel TubeGraphIO::GetReaderConfidenceLevel() const
{
if (AbstractFileIO::GetReaderConfidenceLevel() == Unsupported)
return Unsupported;
return Supported;
}
void TubeGraphIO::Write()
{
OutputStream out(this);
if (!out.good())
{
mitkThrow() << "Stream not good.";
}
std::locale previousLocale(out.getloc());
std::locale I("C");
out.imbue(I);
const auto *tubeGraph = dynamic_cast<const mitk::TubeGraph *>(this->GetInput());
// Get geometry of the tube graph
mitk::Geometry3D::Pointer geometry = dynamic_cast<mitk::Geometry3D *>(tubeGraph->GetGeometry());
// Get property of the tube graph
mitk::TubeGraphProperty::Pointer tubeGraphProperty = dynamic_cast<mitk::TubeGraphProperty *>(
tubeGraph->GetProperty("Tube Graph.Visualization Information").GetPointer());
// Create XML document
- TiXmlDocument documentXML;
+ tinyxml2::XMLDocument documentXML;
{ // Begin document
- auto *declXML = new TiXmlDeclaration("1.0", "", "");
- documentXML.LinkEndChild(declXML);
+ documentXML.InsertEndChild(documentXML.NewDeclaration());
- auto *mainXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_TUBEGRAPH_FILE);
- mainXML->SetAttribute(mitk::TubeGraphDefinitions::XML_FILE_VERSION, mitk::TubeGraphDefinitions::VERSION_STRING);
- documentXML.LinkEndChild(mainXML);
+ auto *mainXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_TUBEGRAPH_FILE.c_str());
+ mainXML->SetAttribute(mitk::TubeGraphDefinitions::XML_FILE_VERSION.c_str(), mitk::TubeGraphDefinitions::VERSION_STRING.c_str());
+ documentXML.InsertEndChild(mainXML);
- auto *geometryXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_GEOMETRY);
+ auto *geometryXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_GEOMETRY.c_str());
{ // begin geometry
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XX, geometry->GetMatrixColumn(0)[0]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XY, geometry->GetMatrixColumn(0)[1]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XZ, geometry->GetMatrixColumn(0)[2]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YX, geometry->GetMatrixColumn(1)[0]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YY, geometry->GetMatrixColumn(1)[1]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YZ, geometry->GetMatrixColumn(1)[2]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZX, geometry->GetMatrixColumn(2)[0]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZY, geometry->GetMatrixColumn(2)[1]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZZ, geometry->GetMatrixColumn(2)[2]);
-
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_X, geometry->GetOrigin()[0]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Y, geometry->GetOrigin()[1]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Z, geometry->GetOrigin()[2]);
-
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_SPACING_X, geometry->GetSpacing()[0]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_SPACING_Y, geometry->GetSpacing()[1]);
- geometryXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_SPACING_Z, geometry->GetSpacing()[2]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XX.c_str(), geometry->GetMatrixColumn(0)[0]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XY.c_str(), geometry->GetMatrixColumn(0)[1]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XZ.c_str(), geometry->GetMatrixColumn(0)[2]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YX.c_str(), geometry->GetMatrixColumn(1)[0]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YY.c_str(), geometry->GetMatrixColumn(1)[1]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YZ.c_str(), geometry->GetMatrixColumn(1)[2]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZX.c_str(), geometry->GetMatrixColumn(2)[0]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZY.c_str(), geometry->GetMatrixColumn(2)[1]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZZ.c_str(), geometry->GetMatrixColumn(2)[2]);
+
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_X.c_str(), geometry->GetOrigin()[0]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Y.c_str(), geometry->GetOrigin()[1]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Z.c_str(), geometry->GetOrigin()[2]);
+
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_SPACING_X.c_str(), geometry->GetSpacing()[0]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_SPACING_Y.c_str(), geometry->GetSpacing()[1]);
+ geometryXML->SetAttribute(mitk::TubeGraphDefinitions::XML_SPACING_Z.c_str(), geometry->GetSpacing()[2]);
} // end geometry
- mainXML->LinkEndChild(geometryXML);
+ mainXML->InsertEndChild(geometryXML);
- auto *verticesXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_VERTICES);
+ auto *verticesXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_VERTICES.c_str());
{ // begin vertices section
std::vector<mitk::TubeGraphVertex> vertexVector = tubeGraph->GetVectorOfAllVertices();
for (unsigned int index = 0; index < vertexVector.size(); index++)
{
- auto *vertexXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_VERTEX);
- vertexXML->SetAttribute(mitk::TubeGraphDefinitions::XML_VERTEX_ID,
- tubeGraph->GetVertexDescriptor(vertexVector[index]));
+ auto *vertexXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_VERTEX.c_str());
+ vertexXML->SetAttribute(mitk::TubeGraphDefinitions::XML_VERTEX_ID.c_str(),
+ static_cast<int>(tubeGraph->GetVertexDescriptor(vertexVector[index])));
// element of each vertex
const mitk::TubeElement *element = vertexVector[index].GetTubeElement();
- auto *elementXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_ELEMENT);
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X,
+ auto *elementXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ELEMENT.c_str());
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(),
element->GetCoordinates().GetElement(0));
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y,
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(),
element->GetCoordinates().GetElement(1));
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z,
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(),
element->GetCoordinates().GetElement(2));
if (dynamic_cast<const mitk::CircularProfileTubeElement *>(element))
- elementXML->SetDoubleAttribute(
- mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER,
+ elementXML->SetAttribute(
+ mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(),
(dynamic_cast<const mitk::CircularProfileTubeElement *>(element))->GetDiameter());
else
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER, 2);
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(), 2);
- vertexXML->LinkEndChild(elementXML);
+ vertexXML->InsertEndChild(elementXML);
- verticesXML->LinkEndChild(vertexXML);
+ verticesXML->InsertEndChild(vertexXML);
}
} // end vertices section
- mainXML->LinkEndChild(verticesXML);
+ mainXML->InsertEndChild(verticesXML);
- auto *edgesXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_EDGES);
+ auto *edgesXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_EDGES.c_str());
{ // begin edges section
std::vector<mitk::TubeGraphEdge> edgeVector = tubeGraph->GetVectorOfAllEdges();
for (unsigned int index = 0; index < edgeVector.size(); index++)
{
- auto *edgeXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_EDGE);
- edgeXML->SetAttribute(mitk::TubeGraphDefinitions::XML_EDGE_ID, index);
+ auto *edgeXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_EDGE.c_str());
+ edgeXML->SetAttribute(mitk::TubeGraphDefinitions::XML_EDGE_ID.c_str(), index);
std::pair<mitk::TubeGraphVertex, mitk::TubeGraphVertex> soureTargetPair =
tubeGraph->GetVerticesOfAnEdge(tubeGraph->GetEdgeDescriptor(edgeVector[index]));
- edgeXML->SetAttribute(mitk::TubeGraphDefinitions::XML_EDGE_SOURCE_ID,
- tubeGraph->GetVertexDescriptor(soureTargetPair.first));
- edgeXML->SetAttribute(mitk::TubeGraphDefinitions::XML_EDGE_TARGET_ID,
- tubeGraph->GetVertexDescriptor(soureTargetPair.second));
+ edgeXML->SetAttribute(mitk::TubeGraphDefinitions::XML_EDGE_SOURCE_ID.c_str(),
+ static_cast<int>(tubeGraph->GetVertexDescriptor(soureTargetPair.first)));
+ edgeXML->SetAttribute(mitk::TubeGraphDefinitions::XML_EDGE_TARGET_ID.c_str(),
+ static_cast<int>(tubeGraph->GetVertexDescriptor(soureTargetPair.second)));
// begin elements of the edge
std::vector<mitk::TubeElement *> elementVector = edgeVector[index].GetElementVector();
for (unsigned int elementIndex = 0; elementIndex < elementVector.size(); elementIndex++)
{
- auto *elementXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_ELEMENT);
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X,
+ auto *elementXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ELEMENT.c_str());
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(),
elementVector[elementIndex]->GetCoordinates().GetElement(0));
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y,
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(),
elementVector[elementIndex]->GetCoordinates().GetElement(1));
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z,
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(),
elementVector[elementIndex]->GetCoordinates().GetElement(2));
if (dynamic_cast<const mitk::CircularProfileTubeElement *>(elementVector[elementIndex]))
- elementXML->SetDoubleAttribute(
- mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER,
+ elementXML->SetAttribute(
+ mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(),
(dynamic_cast<const mitk::CircularProfileTubeElement *>(elementVector[elementIndex]))->GetDiameter());
else
- elementXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER, 2);
- edgeXML->LinkEndChild(elementXML);
- // elementsXML->LinkEndChild(elementXML);
+ elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(), 2);
+ edgeXML->InsertEndChild(elementXML);
+ // elementsXML->InsertEndChild(elementXML);
}
- edgesXML->LinkEndChild(edgeXML);
+ edgesXML->InsertEndChild(edgeXML);
}
} // end edges section
- mainXML->LinkEndChild(edgesXML);
+ mainXML->InsertEndChild(edgesXML);
- auto *labelGroupsXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_LABELGROUPS);
+ auto *labelGroupsXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_LABELGROUPS.c_str());
{ // begin label group section
std::vector<TubeGraphProperty::LabelGroup *> labelGroupVector = tubeGraphProperty->GetLabelGroups();
for (unsigned int index = 0; index < labelGroupVector.size(); index++)
{
- auto *labelGroupXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_LABELGROUP);
- labelGroupXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME,
- labelGroupVector[index]->labelGroupName);
+ auto *labelGroupXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_LABELGROUP.c_str());
+ labelGroupXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME.c_str(),
+ labelGroupVector[index]->labelGroupName.c_str());
// begin labels of the label group
std::vector<TubeGraphProperty::LabelGroup::Label *> labelVector = labelGroupVector[index]->labels;
for (unsigned int labelIndex = 0; labelIndex < labelVector.size(); labelIndex++)
{
- auto *labelXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_LABEL);
- labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_NAME, labelVector[labelIndex]->labelName);
- labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_VISIBILITY,
- labelVector[labelIndex]->isVisible);
- labelXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_R,
+ auto *labelXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_LABEL.c_str());
+ labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_NAME.c_str(), labelVector[labelIndex]->labelName.c_str());
+ labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_VISIBILITY.c_str(),
+ labelVector[labelIndex]->isVisible ? 1 : 0);
+ labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_R.c_str(),
labelVector[labelIndex]->labelColor[0]);
- labelXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_G,
+ labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_G.c_str(),
labelVector[labelIndex]->labelColor[1]);
- labelXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_B,
+ labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_B.c_str(),
labelVector[labelIndex]->labelColor[2]);
- labelGroupXML->LinkEndChild(labelXML);
+ labelGroupXML->InsertEndChild(labelXML);
}
- labelGroupsXML->LinkEndChild(labelGroupXML);
+ labelGroupsXML->InsertEndChild(labelGroupXML);
}
} // end labe group section
- mainXML->LinkEndChild(labelGroupsXML);
+ mainXML->InsertEndChild(labelGroupsXML);
- auto *attributionsXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_ATTRIBUTIONS);
+ auto *attributionsXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ATTRIBUTIONS.c_str());
{ // begin attributions section
std::map<mitk::TubeGraphProperty::TubeToLabelGroupType, std::string> tubeToLabelGroup =
tubeGraphProperty->GetTubesToLabels();
for (auto it =
tubeToLabelGroup.begin();
it != tubeToLabelGroup.end();
it++)
{
- auto *attributXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_ATTRIBUTION);
- attributXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1, it->first.first.first);
- attributXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2, it->first.first.second);
- attributXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME, it->first.second);
- attributXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_NAME, it->second);
- attributionsXML->LinkEndChild(attributXML);
+ auto *attributXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ATTRIBUTION.c_str());
+ attributXML->SetAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1.c_str(), static_cast<int>(it->first.first.first));
+ attributXML->SetAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2.c_str(), static_cast<int>(it->first.first.second));
+ attributXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME.c_str(), it->first.second.c_str());
+ attributXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_NAME.c_str(), it->second.c_str());
+ attributionsXML->InsertEndChild(attributXML);
}
} // end attributions section
- mainXML->LinkEndChild(attributionsXML);
+ mainXML->InsertEndChild(attributionsXML);
- auto *annotationsXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_ANNOTATIONS);
+ auto *annotationsXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ANNOTATIONS.c_str());
{ // begin annotations section
std::vector<mitk::TubeGraphProperty::Annotation *> annotations = tubeGraphProperty->GetAnnotations();
for (unsigned int index = 0; index < annotations.size(); index++)
{
- auto *annotationXML = new TiXmlElement(mitk::TubeGraphDefinitions::XML_ANNOTATION);
- annotationXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_NAME, annotations[index]->name);
- annotationXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_DESCRIPTION,
- annotations[index]->description);
- annotationXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1, annotations[index]->tube.first);
- annotationXML->SetDoubleAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2, annotations[index]->tube.second);
-
- annotationsXML->LinkEndChild(annotationXML);
+ auto *annotationXML = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ANNOTATION.c_str());
+ annotationXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_NAME.c_str(), annotations[index]->name.c_str());
+ annotationXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_DESCRIPTION.c_str(), annotations[index]->description.c_str());
+ annotationXML->SetAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1.c_str(), static_cast<int>(annotations[index]->tube.first));
+ annotationXML->SetAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2.c_str(), static_cast<int>(annotations[index]->tube.second));
+
+ annotationsXML->InsertEndChild(annotationXML);
}
} // end annotations section
- mainXML->LinkEndChild(annotationsXML);
+ mainXML->InsertEndChild(annotationsXML);
} // end document
- TiXmlPrinter printer;
- printer.SetStreamPrinting();
- documentXML.Accept(&printer);
- out << printer.Str();
+ tinyxml2::XMLPrinter printer;
+ documentXML.Print(&printer);
+
+ out << printer.CStr();
}
AbstractFileIO::ConfidenceLevel TubeGraphIO::GetWriterConfidenceLevel() const
{
if (AbstractFileIO::GetWriterConfidenceLevel() == Unsupported)
return Unsupported;
return Supported;
}
TubeGraphIO *TubeGraphIO::IOClone() const { return new TubeGraphIO(*this); }
}
const mitk::BoundingBox::Pointer mitk::TubeGraphIO::ComputeBoundingBox(mitk::TubeGraph::Pointer graph) const
{
BoundingBox::Pointer boundingBox = BoundingBox::New();
BoundingBox::PointIdentifier pointid = 0;
BoundingBox::PointsContainer::Pointer pointscontainer = BoundingBox::PointsContainer::New();
ScalarType nullpoint[] = {0, 0, 0};
BoundingBox::PointType p(nullpoint);
// traverse the tree and add each point to the pointscontainer
mitk::Point3D pos;
std::vector<mitk::TubeGraphVertex> vertexVector = graph->GetVectorOfAllVertices();
for (auto vertex = vertexVector.begin(); vertex != vertexVector.end();
++vertex)
{
pos = vertex->GetTubeElement()->GetCoordinates();
p[0] = pos[0];
p[1] = pos[1];
p[2] = pos[2];
pointscontainer->InsertElement(pointid++, p);
}
std::vector<mitk::TubeGraphEdge> edgeVector = graph->GetVectorOfAllEdges();
for (auto edge = edgeVector.begin(); edge != edgeVector.end(); ++edge)
{
std::vector<mitk::TubeElement *> allElements = edge->GetElementVector();
for (unsigned int index = 0; index < edge->GetNumberOfElements(); index++)
{
pos = allElements[index]->GetCoordinates();
p[0] = pos[0];
p[1] = pos[1];
p[2] = pos[2];
pointscontainer->InsertElement(pointid++, p);
}
}
boundingBox->SetPoints(pointscontainer);
boundingBox->ComputeBoundingBox();
return boundingBox;
}
diff --git a/Modules/US/CMakeLists.txt b/Modules/US/CMakeLists.txt
index 97b6d418c7..ce97594129 100644
--- a/Modules/US/CMakeLists.txt
+++ b/Modules/US/CMakeLists.txt
@@ -1,15 +1,14 @@
MITK_CREATE_MODULE(
INCLUDE_DIRS USControlInterfaces USFilters USModel
INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
- PACKAGE_DEPENDS Poco PRIVATE tinyxml
+ PACKAGE_DEPENDS Poco PRIVATE tinyxml2
DEPENDS MitkOpenCVVideoSupport MitkQtWidgetsExt MitkIGTBase MitkOpenIGTLink
)
## create US config
#CONFIGURE_FILE(mitkUSConfig.h.in ${PROJECT_BINARY_DIR}/mitkUSConfig.h @ONLY)
ADD_SUBDIRECTORY(USHardwareTelemed)
-ADD_SUBDIRECTORY(USHardwareDiPhAS)
ADD_SUBDIRECTORY(USNavigation)
ADD_SUBDIRECTORY(Testing)
diff --git a/Modules/US/USControlInterfaces/mitkUSDiPhASDeviceCustomControls.cpp b/Modules/US/USControlInterfaces/mitkUSDiPhASDeviceCustomControls.cpp
deleted file mode 100644
index 1cda345b0f..0000000000
--- a/Modules/US/USControlInterfaces/mitkUSDiPhASDeviceCustomControls.cpp
+++ /dev/null
@@ -1,202 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkUSDiPhASDeviceCustomControls.h"
-
-mitk::USDiPhASDeviceCustomControls::USDiPhASDeviceCustomControls(itk::SmartPointer<USDevice> device)
- : mitk::USAbstractControlInterface(device.GetPointer()), m_IsActive(false), silentUpdate(false)
-{
-}
-
-mitk::USDiPhASDeviceCustomControls::~USDiPhASDeviceCustomControls()
-{
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetIsActive(bool isActive)
-{
- m_IsActive = isActive;
-}
-
-bool mitk::USDiPhASDeviceCustomControls::GetIsActive()
-{
- return m_IsActive;
-}
-
-void mitk::USDiPhASDeviceCustomControls::passGUIOut(std::function<void(QString)> /*callback*/) {}
-
-void mitk::USDiPhASDeviceCustomControls::SetSilentUpdate(bool silent)
-{
- silentUpdate = silent;
-}
-
-bool mitk::USDiPhASDeviceCustomControls::GetSilentUpdate()
-{
- return silentUpdate;
-}
-
-//Set Functions
-
-void mitk::USDiPhASDeviceCustomControls::SetCompensateEnergy(bool compensate)
-{
- this->OnSetCompensateEnergy(compensate);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetUseBModeFilter(bool isSet)
-{
- this->OnSetUseBModeFilter(isSet);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetRecord(bool record)
-{
- this->OnSetRecord(record);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetVerticalSpacing(float mm)
-{
- this->OnSetVerticalSpacing(mm);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetScatteringCoefficient(float coeff)
-{
- this->OnSetScatteringCoefficient(coeff);
-}
-void mitk::USDiPhASDeviceCustomControls::SetCompensateScattering(bool compensate)
-{
- this->OnSetCompensateScattering(compensate);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetSavingSettings(SavingSettings settings)
-{
- this->OnSetSavingSettings(settings);
-}
-
-//Transmit
-void mitk::USDiPhASDeviceCustomControls::SetTransmitPhaseLength(double us)
-{
- this->OnSetTransmitPhaseLength(us);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetExcitationFrequency(double MHz)
-{
- this->OnSetExcitationFrequency(MHz);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetTransmitEvents(int events)
-{
- this->OnSetTransmitEvents(events);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetVoltage(int voltage)
-{
- this->OnSetVoltage(voltage);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetMode(bool interleaved)
-{
- this->OnSetMode(interleaved);
-}
-
-//Receive
-void mitk::USDiPhASDeviceCustomControls::SetScanDepth(double mm)
-{
- this->OnSetScanDepth(mm);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetAveragingCount(int count)
-{
- this->OnSetAveragingCount(count);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetTGCMin(int min)
-{
- this->OnSetTGCMin(min);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetTGCMax(int max)
-{
- this->OnSetTGCMax(max);
-
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetDataType(DataType type)
-{
- this->OnSetDataType(type);
-}
-
-//Beamforming
-void mitk::USDiPhASDeviceCustomControls::SetPitch(double mm)
-{
- this->OnSetPitch(mm);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetReconstructedSamples(int samples)
-{
- this->OnSetReconstructedSamples(samples);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetReconstructedLines(int lines)
-{
- this->OnSetReconstructedLines(lines);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetSpeedOfSound(int mps)
-{
- this->OnSetSpeedOfSound(mps);
-}
-
-//Bandpass
-void mitk::USDiPhASDeviceCustomControls::SetBandpassEnabled(bool bandpass)
-{
- this->OnSetBandpassEnabled(bandpass);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetLowCut(double MHz)
-{
- this->OnSetLowCut(MHz);
-}
-
-void mitk::USDiPhASDeviceCustomControls::SetHighCut(double MHz)
-{
- this->OnSetHighCut(MHz);
-}
-
-
-//OnSetDummies
-
-void mitk::USDiPhASDeviceCustomControls::OnSetCompensateEnergy(bool /*compensate*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetUseBModeFilter(bool /*isSet*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetRecord(bool /*record*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetVerticalSpacing(float /*mm*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetScatteringCoefficient(float /*coeff*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetCompensateScattering(bool /*compensate*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetSavingSettings(SavingSettings /*settings*/) {}
-//Transmit
-void mitk::USDiPhASDeviceCustomControls::OnSetTransmitPhaseLength(double /*ms*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetExcitationFrequency(double /*MHz*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetTransmitEvents(int /*events*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetVoltage(int /*voltage*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetMode(bool /*interleaved*/) {}
-//Receive
-void mitk::USDiPhASDeviceCustomControls::OnSetScanDepth(double /*mm*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetAveragingCount(int /*count*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetTGCMin(int /*min*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetTGCMax(int /*max*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetDataType(DataType /*type*/) {}
-//Beamforming
-void mitk::USDiPhASDeviceCustomControls::OnSetPitch(double /*mm*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetReconstructedSamples(int /*samples*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetReconstructedLines(int /*lines*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetSpeedOfSound(int /*mps*/) {}
-//Bandpass
-void mitk::USDiPhASDeviceCustomControls::OnSetBandpassEnabled(bool /*bandpass*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetLowCut(double /*MHz*/) {}
-void mitk::USDiPhASDeviceCustomControls::OnSetHighCut(double /*MHz*/) {}
diff --git a/Modules/US/USControlInterfaces/mitkUSDiPhASDeviceCustomControls.h b/Modules/US/USControlInterfaces/mitkUSDiPhASDeviceCustomControls.h
deleted file mode 100644
index b7004e2711..0000000000
--- a/Modules/US/USControlInterfaces/mitkUSDiPhASDeviceCustomControls.h
+++ /dev/null
@@ -1,140 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKUSDiPhASDeviceCustomControls_H_HEADER_INCLUDED_
-#define MITKUSDiPhASDeviceCustomControls_H_HEADER_INCLUDED_
-
-#include "mitkUSAbstractControlInterface.h"
-#include "mitkUSImageVideoSource.h"
-#include "mitkUSDevice.h"
-
-#include <itkObjectFactory.h>
-
-#include <functional>
-#include <qstring.h>
-
-namespace mitk {
-/**
- * \brief Custom controls for mitk::USDiPhASDevice.
- */
-class MITKUS_EXPORT USDiPhASDeviceCustomControls : public USAbstractControlInterface
-{
-public:
- mitkClassMacro(USDiPhASDeviceCustomControls, USAbstractControlInterface);
- mitkNewMacro1Param(Self, itk::SmartPointer<USDevice>);
-
- /**
- * Activate or deactivate the custom controls. This is just for handling
- * widget visibility in a GUI for example.
- */
- void SetIsActive( bool isActive ) override;
-
- enum DataType { Image_uChar, Beamformed_Short };
-
- struct SavingSettings
- {
- bool saveRaw;
- bool saveBeamformed;
- };
- /**
- * \return if this custom controls are currently activated
- */
- bool GetIsActive( ) override;
-
- virtual void SetCompensateEnergy(bool compensate);
- virtual void SetUseBModeFilter(bool isSet);
- virtual void SetVerticalSpacing(float mm);
- virtual void SetRecord(bool record);
- virtual void SetScatteringCoefficient(float coeff);
- virtual void SetCompensateScattering(bool compensate);
- virtual void SetSavingSettings(SavingSettings settings);
-
- //Transmit
- virtual void SetTransmitPhaseLength(double us);
- virtual void SetExcitationFrequency(double MHz);
- virtual void SetTransmitEvents(int events);
- virtual void SetVoltage(int voltage);
- virtual void SetMode(bool interleaved);
-
- //Receive
- virtual void SetScanDepth(double mm);
- virtual void SetAveragingCount(int count);
- virtual void SetTGCMin(int min);
- virtual void SetTGCMax(int max);
- virtual void SetDataType(DataType type);
-
- //Beamforming
- virtual void SetPitch(double mm);
- virtual void SetReconstructedSamples(int samples);
- virtual void SetReconstructedLines(int lines);
- virtual void SetSpeedOfSound(int mps);
-
- //Bandpass
- virtual void SetBandpassEnabled(bool bandpass);
- virtual void SetLowCut(double MHz);
- virtual void SetHighCut(double MHz);
-
- virtual void passGUIOut(std::function<void(QString)> /*callback*/);
- virtual void SetSilentUpdate(bool silent);
- virtual bool GetSilentUpdate();
-
-
-
-protected:
- /**
- * Class needs an mitk::USDevice object for beeing constructed.
- */
- USDiPhASDeviceCustomControls( itk::SmartPointer<USDevice> device );
- ~USDiPhASDeviceCustomControls( ) override;
-
- bool m_IsActive;
- USImageVideoSource::Pointer m_ImageSource;
- bool silentUpdate;
-
- /** virtual handlers implemented in Device Controls
- */
- virtual void OnSetCompensateEnergy(bool /*compensate*/);
- virtual void OnSetSavingSettings(SavingSettings /*settings*/);
- virtual void OnSetUseBModeFilter(bool /*isSet*/);
- virtual void OnSetRecord(bool /*record*/);
- virtual void OnSetVerticalSpacing(float /*mm*/);
- virtual void OnSetScatteringCoefficient(float /*coeff*/);
- virtual void OnSetCompensateScattering(bool /*compensate*/);
- //Transmit
- virtual void OnSetTransmitPhaseLength(double /*us*/);
- virtual void OnSetExcitationFrequency(double /*MHz*/);
- virtual void OnSetTransmitEvents(int /*events*/);
- virtual void OnSetVoltage(int /*voltage*/);
- virtual void OnSetMode(bool /*interleaved*/);
-
- //Receive
- virtual void OnSetScanDepth(double /*mm*/);
- virtual void OnSetAveragingCount(int /*count*/);
- virtual void OnSetTGCMin(int /*min*/);
- virtual void OnSetTGCMax(int /*max*/);
- virtual void OnSetDataType(DataType /*type*/);
-
- //Beamforming
- virtual void OnSetPitch(double /*mm*/);
- virtual void OnSetReconstructedSamples(int /*samples*/);
- virtual void OnSetReconstructedLines(int /*lines*/);
- virtual void OnSetSpeedOfSound(int /*mps*/);
-
- //Bandpass
- virtual void OnSetBandpassEnabled(bool /*bandpass*/);
- virtual void OnSetLowCut(double /*MHz*/);
- virtual void OnSetHighCut(double /*MHz*/);
-
-};
-} // namespace mitk
-
-#endif // MITKUSDiPhASDeviceCustomControls_H_HEADER_INCLUDED_
diff --git a/Modules/US/USHardwareDiPhAS/CMakeLists.txt b/Modules/US/USHardwareDiPhAS/CMakeLists.txt
deleted file mode 100644
index c72b11fa83..0000000000
--- a/Modules/US/USHardwareDiPhAS/CMakeLists.txt
+++ /dev/null
@@ -1,19 +0,0 @@
-if(WIN32)
-
- OPTION(MITK_USE_US_DiPhAS_SDK "Enable support for DiPhAS API devices" OFF)
-
- if(MITK_USE_US_DiPhAS_SDK)
-
- SET(MITK_US_DiPhAS_SDK_PATH "" CACHE PATH "Path to DiPhAS SDK header files.")
-
- MITK_CREATE_MODULE(
- DEPENDS MitkUS MitkPhotoacousticsHardware
- INCLUDE_DIRS PUBLIC "${MITK_US_DiPhAS_SDK_PATH}/Debug" "${MITK_US_DiPhAS_SDK_PATH}/Release"
- INTERNAL_INCLUDE_DIRS ${INCLUDE_DIRS_INTERNAL}
- ADDITIONAL_LIBS "${MITK_US_DiPhAS_SDK_PATH}/Debug/Framework.IBMT.US.CWrapper.lib" "${MITK_US_DiPhAS_SDK_PATH}/Release/Framework.IBMT.US.CWrapper.lib"
- AUTOLOAD_WITH MitkUS
- )
-
- endif()
-
-endif()
diff --git a/Modules/US/USHardwareDiPhAS/FranzTissue.nrrd b/Modules/US/USHardwareDiPhAS/FranzTissue.nrrd
deleted file mode 100644
index 224a89f7ff..0000000000
Binary files a/Modules/US/USHardwareDiPhAS/FranzTissue.nrrd and /dev/null differ
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkAnalyticSignalImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkAnalyticSignalImageFilter.h
deleted file mode 100644
index 0bd53ce42b..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkAnalyticSignalImageFilter.h
+++ /dev/null
@@ -1,139 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkAnalyticSignalImageFilter_h
-#define itkAnalyticSignalImageFilter_h
-
-#include <complex>
-
-#include "itkFFT1DComplexToComplexImageFilter.h"
-#include "itkFFT1DRealToComplexConjugateImageFilter.h"
-#include "itkImageRegionSplitterDirection.h"
-
-namespace itk
-{
-/** \class AnalyticSignalImageFilter
- * \brief Generates the analytic signal from one direction of an image.
- *
- * This filter generates the complex valued analytic signal along one direction
- * of an image. This input is a real valued image, and the output is a complex
- * image.
- *
- * The analytic signal is given by
- *
- * f_a(x) = f(x) - i f_H(x)
- *
- * Where i is the square root of one and f_H(x) is the Hibert transform of f(x).
- *
- * Since the Hilbert transform in the Fourier domain is
- *
- * F_H(k) = F(k) i sign(k),
- *
- * f_a(x) is calculated by
- *
- * f_a(x) = F^{-1}( F(k) 2 U(k) )
- *
- * where U(k) is the unit step function.
- *
- * \ingroup FourierTransform
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage >
-class AnalyticSignalImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension);
-
- typedef AnalyticSignalImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkTypeMacro( AnalyticSignalImageFilter, ImageToImageFilter );
- itkNewMacro( Self );
-
- /** Get the direction in which the filter is to be applied. */
- virtual unsigned int GetDirection() const
- {
- return this->m_FFTRealToComplexFilter->GetDirection();
- }
-
- /** Set the direction in which the filter is to be applied. */
- virtual void SetDirection( const unsigned int direction )
- {
- if( this->m_FFTRealToComplexFilter->GetDirection() != direction )
- {
- this->m_FFTRealToComplexFilter->SetDirection( direction );
- this->m_FFTComplexToComplexFilter->SetDirection( direction );
- this->Modified();
- }
- }
-
-protected:
- AnalyticSignalImageFilter();
- virtual ~AnalyticSignalImageFilter() {}
-
- void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- // These behave like their analogs in FFT1DRealToComplexConjugateImageFilter.
- virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;
- virtual void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- virtual void BeforeThreadedGenerateData() ITK_OVERRIDE;
- virtual void ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId ) ITK_OVERRIDE;
- virtual void AfterThreadedGenerateData() ITK_OVERRIDE;
-
- typedef FFT1DRealToComplexConjugateImageFilter< InputImageType, OutputImageType > FFTRealToComplexType;
- typedef FFT1DComplexToComplexImageFilter< OutputImageType, OutputImageType > FFTComplexToComplexType;
-
- typename FFTRealToComplexType::Pointer m_FFTRealToComplexFilter;
- typename FFTComplexToComplexType::Pointer m_FFTComplexToComplexFilter;
-
- /** Override to return a splitter that does not split along the direction we
- * are performing the transform. */
- virtual const ImageRegionSplitterBase* GetImageRegionSplitter() const ITK_OVERRIDE;
-
-private:
- AnalyticSignalImageFilter( const Self& ); // purposely not implemented
- void operator=( const Self& ); // purposely not implemented
-
- ImageRegionSplitterDirection::Pointer m_ImageRegionSplitter;
-};
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkAnalyticSignalImageFilter.hxx"
-#endif
-
-#endif // itkAnalyticSignalImageFilter_h
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkAnalyticSignalImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkAnalyticSignalImageFilter.hxx
deleted file mode 100644
index 6f9bed0161..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkAnalyticSignalImageFilter.hxx
+++ /dev/null
@@ -1,267 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkAnalyticSignalImageFilter_hxx
-#define itkAnalyticSignalImageFilter_hxx
-
-#include "itkAnalyticSignalImageFilter.h"
-
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.h"
-#include "itkVnlFFT1DComplexToComplexImageFilter.h"
-
-#if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
-#include "itkFFTW1DRealToComplexConjugateImageFilter.h"
-#include "itkFFTW1DComplexToComplexImageFilter.h"
-#endif
-
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::AnalyticSignalImageFilter()
-{
- m_FFTRealToComplexFilter = FFTRealToComplexType::New();
- m_FFTComplexToComplexFilter = FFTComplexToComplexType::New();
-
- m_FFTComplexToComplexFilter->SetTransformDirection( FFTComplexToComplexType::INVERSE );
-
- this->SetDirection( 0 );
-
- this->m_ImageRegionSplitter = ImageRegionSplitterDirection::New();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- typename InputImageType::Pointer inputPtr =
- const_cast<InputImageType *> (this->GetInput());
- typename OutputImageType::Pointer outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->GetDirection();
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast< OutputImageType* >( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- const unsigned int direction = this->GetDirection ();
- enlargedSize[direction] = outputLargeSize[direction];
- enlargedIndex[direction] = outputLargeIndex[direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- const unsigned int direction = this->GetDirection();
- os << indent << "Direction: " << direction << std::endl;
-
- os << indent << "FFTRealToComplexFilter: " << std::endl;
- m_FFTRealToComplexFilter->Print( os, indent );
- os << indent << "FFTComplexToComplexFilter: " << std::endl;
- m_FFTComplexToComplexFilter->Print( os, indent );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-const ImageRegionSplitterBase *
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::GetImageRegionSplitter() const
-{
- return this->m_ImageRegionSplitter.GetPointer();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- this->m_ImageRegionSplitter->SetDirection( this->GetDirection() );
-
- m_FFTRealToComplexFilter->SetInput( this->GetInput() );
- m_FFTRealToComplexFilter->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
- m_FFTRealToComplexFilter->GetOutput()->SetLargestPossibleRegion( this->GetOutput()->GetLargestPossibleRegion() );
- m_FFTRealToComplexFilter->SetNumberOfThreads( this->GetNumberOfThreads() );
- m_FFTRealToComplexFilter->Update ();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType itkNotUsed( threadId ) )
-{
- // get pointers to the input and output
- const typename FFTRealToComplexType::OutputImageType * inputPtr = m_FFTRealToComplexFilter->GetOutput();
- OutputImageType * outputPtr = this->GetOutput();
-
- const typename FFTRealToComplexType::OutputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
- const unsigned int direction = this->GetDirection ();
- const unsigned int size = inputSize[direction];
- unsigned int dub_size;
- bool even;
- if( size % 2 == 0 )
- {
- even = true;
- dub_size = size / 2 - 1;
- }
- else
- {
- even = false;
- dub_size = (size + 1) / 2 - 1;
- }
-
- typedef ImageLinearConstIteratorWithIndex< typename FFTRealToComplexType::OutputImageType > InputIteratorType;
- typedef ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegionForThread );
- OutputIteratorType outputIt( outputPtr, outputRegionForThread );
- inputIt.SetDirection( direction );
- outputIt.SetDirection( direction );
-
- unsigned int i;
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- inputIt.GoToBeginOfLine();
- outputIt.GoToBeginOfLine();
-
- // DC
- outputIt.Set( inputIt.Get() );
- ++inputIt;
- ++outputIt;
-
- for( i = 0; i < dub_size; i++ )
- {
- outputIt.Set( inputIt.Get() * static_cast< typename TInputImage::PixelType >( 2 ) );
- ++outputIt;
- ++inputIt;
- }
- if( even )
- {
- outputIt.Set( inputIt.Get() );
- ++inputIt;
- ++outputIt;
- }
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( static_cast< typename TInputImage::PixelType >( 0 ) );
- ++outputIt;
- }
- }
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-AnalyticSignalImageFilter< TInputImage, TOutputImage >
-::AfterThreadedGenerateData()
-{
- // Trippy, eh?
- m_FFTComplexToComplexFilter->SetInput( this->GetOutput() );
- m_FFTComplexToComplexFilter->GetOutput()->SetRequestedRegion( this->GetOutput()->GetRequestedRegion() );
- m_FFTComplexToComplexFilter->GetOutput()->SetLargestPossibleRegion( this->GetOutput()->GetLargestPossibleRegion() );
- m_FFTComplexToComplexFilter->SetNumberOfThreads( this->GetNumberOfThreads() );
- m_FFTComplexToComplexFilter->Update ();
- this->GraftOutput( m_FFTComplexToComplexFilter->GetOutput() );
-}
-
-} // end namespace itk
-
-#endif // itkAnalyticSignalImageFilter_hxx
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkBModeImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkBModeImageFilter.h
deleted file mode 100644
index ec84eee33f..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkBModeImageFilter.h
+++ /dev/null
@@ -1,152 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkBModeImageFilter_h
-#define itkBModeImageFilter_h
-
-#include "itkAddImageFilter.h"
-#include "itkComplexToModulusImageFilter.h"
-#include "itkConstantPadImageFilter.h"
-#include "itkRegionFromReferenceImageFilter.h"
-#include "itkImageToImageFilter.h"
-#include "itkImage.h"
-#include "itkLog10ImageFilter.h"
-
-#include "itkAnalyticSignalImageFilter.h"
-
-namespace itk
-{
-
-/**
- * \class BModeImageFilter
- *
- * \brief Create an ultrasound B-Mode (Brightness-Mode) image from raw
- * "RF" data. The RF's envelope is calculated from the analytic signal and
- * logarithmic intensity transform is applied.
- *
- * Use SetDirection() to define the axis of propagation.
- *
- * \ingroup Ultrasound
- *
- * \sa AnalyticSignalImageFilter
- *
- */
-template < typename TInputImage, typename TOutputImage=TInputImage, typename TComplexImage=Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
-class BModeImageFilter :
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef BModeImageFilter Self;
- typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- /** The type of input image. */
- typedef TInputImage InputImageType;
-
- /** Dimension of the input and output images. */
- itkStaticConstMacro (ImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- /** Typedef support for the input image scalar value type. */
- typedef typename InputImageType::PixelType InputPixelType;
-
- /** The type of output image. */
- typedef TOutputImage OutputImageType;
-
- /** Typedef support for the output image scalar value type. */
- typedef typename OutputImageType::PixelType OutputPixelType;
-
- /** Typedef of the image used for internal computations that has
- * std::complex pixels. */
- typedef TComplexImage ComplexImageType;
-
- /** Other convenient typedefs */
- typedef typename InputImageType::RegionType InputRegionType;
- typedef typename InputImageType::SizeType InputSizeType;
- typedef typename InputImageType::IndexType InputIndexType;
-
- /** Run-time type information (and related methods) */
- itkTypeMacro( BModeImageFilter, ImageToImageFilter );
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Set the direction in which the envelope is to be calculated. */
- virtual void SetDirection( unsigned int direction )
- {
- this->m_AnalyticFilter->SetDirection( direction );
- this->Modified();
- }
-
- /** Get the direction in which the envelope is to be calculated. */
- virtual unsigned int GetDirection() const
- {
- return m_AnalyticFilter->GetDirection();
- }
-
-protected:
- BModeImageFilter();
- ~BModeImageFilter() {}
-
- virtual void PrintSelf( std::ostream& os, Indent indent ) const ITK_OVERRIDE;
-
- virtual void GenerateData() ITK_OVERRIDE;
-
- // These behave like their analogs in FFT1DRealToComplexConjugateImageFilter.
- virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;
- virtual void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- /** Component filters. */
- typedef AnalyticSignalImageFilter< InputImageType, ComplexImageType > AnalyticType;
- typedef ComplexToModulusImageFilter< typename AnalyticType::OutputImageType, OutputImageType > ComplexToModulusType;
- typedef ConstantPadImageFilter< InputImageType, InputImageType > PadType;
- typedef AddImageFilter< InputImageType, InputImageType > AddConstantType;
- typedef Log10ImageFilter< InputImageType, OutputImageType > LogType;
- typedef RegionFromReferenceImageFilter< OutputImageType, OutputImageType > ROIType;
-
-private:
- BModeImageFilter( const Self& ); // purposely not implemented
- void operator=( const Self& ); // purposely not implemented
-
- typename AnalyticType::Pointer m_AnalyticFilter;
- typename ComplexToModulusType::Pointer m_ComplexToModulusFilter;
- typename PadType::Pointer m_PadFilter;
- typename AddConstantType::Pointer m_AddConstantFilter;
- typename LogType::Pointer m_LogFilter;
- typename ROIType::Pointer m_ROIFilter;
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkBModeImageFilter.hxx"
-#endif
-
-#endif // itkBModeImageFilter_h
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkBModeImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkBModeImageFilter.hxx
deleted file mode 100644
index f45b42fe37..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkBModeImageFilter.hxx
+++ /dev/null
@@ -1,208 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkBModeImageFilter_hxx
-#define itkBModeImageFilter_hxx
-
-#include "itkBModeImageFilter.h"
-
-#include "itkMetaDataDictionary.h"
-
-#include <algorithm>
-#include <sstream>
-#include <string>
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::BModeImageFilter()
-{
- m_AnalyticFilter = AnalyticType::New();
- m_ComplexToModulusFilter = ComplexToModulusType::New();
- m_PadFilter = PadType::New();
- m_AddConstantFilter = AddConstantType::New();
- m_LogFilter = LogType::New();
- m_ROIFilter = ROIType::New();
-
- // Avoid taking the log of zero. Assuming that the original input is coming
- // from a digitizer that outputs integer types, so 1 is small.
- m_AddConstantFilter->SetConstant2( 1 );
- m_PadFilter->SetConstant( 0. );
-
- m_ComplexToModulusFilter->SetInput( m_AnalyticFilter->GetOutput() );
- m_ROIFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
- m_LogFilter->SetInput( m_AddConstantFilter->GetOutput() );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- InputImageType * inputPtr = const_cast<InputImageType *> (this->GetInput());
- OutputImageType * outputPtr = this->GetOutput();
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->GetDirection();
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast< OutputImageType* >( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- const unsigned int direction = this->GetDirection ();
- enlargedSize[direction] = outputLargeSize[direction];
- enlargedIndex[direction] = outputLargeIndex[direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template < typename TInputImage, typename TOutputImage, typename TComplexImage >
-void
-BModeImageFilter< TInputImage, TOutputImage, TComplexImage >
-::GenerateData()
-{
- this->AllocateOutputs();
-
- const InputImageType * inputPtr = this->GetInput();
- OutputImageType * outputPtr = this->GetOutput();
-
- const unsigned int direction = m_AnalyticFilter->GetDirection();
- typename InputImageType::SizeType size = inputPtr->GetLargestPossibleRegion().GetSize();
-
- // Zero padding. FFT direction should be factorable by 2 for all FFT
- // implementations to work.
- unsigned int n = size[direction];
- while( n % 2 == 0 )
- {
- n /= 2;
- }
- bool doPadding;
- if( n == 1 )
- {
- doPadding = false;
- }
- else
- {
- doPadding = true;
- }
- if( doPadding )
- {
- n = size[direction];
- unsigned int newSizeDirection = 1;
- while( newSizeDirection < n )
- {
- newSizeDirection *= 2;
- }
- typename InputImageType::SizeType padSize;
- padSize.Fill( 0 );
- padSize[direction] = newSizeDirection - size[direction];
- size[direction] = newSizeDirection;
- m_PadFilter->SetPadUpperBound( padSize );
- m_PadFilter->SetInput( inputPtr );
- m_AnalyticFilter->SetInput( m_PadFilter->GetOutput() );
- m_ROIFilter->SetReferenceImage( inputPtr );
- m_ROIFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
- m_AddConstantFilter->SetInput( m_ROIFilter->GetOutput() );
- }
- else // padding is not required
- {
- m_AnalyticFilter->SetInput( inputPtr );
- m_AddConstantFilter->SetInput( m_ComplexToModulusFilter->GetOutput() );
- }
- m_LogFilter->GraftOutput( outputPtr );
- m_LogFilter->Update();
- this->GraftOutput( m_LogFilter->GetOutput() );
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h
deleted file mode 100644
index 9c6bede6c1..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.h
+++ /dev/null
@@ -1,138 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DComplexToComplexImageFilter_h
-#define itkFFT1DComplexToComplexImageFilter_h
-
-#include <complex>
-
-#include "itkImage.h"
-#include "itkImageToImageFilter.h"
-#include "itkImageRegionSplitterDirection.h"
-
-namespace itk
-{
-/** \class FFT1DComplexToComplexImageFilter
- * \brief Perform the Fast Fourier Transform, complex input to complex output,
- * but only along one dimension.
- *
- * The direction of the transform, 'Forward' or 'Inverse', can be set with
- * SetTransformDirection() and GetTransformDirection().
- *
- * The dimension along which to apply to filter can be specified with
- * SetDirection() and GetDirection().
- *
- * \ingroup FourierTransform
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=TInputImage >
-class FFT1DComplexToComplexImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- typedef FFT1DComplexToComplexImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension );
-
- itkTypeMacro( FFT1DComplexToComplexImageFilter, ImageToImageFilter );
-
- /** Customized object creation methods that support configuration-based
- * selection of FFT implementation.
- *
- * Default implementation is VnlFFT1D.
- */
- static Pointer New();
-
- /** Transform direction. */
- typedef enum { DIRECT = 1, INVERSE } TransformDirectionType;
-
- /** Set/Get the direction in which the transform will be applied.
- * By selecting DIRECT, this filter will perform a direct (forward) Fourier
- * Transform.
- * By selecting INVERSE, this filter will perform an inverse Fourier
- * Transform. */
- itkSetMacro( TransformDirection, TransformDirectionType );
- itkGetConstMacro( TransformDirection, TransformDirectionType );
-
- /** Get the direction in which the filter is to be applied. */
- itkGetMacro(Direction, unsigned int);
-
- /** Set the direction in which the filter is to be applied. */
- itkSetClampMacro(Direction, unsigned int, 0, ImageDimension - 1);
-
-protected:
- FFT1DComplexToComplexImageFilter();
- virtual ~FFT1DComplexToComplexImageFilter() {}
-
- void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;
- virtual void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- virtual void BeforeThreadedGenerateData() ITK_OVERRIDE;
-
- /** Override to return a splitter that does not split along the direction we
- * are performing the transform. */
- virtual const ImageRegionSplitterBase* GetImageRegionSplitter() const ITK_OVERRIDE;
-
- /** Direction in which the filter is to be applied
- * this should be in the range [0,ImageDimension-1]. */
- unsigned int m_Direction;
-
- /** Direction to apply the transform (forward/inverse). */
- TransformDirectionType m_TransformDirection;
-
-private:
- FFT1DComplexToComplexImageFilter( const Self& );
- void operator=( const Self& );
-
- ImageRegionSplitterDirection::Pointer m_ImageRegionSplitter;
-};
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_h
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_hxx
-#ifndef itkFFTW1DComplexToComplexImageFilter_h
-#ifndef itkFFTW1DComplexToComplexImageFilter_hxx
-#include "itkFFT1DComplexToComplexImageFilter.hxx"
-#endif
-#endif
-#endif
-#endif
-#endif
-
-#endif // itkFFT1DComplexToComplexImageFilter_h
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx
deleted file mode 100644
index af4c9d7b1c..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DComplexToComplexImageFilter.hxx
+++ /dev/null
@@ -1,206 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DComplexToComplexImageFilter_hxx
-#define itkFFT1DComplexToComplexImageFilter_hxx
-
-#include "itkFFT1DComplexToComplexImageFilter.h"
-
-#include "itkVnlFFT1DComplexToComplexImageFilter.h"
-
-#if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
-#include "itkFFTW1DComplexToComplexImageFilter.h"
-#endif
-
-#include "itkMetaDataDictionary.h"
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage >
-typename FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >::Pointer
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::New()
-{
- Pointer smartPtr = ::itk::ObjectFactory< Self >::Create();
-
-#ifdef ITK_USE_FFTWD
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( double ) )
- {
- smartPtr = dynamic_cast< Self* >(
- FFTW1DComplexToComplexImageFilter< double, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-#ifdef ITK_USE_FFTWF
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( float ) )
- {
- smartPtr = dynamic_cast<Self *>(
- FFTW1DComplexToComplexImageFilter< float, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-
- if( smartPtr.IsNull() )
- {
- smartPtr = VnlFFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
- ::New().GetPointer();
- }
-
- return smartPtr;
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::FFT1DComplexToComplexImageFilter():
- m_Direction(0), m_TransformDirection( DIRECT )
-{
- this->m_ImageRegionSplitter = ImageRegionSplitterDirection::New();
-}
-
-
-template <typename TInputImage, typename TOutputImage>
-const ImageRegionSplitterBase*
-FFT1DComplexToComplexImageFilter < TInputImage, TOutputImage >
-::GetImageRegionSplitter(void) const
-{
- return this->m_ImageRegionSplitter.GetPointer();
-}
-
-
-template<typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter < TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- this->m_ImageRegionSplitter->SetDirection( this->GetDirection() );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- typename InputImageType::Pointer inputPtr =
- const_cast<InputImageType *> (this->GetInput());
- typename OutputImageType::Pointer outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->m_Direction;
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast<OutputImageType*>( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- enlargedSize[this->m_Direction] = outputLargeSize[this->m_Direction];
- enlargedIndex[this->m_Direction] = outputLargeIndex[this->m_Direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Direction: " << m_Direction << std::endl;
- os << indent << "TransformDirection: " << m_TransformDirection << std::endl;
-}
-
-
-} // end namespace itk
-
-#endif // itkFFT1DComplexToComplexImageFilter_hxx
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h
deleted file mode 100644
index 6dfb296bc3..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.h
+++ /dev/null
@@ -1,119 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DRealToComplexConjugateImageFilter_h
-#define itkFFT1DRealToComplexConjugateImageFilter_h
-
-#include <complex>
-
-#include "itkImageToImageFilter.h"
-#include "itkImageRegionSplitterDirection.h"
-
-namespace itk
-{
-/** \class FFT1DRealToComplexConjugateImageFilter
- * \brief Perform the Fast Fourier Transform, in the forward direction, with
- * real inputs, but only along one dimension.
- *
- * \ingroup FourierTransform
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
-class FFT1DRealToComplexConjugateImageFilter:
- public ImageToImageFilter< TInputImage, TOutputImage >
-{
-public:
-
- /** Standard class typedefs. */
- typedef TInputImage InputImageType;
- typedef TOutputImage OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- typedef FFT1DRealToComplexConjugateImageFilter Self;
- typedef ImageToImageFilter< InputImageType, OutputImageType > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- itkStaticConstMacro( ImageDimension, unsigned int, InputImageType::ImageDimension );
-
- itkTypeMacro( FFT1DRealToComplexConjugateImageFilter, ImageToImageFilter );
-
- /** Customized object creation methods that support configuration-based
- * selection of FFT implementation.
- *
- * Default implementation is VnlFFT1D.
- */
- static Pointer New();
-
- /** Get the direction in which the filter is to be applied. */
- itkGetMacro(Direction, unsigned int);
-
- /** Set the direction in which the filter is to be applied. */
- itkSetClampMacro(Direction, unsigned int, 0, ImageDimension - 1);
-
-protected:
- FFT1DRealToComplexConjugateImageFilter();
- virtual ~FFT1DRealToComplexConjugateImageFilter() {}
-
- void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;
- virtual void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- virtual void BeforeThreadedGenerateData() ITK_OVERRIDE;
-
- /** Override to return a splitter that does not split along the direction we
- * are performing the transform. */
- virtual const ImageRegionSplitterBase* GetImageRegionSplitter() const ITK_OVERRIDE;
-
-private:
- FFT1DRealToComplexConjugateImageFilter( const Self& );
- void operator=( const Self& );
-
- ImageRegionSplitterDirection::Pointer m_ImageRegionSplitter;
-
- /** Direction in which the filter is to be applied
- * this should be in the range [0,ImageDimension-1]. */
- unsigned int m_Direction;
-
-};
-}
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_h
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_hxx
-#ifndef itkFFTW1DRealToComplexConjugateImageFilter_h
-#ifndef itkFFTW1DRealToComplexConjugateImageFilter_hxx
-#include "itkFFT1DRealToComplexConjugateImageFilter.hxx"
-#endif
-#endif
-#endif
-#endif
-#endif
-
-#endif // itkFFT1DRealToComplexConjugateImageFilter_h
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx
deleted file mode 100644
index 469f702479..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkFFT1DRealToComplexConjugateImageFilter.hxx
+++ /dev/null
@@ -1,203 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkFFT1DRealToComplexConjugateImageFilter_hxx
-#define itkFFT1DRealToComplexConjugateImageFilter_hxx
-
-#include "itkFFT1DRealToComplexConjugateImageFilter.h"
-
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.h"
-
-#if defined(ITK_USE_FFTWD) || defined(ITK_USE_FFTWF)
-#include "itkFFTW1DRealToComplexConjugateImageFilter.h"
-#endif
-
-#include "itkMetaDataObject.h"
-
-namespace itk
-{
-
-template < typename TInputImage, typename TOutputImage >
-typename FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >::Pointer
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::New()
-{
- Pointer smartPtr = ::itk::ObjectFactory< Self >::Create();
-
-#ifdef ITK_USE_FFTWD
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( double ) )
- {
- smartPtr = dynamic_cast< Self* >(
- FFTW1DRealToComplexConjugateImageFilter< double, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-#ifdef ITK_USE_FFTWF
- if( smartPtr.IsNull() )
- {
- if( typeid( TPixel ) == typeid( float ) )
- {
- smartPtr = dynamic_cast<Self *>(
- FFTW1DRealToComplexConjugateImageFilter< float, VDimension >
- ::New().GetPointer() );
- }
- }
-#endif
-
- if( smartPtr.IsNull() )
- {
- smartPtr = VnlFFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
- ::New().GetPointer();
- }
-
- return smartPtr;
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::FFT1DRealToComplexConjugateImageFilter():
- m_Direction( 0 )
-{
- this->m_ImageRegionSplitter = ImageRegionSplitterDirection::New();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-const ImageRegionSplitterBase*
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::GetImageRegionSplitter() const
-{
- return this->m_ImageRegionSplitter.GetPointer();
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::BeforeThreadedGenerateData()
-{
- this->m_ImageRegionSplitter->SetDirection( this->GetDirection() );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::GenerateInputRequestedRegion()
-{
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- typename InputImageType::Pointer inputPtr =
- const_cast<InputImageType *> (this->GetInput());
- typename OutputImageType::Pointer outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->m_Direction;
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize( inputRequestedRegionSize );
- inputRequestedRegion.SetIndex( inputRequestedRegionStartIndex );
-
- inputPtr->SetRequestedRegion( inputRequestedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter < TInputImage, TOutputImage >
-::EnlargeOutputRequestedRegion(DataObject *output)
-{
- OutputImageType* outputPtr = dynamic_cast< OutputImageType * >( output );
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- enlargedSize[this->m_Direction] = outputLargeSize[this->m_Direction];
- enlargedIndex[this->m_Direction] = outputLargeIndex[this->m_Direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize( enlargedSize );
- enlargedRegion.SetIndex( enlargedIndex );
- outputPtr->SetRequestedRegion( enlargedRegion );
-}
-
-
-template< typename TInputImage, typename TOutputImage >
-void
-FFT1DRealToComplexConjugateImageFilter < TInputImage, TOutputImage >
-::PrintSelf( std::ostream& os, Indent indent ) const
-{
- Superclass::PrintSelf( os, indent );
-
- os << indent << "Direction: " << m_Direction << std::endl;
-}
-
-} // end namespace itk
-
-#endif // itkFFT1DRealToComplexConjugateImageFilter_hxx
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkRegionFromReferenceImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkRegionFromReferenceImageFilter.h
deleted file mode 100644
index 41d9bc62d6..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkRegionFromReferenceImageFilter.h
+++ /dev/null
@@ -1,139 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkRegionFromReferenceImageFilter_h
-#define itkRegionFromReferenceImageFilter_h
-
-#include "itkExtractImageFilter.h"
-
-namespace itk
-{
-
-/** \class RegionFromReferenceImageFilter
- * \brief Decrease the image size by cropping the image by an itk::Size at
- * both the upper and lower bounds of the largest possible region.
- *
- * RegionFromReferenceImageFilter changes the image boundary of an image by removing
- * pixels outside the target region. The target region is not specified in
- * advance, but calculated in BeforeThreadedGenerateData().
- *
- * This filter uses ExtractImageFilter to perform the cropping.
- *
- * \ingroup GeometricTransforms
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=TInputImage >
-class RegionFromReferenceImageFilter:
- public ExtractImageFilter<TInputImage,TOutputImage>
-{
-public:
- /** Standard class typedefs. */
- typedef RegionFromReferenceImageFilter Self;
- typedef ExtractImageFilter<TInputImage,TOutputImage> Superclass;
- typedef SmartPointer<Self> Pointer;
- typedef SmartPointer<const Self> ConstPointer;
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(RegionFromReferenceImageFilter, ExtractImageFilter);
-
- /** Typedef to describe the output and input image region types. */
- typedef typename Superclass::OutputImageRegionType OutputImageRegionType;
- typedef typename Superclass::InputImageRegionType InputImageRegionType;
-
- /** Typedef to describe the type of pixel. */
- typedef typename Superclass::OutputImagePixelType OutputImagePixelType;
- typedef typename Superclass::InputImagePixelType InputImagePixelType;
-
- /** Typedef to describe the output and input image index and size types. */
- typedef typename Superclass::OutputImageIndexType OutputImageIndexType;
- typedef typename Superclass::InputImageIndexType InputImageIndexType;
- typedef typename Superclass::OutputImageSizeType OutputImageSizeType;
- typedef typename Superclass::InputImageSizeType InputImageSizeType;
- typedef InputImageSizeType SizeType;
-
- /** ImageDimension constants */
- itkStaticConstMacro(InputImageDimension, unsigned int,
- Superclass::InputImageDimension);
- itkStaticConstMacro(OutputImageDimension, unsigned int,
- Superclass::OutputImageDimension);
- itkStaticConstMacro(ImageDimension, unsigned int,
- Superclass::OutputImageDimension);
-
- typedef ImageBase< itkGetStaticConstMacro( ImageDimension ) > ReferenceImageType;
-
- /** Copy the output information from another Image. */
- void SetReferenceImage ( const ReferenceImageType *image );
-
- const ReferenceImageType * GetReferenceImage() const;
-
- /** Set the input image */
- void SetInput1(const TInputImage *input)
- {
- this->SetInput( input );
- }
-
- /** Set the reference image */
- void SetInput2(const ReferenceImageType *input)
- {
- this->SetReferenceImage( input );
- }
-
-
-#ifdef ITK_USE_CONCEPT_CHECKING
- /** Begin concept checking */
- itkConceptMacro(InputConvertibleToOutputCheck,
- (Concept::Convertible<InputImagePixelType, OutputImagePixelType>));
- itkConceptMacro(SameDimensionCheck,
- (Concept::SameDimension<InputImageDimension, OutputImageDimension>));
- /** End concept checking */
-#endif
-
-protected:
- RegionFromReferenceImageFilter()
- {
- this->SetNumberOfRequiredInputs(2);
- }
- ~RegionFromReferenceImageFilter() {}
-
- virtual void GenerateOutputInformation() ITK_OVERRIDE;
-
-private:
- RegionFromReferenceImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkRegionFromReferenceImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx
deleted file mode 100644
index 277794c7f2..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkRegionFromReferenceImageFilter.hxx
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkRegionFromReferenceImageFilter_hxx
-#define itkRegionFromReferenceImageFilter_hxx
-
-#include "itkRegionFromReferenceImageFilter.h"
-
-namespace itk
-{
-
-template <typename TInputImage, typename TOutputImage>
-void
-RegionFromReferenceImageFilter<TInputImage, TOutputImage>
-::GenerateOutputInformation()
-{
- if( !this->GetInput() || !this->GetReferenceImage() )
- {
- return;
- }
-
- // Superclass::Superclass::GenerateOutputInformation();
- this->SetExtractionRegion( this->GetReferenceImage()->GetLargestPossibleRegion() );
- Superclass::GenerateOutputInformation();
-}
-
-
-template <typename TInputImage, typename TOutputImage>
-void
-RegionFromReferenceImageFilter<TInputImage,TOutputImage>
-::SetReferenceImage ( const ReferenceImageType *image )
-{
- itkDebugMacro("setting input ReferenceImage to " << image);
- if( image != static_cast<const ReferenceImageType *>(this->GetInput( 1 )) )
- {
- this->ProcessObject::SetNthInput(1, const_cast< ReferenceImageType *>( image ) );
- this->Modified();
- }
-}
-
-
-template <typename TInputImage, typename TOutputImage>
-const typename RegionFromReferenceImageFilter<TInputImage,TOutputImage>::ReferenceImageType *
-RegionFromReferenceImageFilter<TInputImage,TOutputImage>
-::GetReferenceImage() const
-{
- Self * surrogate = const_cast< Self * >( this );
-
- const DataObject * input = surrogate->ProcessObject::GetInput(1);
-
- const ReferenceImageType * referenceImage = static_cast<const ReferenceImageType *>( input );
-
- return referenceImage;
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h
deleted file mode 100644
index bf225d99de..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.h
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexConjugateToRealImageFilter_h
-#define itkVnlFFT1DComplexConjugateToRealImageFilter_h
-
-#include "itkFFT1DComplexConjugateToRealImageFilter.h"
-#include <complex>
-
-namespace itk
-{
-
-/** \class VnlFFT1DComplexConjugateToRealImageFilter
- *
- * \brief Perform the FFT along one dimension of an image using Vnl as a
- * backend.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=Image< typename NumericTraits< typename TInputImage::PixelType >::ValueType, TInputImage::ImageDimension > >
-class VnlFFT1DComplexConjugateToRealImageFilter:
- public FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef VnlFFT1DComplexConjugateToRealImageFilter Self;
- typedef FFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- typedef typename Superclass::InputImageType InputImageType;
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Run-time type information (and related methods). */
- itkTypeMacro( VnlFFT1DComplexConjugateToRealImageFilter, FFT1DComplexConjugateToRealImageFilter );
-
-protected:
- virtual void ThreadedGenerateData( const OutputImageRegionType&, ThreadIdType threadID ); // generates output from input
-
- VnlFFT1DComplexConjugateToRealImageFilter() { }
- virtual ~VnlFFT1DComplexConjugateToRealImageFilter() { }
-
-private:
- VnlFFT1DComplexConjugateToRealImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkVnlFFT1DComplexConjugateToRealImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx
deleted file mode 100644
index d77ad681a1..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexConjugateToRealImageFilter.hxx
+++ /dev/null
@@ -1,110 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexConjugateToRealImageFilter_hxx
-#define itkVnlFFT1DComplexConjugateToRealImageFilter_hxx
-
-#include "itkVnlFFT1DComplexConjugateToRealImageFilter.h"
-
-#include "itkFFT1DComplexConjugateToRealImageFilter.hxx"
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkIndent.h"
-#include "itkMetaDataObject.h"
-#include "itkExceptionObject.h"
-#include "vnl/algo/vnl_fft_base.h"
-#include "vnl/algo/vnl_fft_1d.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-void
-VnlFFT1DComplexConjugateToRealImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegion, ThreadIdType itkNotUsed( threadID ) )
-{
- // get pointers to the input and output
- const typename Superclass::InputImageType * inputPtr = this->GetInput();
- typename Superclass::OutputImageType * outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- const typename Superclass::InputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
-
- unsigned int vec_size = inputSize[this->m_Direction];
-
- typedef itk::ImageLinearConstIteratorWithIndex< InputImageType > InputIteratorType;
- typedef itk::ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegion );
- OutputIteratorType outputIt( outputPtr, outputRegion );
-
- inputIt.SetDirection(this->m_Direction);
- outputIt.SetDirection(this->m_Direction);
-
- typedef typename TOutputImage::PixelType OutputPixelType;
- vnl_vector< vcl_complex< OutputPixelType > > inputBuffer( vec_size );
- typename vnl_vector< vcl_complex< OutputPixelType > >::iterator inputBufferIt = inputBuffer.begin();
- // fft is done in-place
- typename vnl_vector< vcl_complex< OutputPixelType > >::iterator outputBufferIt = inputBuffer.begin();
- vnl_fft_1d< OutputPixelType > v1d(vec_size);
-
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- // copy the input line into our buffer
- inputIt.GoToBeginOfLine();
- inputBufferIt = inputBuffer.begin();
- while( !inputIt.IsAtEndOfLine() )
- {
- *inputBufferIt = inputIt.Get();
- ++inputIt;
- ++inputBufferIt;
- }
-
- // do the transform
- v1d.fwd_transform(inputBuffer);
-
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( (*outputBufferIt).real() / vec_size );
- ++outputIt;
- ++outputBufferIt;
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h
deleted file mode 100644
index 8c8c6e2614..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.h
+++ /dev/null
@@ -1,85 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_h
-#define itkVnlFFT1DComplexToComplexImageFilter_h
-
-#include "itkFFT1DComplexToComplexImageFilter.h"
-#include <complex>
-
-namespace itk
-{
-
-/** \class VnlFFT1DComplexToComplexImageFilter
- *
- * \brief Perform the FFT along one dimension of an image using Vnl as a
- * backend.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage >
-class VnlFFT1DComplexToComplexImageFilter:
- public FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef VnlFFT1DComplexToComplexImageFilter Self;
- typedef FFT1DComplexToComplexImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- typedef typename Superclass::InputImageType InputImageType;
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- typedef typename Superclass::TransformDirectionType TransformDirectionType;
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Run-time type information (and related methods). */
- itkTypeMacro( VnlFFT1DComplexToComplexImageFilter, FFT1DComplexToComplexImageFilter );
-
-protected:
- VnlFFT1DComplexToComplexImageFilter() {}
- virtual ~VnlFFT1DComplexToComplexImageFilter() {}
-
- virtual void ThreadedGenerateData( const OutputImageRegionType&, ThreadIdType threadID ) ITK_OVERRIDE;
-
-private:
- VnlFFT1DComplexToComplexImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkVnlFFT1DComplexToComplexImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx
deleted file mode 100644
index 3ab41c2caa..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DComplexToComplexImageFilter.hxx
+++ /dev/null
@@ -1,127 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DComplexToComplexImageFilter_hxx
-#define itkVnlFFT1DComplexToComplexImageFilter_hxx
-
-#include "itkVnlFFT1DComplexToComplexImageFilter.h"
-
-#include "itkFFT1DComplexToComplexImageFilter.hxx"
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkIndent.h"
-#include "itkMetaDataObject.h"
-#include "itkExceptionObject.h"
-#include "vnl/algo/vnl_fft_base.h"
-#include "vnl/algo/vnl_fft_1d.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-void
-VnlFFT1DComplexToComplexImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegion, ThreadIdType itkNotUsed( threadID ) )
-{
- // get pointers to the input and output
- const typename Superclass::InputImageType * inputPtr = this->GetInput();
- typename Superclass::OutputImageType * outputPtr = this->GetOutput();
-
- if ( !inputPtr || !outputPtr )
- {
- return;
- }
-
- const typename Superclass::InputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
-
- const unsigned int direction = this->GetDirection();
- const unsigned int vectorSize = inputSize[direction];
-
- typedef itk::ImageLinearConstIteratorWithIndex< InputImageType > InputIteratorType;
- typedef itk::ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegion );
- OutputIteratorType outputIt( outputPtr, outputRegion );
-
- inputIt.SetDirection( direction );
- outputIt.SetDirection( direction );
-
- typedef typename TInputImage::PixelType PixelType;
- typedef vnl_vector< PixelType > VNLVectorType;
- VNLVectorType inputBuffer( vectorSize );
- typename VNLVectorType::iterator inputBufferIt = inputBuffer.begin();
- // fft is done in-place
- typename VNLVectorType::iterator outputBufferIt = inputBuffer.begin();
- vnl_fft_1d< typename NumericTraits< PixelType >::ValueType > v1d(vectorSize);
-
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin(); !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- // copy the input line into our buffer
- inputIt.GoToBeginOfLine();
- inputBufferIt = inputBuffer.begin();
- while( !inputIt.IsAtEndOfLine() )
- {
- *inputBufferIt = inputIt.Get();
- ++inputIt;
- ++inputBufferIt;
- }
-
- // do the transform
- if( this->m_TransformDirection == Superclass::DIRECT )
- {
- v1d.bwd_transform(inputBuffer);
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( *outputBufferIt );
- ++outputIt;
- ++outputBufferIt;
- }
- }
- else // m_TransformDirection == INVERSE
- {
- v1d.fwd_transform(inputBuffer);
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( (*outputBufferIt) / static_cast< PixelType >( vectorSize ));
- ++outputIt;
- ++outputBufferIt;
- }
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h
deleted file mode 100644
index 679b4b5bae..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.h
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_h
-#define itkVnlFFT1DRealToComplexConjugateImageFilter_h
-
-#include "itkFFT1DRealToComplexConjugateImageFilter.h"
-#include <complex>
-
-namespace itk
-{
-
-/** \class VnlFFT1DRealToComplexConjugateImageFilter
- *
- * \brief Perform the FFT along one dimension of an image using Vnl as a
- * backend.
- *
- * \ingroup Ultrasound
- */
-template< typename TInputImage, typename TOutputImage=Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
-class VnlFFT1DRealToComplexConjugateImageFilter :
- public FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-{
-public:
- /** Standard class typedefs. */
- typedef VnlFFT1DRealToComplexConjugateImageFilter Self;
- typedef FFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- typedef typename Superclass::InputImageType InputImageType;
- typedef typename Superclass::OutputImageType OutputImageType;
- typedef typename OutputImageType::RegionType OutputImageRegionType;
-
- /** Method for creation through the object factory. */
- itkNewMacro( Self );
-
- /** Run-time type information (and related methods). */
- itkTypeMacro( VnlFFT1DRealToComplexConjugateImageFilter, FFT1DRealToComplexConjugateImageFilter );
-
-protected:
- virtual void ThreadedGenerateData( const OutputImageRegionType&, ThreadIdType threadID ) ITK_OVERRIDE;
-
- VnlFFT1DRealToComplexConjugateImageFilter() { }
- ~VnlFFT1DRealToComplexConjugateImageFilter() { }
-
-private:
- VnlFFT1DRealToComplexConjugateImageFilter(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
-};
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.hxx"
-#endif
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx b/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx
deleted file mode 100644
index 0d38c0d745..0000000000
--- a/Modules/US/USHardwareDiPhAS/ITKUltrasound/itkVnlFFT1DRealToComplexConjugateImageFilter.hxx
+++ /dev/null
@@ -1,115 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
- *
- * Copyright Insight Software Consortium
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0.txt
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- *
- *=========================================================================*/
-#ifndef itkVnlFFT1DRealToComplexConjugateImageFilter_hxx
-#define itkVnlFFT1DRealToComplexConjugateImageFilter_hxx
-
-#include "itkVnlFFT1DRealToComplexConjugateImageFilter.h"
-
-#include "itkFFT1DRealToComplexConjugateImageFilter.hxx"
-#include "itkImageLinearConstIteratorWithIndex.h"
-#include "itkImageLinearIteratorWithIndex.h"
-#include "itkIndent.h"
-#include "itkMetaDataObject.h"
-#include "itkExceptionObject.h"
-#include "itkVnlFFTCommon.h"
-#include "vnl/algo/vnl_fft_base.h"
-#include "vnl/algo/vnl_fft_1d.h"
-
-namespace itk
-{
-
-template< typename TInputImage, typename TOutputImage >
-void
-VnlFFT1DRealToComplexConjugateImageFilter< TInputImage, TOutputImage >
-::ThreadedGenerateData( const OutputImageRegionType& outputRegion, ThreadIdType itkNotUsed( threadID ) )
-{
- // get pointers to the input and output
- const typename Superclass::InputImageType * inputPtr = this->GetInput();
- typename Superclass::OutputImageType * outputPtr = this->GetOutput();
-
- const typename Superclass::InputImageType::SizeType & inputSize = inputPtr->GetRequestedRegion().GetSize();
-
- const unsigned int direction = this->GetDirection();
- unsigned int vectorSize = inputSize[direction];
- if( ! VnlFFTCommon::IsDimensionSizeLegal(vectorSize) )
- {
- itkExceptionMacro("Illegal Array DIM for FFT");
- }
-
-
- typedef ImageLinearConstIteratorWithIndex< InputImageType > InputIteratorType;
- typedef ImageLinearIteratorWithIndex< OutputImageType > OutputIteratorType;
- InputIteratorType inputIt( inputPtr, outputRegion );
- OutputIteratorType outputIt( outputPtr, outputRegion );
-
- inputIt.SetDirection( direction );
- outputIt.SetDirection( direction );
-
- typedef typename TInputImage::PixelType PixelType;
- typedef vcl_complex< PixelType > ComplexType;
- typedef vnl_vector< ComplexType > ComplexVectorType;
- ComplexVectorType inputBuffer( vectorSize );
- typename ComplexVectorType::iterator inputBufferIt = inputBuffer.begin();
- // fft is done in-place
- typename ComplexVectorType::iterator outputBufferIt = inputBuffer.begin();
- vnl_fft_1d< PixelType > v1d( vectorSize );
-
- // for every fft line
- for( inputIt.GoToBegin(), outputIt.GoToBegin();
- !inputIt.IsAtEnd();
- outputIt.NextLine(), inputIt.NextLine() )
- {
- // copy the input line into our buffer
- inputIt.GoToBeginOfLine();
- inputBufferIt = inputBuffer.begin();
- while( !inputIt.IsAtEndOfLine() )
- {
- *inputBufferIt = inputIt.Value();
- ++inputIt;
- ++inputBufferIt;
- }
-
- // do the transform
- v1d.bwd_transform( inputBuffer );
-
- // copy the output from the buffer into our line
- outputBufferIt = inputBuffer.begin();
- outputIt.GoToBeginOfLine();
- while( !outputIt.IsAtEndOfLine() )
- {
- outputIt.Set( *outputBufferIt );
- ++outputIt;
- ++outputBufferIt;
- }
- }
-}
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/Resources/Fluence05.nrrd b/Modules/US/USHardwareDiPhAS/Resources/Fluence05.nrrd
deleted file mode 100644
index 224a89f7ff..0000000000
Binary files a/Modules/US/USHardwareDiPhAS/Resources/Fluence05.nrrd and /dev/null differ
diff --git a/Modules/US/USHardwareDiPhAS/Resources/Fluence06.nrrd b/Modules/US/USHardwareDiPhAS/Resources/Fluence06.nrrd
deleted file mode 100644
index 224a89f7ff..0000000000
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diff --git a/Modules/US/USHardwareDiPhAS/Resources/Fluence25.nrrd b/Modules/US/USHardwareDiPhAS/Resources/Fluence25.nrrd
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diff --git a/Modules/US/USHardwareDiPhAS/files.cmake b/Modules/US/USHardwareDiPhAS/files.cmake
deleted file mode 100644
index 84d6550ddb..0000000000
--- a/Modules/US/USHardwareDiPhAS/files.cmake
+++ /dev/null
@@ -1,34 +0,0 @@
-SET(CPP_FILES
-mitkUSDiPhASActivator.cpp
-mitkUSDiPhASDevice.cpp
-mitkUSDiPhASImageSource.cpp
-mitkUSDiPhASProbe.cpp
-mitkUSDiPhASProbesControls.cpp
-mitkUSDiPhASCustomControls.cpp
-mitkUSDiPhASBModeImageFilter.hxx
-mitkUSDiPhASBModeImageFilter.h
-)
-
-set(RESOURCE_FILES
- Fluence05.nrrd
- Fluence06.nrrd
- Fluence07.nrrd
- Fluence08.nrrd
- Fluence09.nrrd
- Fluence10.nrrd
- Fluence11.nrrd
- Fluence12.nrrd
- Fluence13.nrrd
- Fluence14.nrrd
- Fluence15.nrrd
- Fluence16.nrrd
- Fluence17.nrrd
- Fluence18.nrrd
- Fluence19.nrrd
- Fluence20.nrrd
- Fluence21.nrrd
- Fluence22.nrrd
- Fluence23.nrrd
- Fluence24.nrrd
- Fluence25.nrrd
- )
\ No newline at end of file
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASActivator.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASActivator.cpp
deleted file mode 100644
index e3a7d7c8f4..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASActivator.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkUSDiPhASActivator.h"
-
-mitk::USDiPhASActivator::USDiPhASActivator()
-{
- MITK_INFO << "USDiPhASActivator created";
-}
-
-mitk::USDiPhASActivator::~USDiPhASActivator()
-{
-}
-
-void mitk::USDiPhASActivator::Load(us::ModuleContext* context)
-{
- // create a new device
- m_Device = mitk::USDiPhASDevice::New("DiPhAS", "Ultrasound System");
- m_Device->Initialize();
-}
-
-void mitk::USDiPhASActivator::Unload(us::ModuleContext* context)
-{
- // set smart pointer to null (device will be unregistered from
- // micro service in it's destrcutor)
- m_Device = 0;
-}
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASActivator.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASActivator.h
deleted file mode 100644
index 172e6656b8..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASActivator.h
+++ /dev/null
@@ -1,49 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef __mitkUSDiPhASActivator_h
-#define __mitkUSDiPhASActivator_h
-
-#include "mitkUSDiPhASDevice.h"
-
-// Microservices
-#include <usModuleContext.h>
-#include <usModuleActivator.h>
-
-namespace mitk
-{
- class USDiPhASActivator : public us::ModuleActivator {
- public:
-
- USDiPhASActivator();
- virtual ~USDiPhASActivator();
-
- /**
- * \brief DiPhAS device is created and initialized on module load.
- * Service registration is done during the initialization process.
- */
- void Load(us::ModuleContext* context);
-
- /**
- * \brief Device pointer is removed on module unload.
- * Service deregistration is done in the device destructor.
- */
- void Unload(us::ModuleContext* context);
-
- protected:
- USDiPhASDevice::Pointer m_Device;
- };
-} // namespace mitk
-
-US_EXPORT_MODULE_ACTIVATOR(mitk::USDiPhASActivator)
-
-#endif // __mitkUSDiPhASActivator_h
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASBModeImageFilter.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASBModeImageFilter.h
deleted file mode 100644
index ba7eb074e3..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASBModeImageFilter.h
+++ /dev/null
@@ -1,143 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
-*
-* Copyright Insight Software Consortium
-*
-* Licensed under the Apache License, Version 2.0 (the "License");
-* you may not use this file except in compliance with the License.
-* You may obtain a copy of the License at
-*
-* http://www.apache.org/licenses/LICENSE-2.0.txt
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*
-*=========================================================================*/
-#ifndef itkPhotoacousticBModeImageFilter_h
-#define itkPhotoacousticBModeImageFilter_h
-
-#include "itkComplexToModulusImageFilter.h"
-#include "itkConstantPadImageFilter.h"
-#include "itkImageToImageFilter.h"
-#include "itkImage.h"
-
-#include "ITKUltrasound/itkRegionFromReferenceImageFilter.h"
-#include "ITKUltrasound/itkAnalyticSignalImageFilter.h"
-
-namespace itk
-{
-
- /**
- * \class PhotoacousticBModeImageFilter
- *
- * \brief Create an Photoacoustic B-Mode (Brightness-Mode) image from raw
- * "RF" data. The RF's envelope is calculated from the analytic signal and
- * logarithmic intensity transform is NOT applied. This is for now the only
- * difference to the "normal" BModeImageFilter.
- *
- * Use SetDirection() to define the axis of propagation.
- *
- */
- template < typename TInputImage, typename TOutputImage = TInputImage, typename TComplexImage = Image< std::complex< typename TInputImage::PixelType >, TInputImage::ImageDimension > >
- class PhotoacousticBModeImageFilter :
- public ImageToImageFilter< TInputImage, TOutputImage >
- {
- public:
- /** Standard class typedefs. */
- typedef PhotoacousticBModeImageFilter Self;
- typedef ImageToImageFilter< TInputImage, TOutputImage > Superclass;
- typedef SmartPointer< Self > Pointer;
- typedef SmartPointer< const Self > ConstPointer;
-
- /** The type of input image. */
- typedef TInputImage InputImageType;
-
- /** Dimension of the input and output images. */
- itkStaticConstMacro(ImageDimension, unsigned int,
- TInputImage::ImageDimension);
-
- /** Typedef support for the input image scalar value type. */
- typedef typename InputImageType::PixelType InputPixelType;
-
- /** The type of output image. */
- typedef TOutputImage OutputImageType;
-
- /** Typedef support for the output image scalar value type. */
- typedef typename OutputImageType::PixelType OutputPixelType;
-
- /** Typedef of the image used for internal computations that has
- * std::complex pixels. */
- typedef TComplexImage ComplexImageType;
-
- /** Other convenient typedefs */
- typedef typename InputImageType::RegionType InputRegionType;
- typedef typename InputImageType::SizeType InputSizeType;
- typedef typename InputImageType::IndexType InputIndexType;
-
- /** Run-time type information (and related methods) */
- itkTypeMacro(PhotoacousticBModeImageFilter, ImageToImageFilter);
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Set the direction in which the envelope is to be calculated. */
- virtual void SetDirection(unsigned int direction)
- {
- this->m_AnalyticFilter->SetDirection(direction);
- this->Modified();
- }
-
- /** Get the direction in which the envelope is to be calculated. */
- virtual unsigned int GetDirection() const
- {
- return m_AnalyticFilter->GetDirection();
- }
-
- protected:
- PhotoacousticBModeImageFilter();
- ~PhotoacousticBModeImageFilter() {}
-
- virtual void PrintSelf(std::ostream& os, Indent indent) const ITK_OVERRIDE;
-
- virtual void GenerateData() ITK_OVERRIDE;
-
- // These behave like their analogs in FFT1DRealToComplexConjugateImageFilter.
- virtual void GenerateInputRequestedRegion() ITK_OVERRIDE;
- virtual void EnlargeOutputRequestedRegion(DataObject *output) ITK_OVERRIDE;
-
- /** Component filters. */
- typedef AnalyticSignalImageFilter< InputImageType, ComplexImageType > AnalyticType;
- typedef ComplexToModulusImageFilter< typename AnalyticType::OutputImageType, OutputImageType > ComplexToModulusType;
- typedef ConstantPadImageFilter< InputImageType, InputImageType > PadType;
- typedef RegionFromReferenceImageFilter< OutputImageType, OutputImageType > ROIType;
-
- private:
- PhotoacousticBModeImageFilter(const Self&); // purposely not implemented
- void operator=(const Self&); // purposely not implemented
-
- typename AnalyticType::Pointer m_AnalyticFilter;
- typename ComplexToModulusType::Pointer m_ComplexToModulusFilter;
- typename PadType::Pointer m_PadFilter;
- typename ROIType::Pointer m_ROIFilter;
- };
-
-} // end namespace itk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "mitkUSDiPhASBModeImageFilter.hxx"
-#endif
-
-#endif // itkPhotoacousticBModeImageFilter_h
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASBModeImageFilter.hxx b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASBModeImageFilter.hxx
deleted file mode 100644
index 4b34a1ae0e..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASBModeImageFilter.hxx
+++ /dev/null
@@ -1,203 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-/*=========================================================================
-*
-* Copyright Insight Software Consortium
-*
-* Licensed under the Apache License, Version 2.0 (the "License");
-* you may not use this file except in compliance with the License.
-* You may obtain a copy of the License at
-*
-* http://www.apache.org/licenses/LICENSE-2.0.txt
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*
-*=========================================================================*/
-#ifndef itkPhotoacousticBModeImageFilter_hxx
-#define itkPhotoacousticBModeImageFilter_hxx
-
-#include "mitkUSDiPhASBModeImageFilter.h"
-
-#include "itkMetaDataDictionary.h"
-
-#include <algorithm>
-#include <sstream>
-#include <string>
-
-namespace itk
-{
-
- template < typename TInputImage, typename TOutputImage, typename TComplexImage >
- PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
- ::PhotoacousticBModeImageFilter()
- {
- m_AnalyticFilter = AnalyticType::New();
- m_ComplexToModulusFilter = ComplexToModulusType::New();
- m_PadFilter = PadType::New();
- m_ROIFilter = ROIType::New();
-
- m_PadFilter->SetConstant(0.);
- m_ComplexToModulusFilter->SetInput(m_AnalyticFilter->GetOutput());
- m_ROIFilter->SetInput(m_ComplexToModulusFilter->GetOutput());
- }
-
-
- template < typename TInputImage, typename TOutputImage, typename TComplexImage >
- void
- PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
- ::PrintSelf(std::ostream& os, Indent indent) const
- {
- Superclass::PrintSelf(os, indent);
- }
-
-
- template < typename TInputImage, typename TOutputImage, typename TComplexImage >
- void
- PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
- ::GenerateInputRequestedRegion()
- {
- // call the superclass' implementation of this method
- Superclass::GenerateInputRequestedRegion();
-
- // get pointers to the inputs
- InputImageType * inputPtr = const_cast<InputImageType *> (this->GetInput());
- OutputImageType * outputPtr = this->GetOutput();
-
- // we need to compute the input requested region (size and start index)
- typedef const typename OutputImageType::SizeType& OutputSizeType;
- OutputSizeType outputRequestedRegionSize =
- outputPtr->GetRequestedRegion().GetSize();
- typedef const typename OutputImageType::IndexType& OutputIndexType;
- OutputIndexType outputRequestedRegionStartIndex =
- outputPtr->GetRequestedRegion().GetIndex();
-
- //// the regions other than the fft direction are fine
- typename InputImageType::SizeType inputRequestedRegionSize = outputRequestedRegionSize;
- typename InputImageType::IndexType inputRequestedRegionStartIndex = outputRequestedRegionStartIndex;
-
- // we but need all of the input in the fft direction
- const unsigned int direction = this->GetDirection();
- const typename InputImageType::SizeType& inputLargeSize =
- inputPtr->GetLargestPossibleRegion().GetSize();
- inputRequestedRegionSize[direction] = inputLargeSize[direction];
- const typename InputImageType::IndexType& inputLargeIndex =
- inputPtr->GetLargestPossibleRegion().GetIndex();
- inputRequestedRegionStartIndex[direction] = inputLargeIndex[direction];
-
- typename InputImageType::RegionType inputRequestedRegion;
- inputRequestedRegion.SetSize(inputRequestedRegionSize);
- inputRequestedRegion.SetIndex(inputRequestedRegionStartIndex);
-
- inputPtr->SetRequestedRegion(inputRequestedRegion);
- }
-
-
- template < typename TInputImage, typename TOutputImage, typename TComplexImage >
- void
- PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
- ::EnlargeOutputRequestedRegion(DataObject *output)
- {
- OutputImageType* outputPtr = dynamic_cast< OutputImageType* >(output);
-
- // we need to enlarge the region in the fft direction to the
- // largest possible in that direction
- typedef const typename OutputImageType::SizeType& ConstOutputSizeType;
- ConstOutputSizeType requestedSize =
- outputPtr->GetRequestedRegion().GetSize();
- ConstOutputSizeType outputLargeSize =
- outputPtr->GetLargestPossibleRegion().GetSize();
- typedef const typename OutputImageType::IndexType& ConstOutputIndexType;
- ConstOutputIndexType requestedIndex =
- outputPtr->GetRequestedRegion().GetIndex();
- ConstOutputIndexType outputLargeIndex =
- outputPtr->GetLargestPossibleRegion().GetIndex();
-
- typename OutputImageType::SizeType enlargedSize = requestedSize;
- typename OutputImageType::IndexType enlargedIndex = requestedIndex;
- const unsigned int direction = this->GetDirection();
- enlargedSize[direction] = outputLargeSize[direction];
- enlargedIndex[direction] = outputLargeIndex[direction];
-
- typename OutputImageType::RegionType enlargedRegion;
- enlargedRegion.SetSize(enlargedSize);
- enlargedRegion.SetIndex(enlargedIndex);
- outputPtr->SetRequestedRegion(enlargedRegion);
- }
-
-
- template < typename TInputImage, typename TOutputImage, typename TComplexImage >
- void
- PhotoacousticBModeImageFilter< TInputImage, TOutputImage, TComplexImage >
- ::GenerateData()
- {
- this->AllocateOutputs();
-
- const InputImageType * inputPtr = this->GetInput();
- OutputImageType * outputPtr = this->GetOutput();
-
- const unsigned int direction = m_AnalyticFilter->GetDirection();
- typename InputImageType::SizeType size = inputPtr->GetLargestPossibleRegion().GetSize();
-
- // Zero padding. FFT direction should be factorable by 2 for all FFT
- // implementations to work.
- unsigned int n = size[direction];
- while (n % 2 == 0)
- {
- n /= 2;
- }
- bool doPadding;
- if (n == 1)
- {
- doPadding = false;
- }
- else
- {
- doPadding = true;
- }
- if (doPadding)
- {
- n = size[direction];
- unsigned int newSizeDirection = 1;
- while (newSizeDirection < n)
- {
- newSizeDirection *= 2;
- }
- typename InputImageType::SizeType padSize;
- padSize.Fill(0);
- padSize[direction] = newSizeDirection - size[direction];
- size[direction] = newSizeDirection;
- m_PadFilter->SetPadUpperBound(padSize);
- m_PadFilter->SetInput(inputPtr);
- m_AnalyticFilter->SetInput(m_PadFilter->GetOutput());
- m_ROIFilter->SetReferenceImage(inputPtr);
- m_ROIFilter->SetInput(m_ComplexToModulusFilter->GetOutput());
- m_ROIFilter->GraftOutput(outputPtr);
- m_ROIFilter->Update();
- this->GraftOutput(m_ROIFilter->GetOutput());
- }
- else // padding is not required
- {
- m_AnalyticFilter->SetInput(inputPtr);
- m_ComplexToModulusFilter->GraftOutput(outputPtr);
- m_ComplexToModulusFilter->Update();
- this->GraftOutput(m_ComplexToModulusFilter->GetOutput());
- }
-
- }
-
-} // end namespace itk
-
-#endif
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASCustomControls.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASCustomControls.cpp
deleted file mode 100644
index 824a71f279..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASCustomControls.cpp
+++ /dev/null
@@ -1,224 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkUSDiPhASCustomControls.h"
-#include <cmath>
-
-mitk::USDiPhASCustomControls::USDiPhASCustomControls(USDiPhASDevice* device)
- : mitk::USDiPhASDeviceCustomControls(device), m_IsActive(false), m_device(device), currentBeamformingAlgorithm((int)Beamforming::PlaneWaveCompound)
-{
-}
-
-mitk::USDiPhASCustomControls::~USDiPhASCustomControls()
-{
-}
-
-void mitk::USDiPhASCustomControls::SetIsActive(bool isActive)
-{
- m_IsActive = isActive;
-}
-
-bool mitk::USDiPhASCustomControls::GetIsActive()
-{
- return m_IsActive;
-}
-
-void mitk::USDiPhASCustomControls::passGUIOut(std::function<void(QString)> callback)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- callback("initializing");
- imageSource->SetGUIOutput(callback);
-}
-
-// OnSet methods
-
-void mitk::USDiPhASCustomControls::OnSetCompensateEnergy(bool compensate)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- imageSource->ModifyEnergyCompensation(compensate);
-}
-
-void mitk::USDiPhASCustomControls::OnSetUseBModeFilter(bool isSet)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- imageSource->ModifyUseBModeFilter(isSet);
-}
-
-void mitk::USDiPhASCustomControls::OnSetRecord(bool record)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- imageSource->SetRecordingStatus(record);
-}
-
-void mitk::USDiPhASCustomControls::OnSetVerticalSpacing(float mm)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- imageSource->SetVerticalSpacing(mm);
-}
-
-void mitk::USDiPhASCustomControls::OnSetScatteringCoefficient(float coeff)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- imageSource->ModifyScatteringCoefficient(coeff);
-}
-
-void mitk::USDiPhASCustomControls::OnSetCompensateScattering(bool compensate)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- imageSource->ModifyCompensateForScattering(compensate);
-}
-
-void mitk::USDiPhASCustomControls::OnSetSavingSettings(SavingSettings settings)
-{
- mitk::USDiPhASImageSource* imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- imageSource->SetSavingSettings(settings);
-}
-
-//Transmit
-void mitk::USDiPhASCustomControls::OnSetTransmitPhaseLength(double us)
-{
- m_device->GetScanMode().transmitPhaseLengthSeconds = us/1000000;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetExcitationFrequency(double MHz)
-{
- m_device->SetBursts(round(((120 / MHz) - 2) / 2));
- m_device->UpdateScanmode();
- // b = (c/f - 2) * 1/2, where c is the internal clock, f the wanted frequency, b the burst count
-}
-
-void mitk::USDiPhASCustomControls::OnSetTransmitEvents(int events)
-{
- m_device->GetScanMode().transmitEventsCount = events;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetVoltage(int voltage)
-{
- m_device->GetScanMode().voltageV = voltage;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetMode(bool interleaved)
-{
- m_device->SetInterleaved(interleaved);
- m_device->UpdateScanmode();
-}
-
-//Receive
-void mitk::USDiPhASCustomControls::OnSetScanDepth(double mm)
-{
- auto& scanMode = m_device->GetScanMode();
- float time = 2 * (0.001 * (mm)) / scanMode.averageSpeedOfSound;
- float timeInMicroSeconds = floor(time *1e6); // this is necessary because sub-microsecond accuracy causes undefined behaviour
- m_device->GetScanMode().receivePhaseLengthSeconds = timeInMicroSeconds*1e-6;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetAveragingCount(int count)
-{
- m_device->GetScanMode().averagingCount = count;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetTGCMin(int min)
-{
- auto& scanMode = m_device->GetScanMode();
- char range = scanMode.tgcdB[7] - min;
- for (int tgc = 0; tgc < 7; ++tgc)
- scanMode.tgcdB[tgc] = round(tgc*range / 7 + min);
-
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetTGCMax(int max)
-{
- auto& scanMode = m_device->GetScanMode();
- char range = max - scanMode.tgcdB[0];
- for (int tgc = 1; tgc < 8; ++tgc)
- scanMode.tgcdB[tgc] = round(tgc*range / 7 + scanMode.tgcdB[0]);
-
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetDataType(DataType type)
-{
- auto& scanMode = m_device->GetScanMode();
- auto imageSource = dynamic_cast<mitk::USDiPhASImageSource*>(m_device->GetUSImageSource().GetPointer());
- switch (type) {
- case DataType::Image_uChar : {
- scanMode.transferBeamformedData = false;
- scanMode.transferImageData = true;
- m_device->UpdateScanmode();
- imageSource->ModifyDataType(DataType::Image_uChar);
- break;
- }
- case DataType::Beamformed_Short : {
- scanMode.transferBeamformedData = true;
- scanMode.transferImageData = false;
- m_device->UpdateScanmode();
- imageSource->ModifyDataType(DataType::Beamformed_Short);
- break;
- }
-
- default:
- MITK_INFO << "Unknown Data Type requested";
- break;
- }
-}
-// 0= image; 1= beamformed
-
-//Beamforming
-void mitk::USDiPhASCustomControls::OnSetPitch(double mm)
-{
- m_device->GetScanMode().reconstructedLinePitchMmOrAngleDegree = mm;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetReconstructedSamples(int samples)
-{
- m_device->GetScanMode().reconstructionSamplesPerLine = samples;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetReconstructedLines(int lines)
-{
- m_device->GetScanMode().reconstructionLines = lines;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetSpeedOfSound(int mps)
-{
- m_device->GetScanMode().averageSpeedOfSound = mps;
- m_device->SetInterleaved(m_device->IsInterleaved()); //update transmit parameters
- m_device->UpdateScanmode();
-}
-
-//Bandpass
-void mitk::USDiPhASCustomControls::OnSetBandpassEnabled(bool bandpass)
-{
- m_device->GetScanMode().bandpassApply = bandpass;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetLowCut(double MHz)
-{
- m_device->GetScanMode().bandpassFrequencyLowHz = MHz*1000*1000;
- m_device->UpdateScanmode();
-}
-
-void mitk::USDiPhASCustomControls::OnSetHighCut(double MHz)
-{
- m_device->GetScanMode().bandpassFrequencyHighHz = MHz*1000*1000;
- m_device->UpdateScanmode();
-}
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASCustomControls.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASCustomControls.h
deleted file mode 100644
index e58f8ea3d8..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASCustomControls.h
+++ /dev/null
@@ -1,102 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKUSDiPhASCustomControls_H_HEADER_INCLUDED_
-#define MITKUSDiPhASCustomControls_H_HEADER_INCLUDED_
-
-#include "mitkUSDiPhASDeviceCustomControls.h"
-#include "mitkUSDevice.h"
-#include "mitkUSDiPhASDevice.h"
-#include "Framework.IBMT.US.CWrapper.h"
-
-#include <itkObjectFactory.h>
-
-namespace mitk {
-/**
- * \brief Custom controls for mitk::USDiPhASDevice.
- */
-class USDiPhASDevice;
-class USDiPhASCustomControls : public USDiPhASDeviceCustomControls
-{
-public:
- mitkClassMacro(USDiPhASCustomControls, USAbstractControlInterface);
- mitkNewMacro1Param(Self, mitk::USDiPhASDevice*);
-
- typedef USDiPhASDeviceCustomControls::DataType DataType;
- typedef USDiPhASDeviceCustomControls::SavingSettings SavingSettings;
- /**
- * Activate or deactivate the custom controls. This is just for handling
- * widget visibility in a GUI for example.
- */
- virtual void SetIsActive( bool isActive ) override;
-
- /**
- * \return if this custom controls are currently activated
- */
- virtual bool GetIsActive( ) override;
-
- virtual void passGUIOut(std::function<void(QString)> callback) override;
-
- BeamformingParametersPlaneWaveCompound parametersPW;
- BeamformingParametersInterleaved_OA_US parametersOSUS;
-
-protected:
- /**
- * Class needs an mitk::USDiPhASDevice object for beeing constructed.
- * This object's ScanMode will be manipulated by the custom controls methods.
- */
- USDiPhASCustomControls(USDiPhASDevice* device);
- virtual ~USDiPhASCustomControls( );
-
- bool m_IsActive;
- USImageVideoSource::Pointer m_ImageSource;
- USDiPhASDevice* m_device;
- int currentBeamformingAlgorithm;
-
- /** handlers for value changes
- */
- virtual void OnSetCompensateEnergy(bool compensate) override;
- virtual void OnSetUseBModeFilter(bool isSet) override;
- virtual void OnSetRecord(bool record) override;
- virtual void OnSetVerticalSpacing(float mm) override;
- virtual void OnSetScatteringCoefficient(float coeff) override;
- virtual void OnSetCompensateScattering(bool compensate) override;
- virtual void OnSetSavingSettings(SavingSettings settings) override;
-
- //Transmit
- virtual void OnSetTransmitPhaseLength(double us) override;
- virtual void OnSetExcitationFrequency(double MHz) override;
- virtual void OnSetTransmitEvents(int events) override;
- virtual void OnSetVoltage(int voltage) override;
- virtual void OnSetMode(bool interleaved) override;
-
- //Receive
- virtual void OnSetScanDepth(double mm) override;
- virtual void OnSetAveragingCount(int count) override;
- virtual void OnSetTGCMin(int min) override;
- virtual void OnSetTGCMax(int max) override;
- virtual void OnSetDataType(DataType type) override;
-
- //Beamforming
- virtual void OnSetPitch(double mm) override;
- virtual void OnSetReconstructedSamples(int samples) override;
- virtual void OnSetReconstructedLines(int lines) override;
- virtual void OnSetSpeedOfSound(int mps) override;
-
- //Bandpass
- virtual void OnSetBandpassEnabled(bool bandpass) override;
- virtual void OnSetLowCut(double MHz) override;
- virtual void OnSetHighCut(double MHz) override;
-};
-} // namespace mitk
-
-#endif // MITKUSDiPhASCustomControls_H_HEADER_INCLUDED_
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp
deleted file mode 100644
index e5edeadebe..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.cpp
+++ /dev/null
@@ -1,303 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkUSDiPhASDevice.h"
-#include "mitkUSDiPhASCustomControls.h"
-
-mitk::USDiPhASDevice::USDiPhASDevice(std::string manufacturer, std::string model)
- : mitk::USDevice(manufacturer, model), m_ControlsProbes(mitk::USDiPhASProbesControls::New(this)),
- m_ImageSource(mitk::USDiPhASImageSource::New(this)),
- m_ControlInterfaceCustom(mitk::USDiPhASCustomControls::New(this)),
- m_IsRunning(false),
- m_BurstHalfwaveClockCount(7),
- m_Interleaved(true)
-{
- m_NumberOfOutputs = 2;
- this->SetNumberOfIndexedOutputs(m_NumberOfOutputs);
-
- SetNthOutput(0, this->MakeOutput(0));
- SetNthOutput(1, this->MakeOutput(1));
-}
-
-mitk::USDiPhASDevice::~USDiPhASDevice()
-{
-}
-
-//Gets
-
-std::string mitk::USDiPhASDevice::GetDeviceClass()
-{
- return "org.mitk.modules.us.USDiPhASDevice";
-}
-
-mitk::USControlInterfaceProbes::Pointer mitk::USDiPhASDevice::GetControlInterfaceProbes()
-{
- return m_ControlsProbes.GetPointer();
-};
-
-mitk::USAbstractControlInterface::Pointer mitk::USDiPhASDevice::GetControlInterfaceCustom()
-{
- return m_ControlInterfaceCustom.GetPointer();
-}
-
-mitk::USImageSource::Pointer mitk::USDiPhASDevice::GetUSImageSource()
-{
- return m_ImageSource.GetPointer();
-}
-
-ScanModeNative& mitk::USDiPhASDevice::GetScanMode()
-{
- return m_ScanMode;
-}
-
-// Setup and Cleanup
-
-bool mitk::USDiPhASDevice::OnInitialization()
-{
- return true;
-}
-
-//----------------------------------------------------------------------------------------------------------------------------
-/* ugly wrapper stuff - find better solution so it isn't necessary to create a global pointer to USDiPhASDevice...
- * passing a lambda function would be nicer - sadly something goes wrong when passing the adress of a lambda function:
- * the API produces access violations. Passing the Lambda function itself would be preferable, but that's not possible
-*/
-
-mitk::USDiPhASDevice* w_device;
-mitk::USDiPhASImageSource* w_ISource;
-
-void WrapperMessageCallback(const char* message)
-{
- w_device->MessageCallback(message);
-}
-
-void WrapperImageDataCallback(
- short* rfDataChannelData, int channelDatalinesPerDataset, int channelDataSamplesPerChannel, int channelDataTotalDatasets,
- short* rfDataArrayBeamformed, int beamformedLines, int beamformedSamples, int beamformedTotalDatasets,
- unsigned char* imageData, int imageWidth, int imageHeight, int imagePixelFormat, int imageSetsTotal, double timeStamp)
-{
- w_ISource->ImageDataCallback(
- rfDataChannelData, channelDatalinesPerDataset, channelDataSamplesPerChannel, channelDataTotalDatasets,
- rfDataArrayBeamformed, beamformedLines, beamformedSamples, beamformedTotalDatasets,
- imageData, imageWidth, imageHeight, imagePixelFormat, imageSetsTotal, timeStamp);
-}
-
-//----------------------------------------------------------------------------------------------------------------------------
-
-bool mitk::USDiPhASDevice::OnConnection()
-{
- w_device = this;
- w_ISource = m_ImageSource;
- // Need those pointers for the forwarders to call member functions; createBeamformer expects non-member function pointers.
- createBeamformer((StringMessageCallback)&WrapperMessageCallback, (NewDataCallback)&WrapperImageDataCallback);
-
- InitializeScanMode();
- initBeamformer(); //start the hardware connection
-
- m_ImageSource->UpdateImageGeometry(); //make sure the image geometry is initialized!
- // pass the new scanmode to the device:
- setupScan(this->m_ScanMode);
- return true;
-}
-
-bool mitk::USDiPhASDevice::OnDisconnection()
-{
- //close the beamformer so hardware is disconnected
- closeBeamformer();
- return true;
-}
-
-bool mitk::USDiPhASDevice::OnActivation()
-{
- // probe controls are available now
- m_ControlsProbes->SetIsActive(true);
-
- if (m_ControlsProbes->GetProbesCount() < 1)
- {
- MITK_WARN("USDevice")("USDiPhASDevice") << "No probe found.";
- return false;
- }
-
- m_ControlsProbes->SelectProbe(0);
-
- // toggle the beamformer of the API
- if(!m_IsRunning)
- m_IsRunning=toggleFreeze();
- return true;
-}
-
-bool mitk::USDiPhASDevice::OnDeactivation()
-{
- if(m_IsRunning)
- m_IsRunning=toggleFreeze();
- return true;
-}
-
-void mitk::USDiPhASDevice::OnFreeze(bool freeze)
-{
- if(m_IsRunning==freeze)
- m_IsRunning=toggleFreeze(); // toggleFreeze() returns true if it starts running the beamformer, otherwise false
-}
-
-void mitk::USDiPhASDevice::UpdateScanmode()
-{
- OnFreeze(true);
- SetInterleaved(m_Interleaved); // update the beamforming parameters...
- UpdateTransmitEvents();
-
- if (!(dynamic_cast<mitk::USDiPhASCustomControls*>(this->m_ControlInterfaceCustom.GetPointer())->GetSilentUpdate()))
- {
- setupScan(this->m_ScanMode);
- m_ImageSource->UpdateImageGeometry();
- }
-
- OnFreeze(false);
-}
-
-void mitk::USDiPhASDevice::UpdateTransmitEvents()
-{
- int numChannels = m_ScanMode.reconstructionLines;
-
- // transmitEventsCount defines only the number of acoustic measurements (angles); there will be one event added to the start for OA measurement
- m_ScanMode.TransmitEvents = new TransmitEventNative[m_ScanMode.transmitEventsCount];
-
- for (int ev = 0; ev < m_ScanMode.transmitEventsCount; ++ev)
- {
- m_ScanMode.TransmitEvents[ev].transmitEventDelays = new float[numChannels];
- m_ScanMode.TransmitEvents[ev].BurstHalfwaveClockCountPerChannel = new int[numChannels];
- m_ScanMode.TransmitEvents[ev].BurstCountPerChannel = new int[numChannels];
- m_ScanMode.TransmitEvents[ev].BurstUseNegativePolarityPerChannel = new bool[numChannels];
- m_ScanMode.TransmitEvents[ev].ChannelMultiplexerSetups = nullptr;
- float tiltStrength = ((m_ScanMode.transmitEventsCount - 1) / 2 - ev) * 20e-9f;
-
- for (int i = 0; i < numChannels; ++i)
- {
- m_ScanMode.TransmitEvents[ev].BurstHalfwaveClockCountPerChannel[i] = m_BurstHalfwaveClockCount; // 120 MHz / (2 * (predefinedBurstHalfwaveClockCount + 1)) --> 7.5 MHz
- m_ScanMode.TransmitEvents[ev].BurstCountPerChannel[i] = 1; // Burst with 1 cycle
- m_ScanMode.TransmitEvents[ev].BurstUseNegativePolarityPerChannel[i] = true;
- m_ScanMode.TransmitEvents[ev].transmitEventDelays[i] = 2e-6f + (i - numChannels / 2) * tiltStrength;
- }
- }
-
- m_ScanMode.transmitSequenceCount = 1;
- m_ScanMode.transmitSequences = new SequenceNative[m_ScanMode.transmitSequenceCount];
- m_ScanMode.transmitSequences[0].startEvent = 0;
- m_ScanMode.transmitSequences[0].endEvent = m_ScanMode.transmitEventsCount;
-}
-
-
-
-void mitk::USDiPhASDevice::InitializeScanMode()
-{
- // create a scanmode to be used for measurements:
- m_ScanMode.scanModeName = "InterleavedMode";
-
- // configure a linear transducer
- m_ScanMode.transducerName = "L5-10";
- m_ScanMode.transducerCurvedRadiusMeter = 0;
- m_ScanMode.transducerElementCount = 128;
- m_ScanMode.transducerFrequencyHz = 7500000;
- m_ScanMode.transducerPitchMeter = 0.0003f;
- m_ScanMode.transducerType = 1;
-
- // configure the receive paramters:
- m_ScanMode.receivePhaseLengthSeconds = 185e-6f; // about 15 cm imaging depth
- m_ScanMode.tgcdB = new unsigned char[8];
- for (int tgc = 0; tgc < 8; ++tgc)
- m_ScanMode.tgcdB[tgc] = tgc * 2 + 10;
- m_ScanMode.accumulation = 1;
- m_ScanMode.bandpassApply = false;
- m_ScanMode.averagingCount = 1;
-
- // configure general processing:
- m_ScanMode.transferChannelData = true;
-
- // configure reconstruction processing:
- m_ScanMode.averageSpeedOfSound = 1540;
- m_ScanMode.computeBeamforming = true;
-
- // setup beamforming parameters:
- SetInterleaved(true);
-
- m_ScanMode.reconstructedLinePitchMmOrAngleDegree = 0.3f;
- m_ScanMode.reconstructionLines = 128;
- m_ScanMode.reconstructionSamplesPerLine = 2048;
- m_ScanMode.transferBeamformedData = true;
-
- // configure the transmit sequence(s):
- m_ScanMode.transmitEventsCount = 1;
- m_ScanMode.transmitPhaseLengthSeconds = 1e-6f;
- m_ScanMode.voltageV = 75;
- UpdateTransmitEvents();
-
- // configure bandpass:
- m_ScanMode.bandpassApply = false;
- m_ScanMode.bandpassFrequencyLowHz = 1e6f;
- m_ScanMode.bandpassFrequencyHighHz = 20e6f;
-
- // configure image generation:
- m_ScanMode.imageWidth = 512;
- m_ScanMode.imageHeight = 512;
- m_ScanMode.imageMultiplier = 1;
- m_ScanMode.imageLeveling = 0;
- m_ScanMode.transferImageData = false;
-
- // Trigger setup:
- m_ScanMode.triggerSetup.enabled = true;
- m_ScanMode.triggerSetup.constantPulseRepetitionRateHz = 20;
- m_ScanMode.triggerSetup.triggerWidthMicroseconds = 15;
- m_ScanMode.triggerSetup.delayTrigger2Microseconds = 300;
-}
-
-// callback for the DiPhAS API
-
-void mitk::USDiPhASDevice::MessageCallback(const char* message)
-{
- MITK_INFO << "DiPhAS API: " << message << '\n';
-}
-
-void mitk::USDiPhASDevice::SetBursts(int bursts)
-{
- m_BurstHalfwaveClockCount = bursts;
-}
-
-bool mitk::USDiPhASDevice::IsInterleaved()
-{
- return m_Interleaved;
-}
-
-void mitk::USDiPhASDevice::SetInterleaved(bool interleaved)
-{
- m_Interleaved = interleaved;
- if (interleaved) {
- m_ScanMode.scanModeName = "Interleaved Beamforming Mode";
- m_CurrentBeamformingAlgorithm = Beamforming::Interleaved_OA_US;
-
- paramsInterleaved.SpeedOfSoundMeterPerSecond = m_ScanMode.averageSpeedOfSound;
- paramsInterleaved.angleSkipFactor = 1;
- paramsInterleaved.OptoacousticDelay = 0.0000003; // 300ns
- paramsInterleaved.filter = Filter::None;
-
- m_ScanMode.beamformingAlgorithmParameters = ¶msInterleaved;
- }
- else {
- m_ScanMode.scanModeName = "Plane Wave Beamforming Mode";
- m_CurrentBeamformingAlgorithm = Beamforming::PlaneWaveCompound;
-
- paramsPlaneWave.SpeedOfSoundMeterPerSecond = m_ScanMode.averageSpeedOfSound;
- paramsPlaneWave.angleSkipFactor = 0;
- paramsPlaneWave.usePhaseCoherence = 0;
-
- m_ScanMode.beamformingAlgorithmParameters = ¶msPlaneWave;
- }
- m_ScanMode.beamformingAlgorithm = m_CurrentBeamformingAlgorithm;
-}
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.h
deleted file mode 100644
index 1e97950225..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASDevice.h
+++ /dev/null
@@ -1,169 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKUSDiPhASDevice_H_HEADER_INCLUDED_
-#define MITKUSDiPhASDevice_H_HEADER_INCLUDED_
-
-#include <functional>
-#include "mitkUSDiPhASImageSource.h"
-#include "mitkUSDevice.h"
-#include "mitkUSDiPhASProbesControls.h"
-#include "mitkUSDiPhASImageSource.h"
-#include "mitkUSDiPhASCustomControls.h"
-
-#include "Framework.IBMT.US.CWrapper.h"
-
-#include <Windows.h>
-#include <iostream>
-#include <SDKDDKVer.h>
-#include <stdio.h>
-#include <tchar.h>
-
-#include <itkObjectFactory.h>
-
-
-namespace mitk {
- /**
- * \brief Implementation of mitk::USDevice for DiPhAS API devices.
- * Connects to a DiPhAS API device through its COM library interface.
- *
- * This class handles all API communications and creates interfaces for
- * b mode, doppler and probes controls.
- * Images given by the device are put into an object of
- * mitk::USDiPhASImageSource.
- */
- class USDiPhASImageSource;
-
- class USDiPhASDevice : public USDevice
- {
- public:
- mitkClassMacro(USDiPhASDevice, mitk::USDevice);
- mitkNewMacro2Param(Self, std::string, std::string);
-
- /**
- * \brief Returns the class of the device.
- */
- virtual std::string GetDeviceClass();
-
- virtual USControlInterfaceProbes::Pointer GetControlInterfaceProbes();
- virtual itk::SmartPointer<USAbstractControlInterface> GetControlInterfaceCustom();
-
- /**
- * \brief Is called during the initialization process.
- * There is nothing done on the initialization of a mik::USDiPhASDevive object.
- *
- * \return always true
- */
- virtual bool OnInitialization();
-
- /**
- * \brief Is called during the connection process.
- * Connect to the DiPhAS API.
- *
- * \return true if successfull, false if no device is connected to the pc
- * \throws mitk::Exception if something goes wrong at the API calls
- */
- virtual bool OnConnection();
-
- /**
- * \brief Is called during the disconnection process.
- * Deactivate and remove all DiPhAS API controls. A disconnect from the
- * DiPhAS API is not possible for which reason the hardware stays in connected
- * state even after calling this method.
- *
- * \return always true
- * \throws mitk::Exception if something goes wrong at the API calls
- */
- virtual bool OnDisconnection();
-
- /**
- * \brief Is called during the activation process.
- * After this method is finished, the device is generating images in b mode.
- * Changing scanning mode is possible afterwards by using the appropriate
- * control interfaces.
- *
- * \return always true
- * \throws mitk::Exception if something goes wrong at the API calls
- */
- virtual bool OnActivation();
-
- /**
- * \brief Is called during the deactivation process.
- * After a call to this method the device is connected, but not producing images anymore.
- *
- * \return always true
- * \throws mitk::Exception if something goes wrong at the API calls
- */
- virtual bool OnDeactivation();
-
- /**
- * \brief Changes scan state of the device if freeze is toggeled in mitk::USDevice.
- */
- virtual void OnFreeze(bool freeze);
-
- /** @return Returns the current image source of this device. */
- USImageSource::Pointer GetUSImageSource( );
-
- /** @return Returns the currently used scanmode of this device*/
- ScanModeNative& GetScanMode();
-
- /** Updates the Scanmode and feeds it to the hardware
- */
- void UpdateScanmode();
- /** This method forwards messages from the API to the user*/
- void MessageCallback(const char* message);
- void SetBursts(int bursts);
- void SetInterleaved(bool interleaved);
- bool IsInterleaved();
-
- BeamformingParametersInterleaved_OA_US paramsInterleaved;
- BeamformingParametersPlaneWaveCompound paramsPlaneWave;
-
- protected:
- /**
- * Constructs a mitk::USDiPhASDevice object by given manufacturer
- * and model string. These strings are just for labeling the device
- * in the micro service.
- *
- * Control interfaces and image source are available directly after
- * construction. Registration at the micro service happens not before
- * initialization method was called.
- */
- USDiPhASDevice(std::string manufacturer, std::string model);
- virtual ~USDiPhASDevice();
-
- /**
- * The DiPhAS API expects callback functions to pass
- * both status messages and the processed images to the user.
- * The message callback is here, the data itself is given directly to the image source.
- */
-
- /**
- * This method sets up the scanmode at the begining
- */
- void InitializeScanMode();
- void UpdateTransmitEvents();
-
- USDiPhASProbesControls::Pointer m_ControlsProbes;
- itk::SmartPointer<USAbstractControlInterface> m_ControlInterfaceCustom;
-
- mitk::USDiPhASImageSource::Pointer m_ImageSource;
-
- bool m_IsRunning;
- ScanModeNative m_ScanMode;
- int m_BurstHalfwaveClockCount;
- Beamforming m_CurrentBeamformingAlgorithm;
- bool m_Interleaved;
- };
-} // namespace mitk
-
-#endif // MITKUSDiPhASDevice_H_HEADER_INCLUDED_
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp
deleted file mode 100644
index 45b4c65fd5..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.cpp
+++ /dev/null
@@ -1,927 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-// std dependencies
-#include <ctime>
-#include <chrono>
-#include <algorithm>
-
-// mitk dependencies
-#include "mitkUSDiPhASDevice.h"
-#include "mitkUSDiPhASImageSource.h"
-#include <mitkIOUtil.h>
-#include "mitkUSDiPhASBModeImageFilter.h"
-#include "ITKUltrasound/itkBModeImageFilter.h"
-#include "mitkImageCast.h"
-#include "mitkITKImageImport.h"
-
-// itk dependencies
-#include "itkImage.h"
-#include "itkResampleImageFilter.h"
-#include "itkCastImageFilter.h"
-#include "itkCropImageFilter.h"
-#include "itkRescaleIntensityImageFilter.h"
-#include "itkIntensityWindowingImageFilter.h"
-#include <itkIndex.h>
-#include "itkMultiplyImageFilter.h"
-
-mitk::USDiPhASImageSource::USDiPhASImageSource(mitk::USDiPhASDevice* device)
- : m_Device(device),
- m_StartTime(((float)std::clock()) / CLOCKS_PER_SEC),
- m_UseGUIOutPut(false),
- m_DataType(DataType::Image_uChar),
- m_GUIOutput(nullptr),
- m_UseBModeFilter(false),
- m_CurrentlyRecording(false),
- m_DataTypeModified(true),
- m_DataTypeNext(DataType::Image_uChar),
- m_CurrentImageTimestamp(0),
- m_PyroConnected(false),
- m_ImageTimestampBuffer(),
- m_VerticalSpacing(0),
- m_UseBModeFilterModified(false),
- m_UseBModeFilterNext(false),
- m_ScatteringCoefficientModified(false),
- m_CompensateForScatteringModified(false),
- m_VerticalSpacingModified(false),
- m_ScatteringCoefficient(15),
- m_CompensateForScattering(false),
- m_CompensateEnergy(false),
- m_CompensateEnergyNext(false),
- m_CompensateEnergyModified(false)
-{
- m_BufferSize = 100;
- m_ImageTimestampBuffer.insert(m_ImageTimestampBuffer.begin(), m_BufferSize, 0);
- m_LastWrittenImage = m_BufferSize - 1;
- m_ImageBuffer.insert(m_ImageBuffer.begin(), m_BufferSize, nullptr);
-
- us::ModuleResource resourceFile;
- std::string name;
- m_FluenceCompOriginal.insert(m_FluenceCompOriginal.begin(), 5, Image::New());
- for (int i = 5; i <= 25; ++i)
- {
- name = "c:\\HomogeneousScatteringAssumptions\\Scattering" + std::to_string(i) + ".nrrd";
-
- m_FluenceCompOriginal.push_back(mitk::IOUtil::Load<mitk::Image>(name));
- }
-
- m_FluenceCompResized.insert(m_FluenceCompResized.begin(), 26, Image::New());
- m_FluenceCompResizedItk.insert(m_FluenceCompResizedItk.begin(), 26, itk::Image<float,3>::New());
-}
-
-mitk::USDiPhASImageSource::~USDiPhASImageSource()
-{
- // close the pyro
- MITK_INFO("Pyro Debug") << "StopDataAcquisition: " << m_Pyro->StopDataAcquisition();
- MITK_INFO("Pyro Debug") << "CloseConnection: " << m_Pyro->CloseConnection();
- m_PyroConnected = false;
- m_Pyro = nullptr;
-}
-
-void mitk::USDiPhASImageSource::GetNextRawImage(std::vector<mitk::Image::Pointer>& imageVector)
-{
- // modify all settings that have been changed here, so we don't get multithreading issues
- if (m_DataTypeModified)
- {
- SetDataType(m_DataTypeNext);
- m_DataTypeModified = false;
- UpdateImageGeometry();
- }
- if (m_UseBModeFilterModified)
- {
- SetUseBModeFilter(m_UseBModeFilterNext);
- m_UseBModeFilterModified = false;
- }
- if (m_VerticalSpacingModified)
- {
- m_VerticalSpacing = m_VerticalSpacingNext;
- m_VerticalSpacingModified = false;
- }
- if (m_ScatteringCoefficientModified)
- {
- m_ScatteringCoefficient = m_ScatteringCoefficientNext;
- m_ScatteringCoefficientModified = false;
- }
- if (m_CompensateForScatteringModified)
- {
- m_CompensateForScattering = m_CompensateForScatteringNext;
- m_CompensateForScatteringModified = false;
- }
- if (m_CompensateEnergyModified)
- {
- m_CompensateEnergy = m_CompensateEnergyNext;
- m_CompensateEnergyModified = false;
- }
-
- if (imageVector.size() != 2)
- {
- imageVector.resize(2);
- }
-
- // make sure image is nullptr
- mitk::Image::Pointer image = nullptr;
- float ImageEnergyValue = 0;
-
- for (int i = 100; i > 90 && ImageEnergyValue <= 0; --i)
- {
- if (m_ImageTimestampBuffer[(m_LastWrittenImage + i) % 100] != 0)
- {
- ImageEnergyValue = m_Pyro->GetClosestEnergyInmJ(m_ImageTimestampBuffer[(m_LastWrittenImage + i) % 100]);
- if (ImageEnergyValue > 0) {
- image = &(*m_ImageBuffer[(m_LastWrittenImage + i) % 100]);
- }
- }
- }
- // if we did not get any usable Energy value, compensate using this default value
- if (image == nullptr)
- {
- image = &(*m_ImageBuffer[m_LastWrittenImage]);
- ImageEnergyValue = 40;
- if (image == nullptr)
- return;
- }
-
- // do image processing before displaying it
- if (image.IsNotNull())
- {
- itkFloatImageType::Pointer itkImage;
-
- mitk::CastToItkImage(image, itkImage);
- image = mitk::GrabItkImageMemory(itkImage); //thereby using float images
- image = CutOffTop(image, 165);
-
- // now apply filters to the image, if the options have been selected.
- if ((m_CompensateForScattering || m_UseBModeFilter) && m_DataType == DataType::Beamformed_Short)
- {
- if (m_Device->GetScanMode().beamformingAlgorithm == Beamforming::PlaneWaveCompound) // this is for ultrasound only mode
- {
- if (m_UseBModeFilter)
- {
- image = ApplyBmodeFilter(image, true);
- if (m_VerticalSpacing)
- image = ResampleOutputVertical(image, m_VerticalSpacing);
- }
- }
-
- else
- {
- Image::Pointer imagePA = Image::New();
- unsigned int dim[] = { image->GetDimension(0),image->GetDimension(1),1};
- imagePA->Initialize(image->GetPixelType(), 3, dim);
- imagePA->SetGeometry(image->GetGeometry());
-
- Image::Pointer imageUS = Image::New();
- imageUS->Initialize(image->GetPixelType(), 3, dim);
- imageUS->SetGeometry(image->GetGeometry());
-
- ImageReadAccessor inputReadAccessorCopyPA(image, image->GetSliceData(0));
- imagePA->SetSlice(inputReadAccessorCopyPA.GetData(), 0);
- ImageReadAccessor inputReadAccessorCopyUS(image, image->GetSliceData(1));
- imageUS->SetSlice(inputReadAccessorCopyUS.GetData(), 0);
-
- // first, seperate the PA image from the USImages
-
- // then, we compensate the PAImage using our ImageEnergyValue
- if(m_CompensateEnergy)
- imagePA = MultiplyImage(imagePA, 1/ImageEnergyValue); // TODO: add the correct prefactor here!!!!
-
- // now we apply the BModeFilter
- if (m_UseBModeFilter)
- {
- imageUS = ApplyBmodeFilter(imageUS, true); // the US Images get a logarithmic filter
- imagePA = ApplyBmodeFilter(imagePA, false);
- }
-
- ImageReadAccessor inputReadAccessorPA(imagePA, imagePA->GetSliceData(0));
- image->SetSlice(inputReadAccessorPA.GetData(), 0);
- ImageReadAccessor inputReadAccessorUS(imageUS, imageUS->GetSliceData(0));
- image->SetSlice(inputReadAccessorUS.GetData(), 1);
- if (m_VerticalSpacing)
- {
- image = ResampleOutputVertical(image, m_VerticalSpacing);
- }
-
- // and finally the scattering corrections
- if (m_CompensateForScattering)
- {
- auto curResizeImage = m_FluenceCompResized.at(m_ScatteringCoefficient); // just for convenience
-
- // update the fluence reference images!
- bool doResampling = image->GetDimension(0) != curResizeImage->GetDimension(0) || image->GetDimension(1) != curResizeImage->GetDimension(1)
- || image->GetGeometry()->GetSpacing()[0] != curResizeImage->GetGeometry()->GetSpacing()[0] || image->GetGeometry()->GetSpacing()[1] != curResizeImage->GetGeometry()->GetSpacing()[1];
- if (doResampling)
- {
- curResizeImage = ApplyResampling(m_FluenceCompOriginal.at(m_ScatteringCoefficient), image->GetGeometry()->GetSpacing(), image->GetDimensions());
-
- double* rawOutputData = new double[image->GetDimension(0)*image->GetDimension(1)];
- double* rawScatteringData = (double*)curResizeImage->GetData();
- int sizeRawScatteringData = curResizeImage->GetDimension(0) * curResizeImage->GetDimension(1);
- int imageSize = image->GetDimension(0)*image->GetDimension(1);
-
- //everything above 1.5mm is still inside the transducer; therefore the fluence compensation image has to be positioned a little lower
- float upperCutoffmm = 1.5;
- int lowerBound = std::round(upperCutoffmm / image->GetGeometry()->GetSpacing()[1])*image->GetDimension(0);
- int upperBound = lowerBound + sizeRawScatteringData;
-
- for (int i = 0; i < lowerBound && i < imageSize; ++i)
- {
- rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage, here the upper 0.15mm
- }
- for (int i = lowerBound; i < upperBound && i < imageSize; ++i)
- {
- rawOutputData[i] = 1 / rawScatteringData[i-lowerBound];
- }
- for (int i = upperBound; i < imageSize; ++i)
- {
- rawOutputData[i] = 0; // everything than cannot be compensated shall be treated as garbage
- }
-
-
- unsigned int dim[] = { image->GetDimension(0), image->GetDimension(1), 1 };
- curResizeImage->Initialize(mitk::MakeScalarPixelType<double>(), 3, dim);
- curResizeImage->SetGeometry(image->GetGeometry());
- curResizeImage->SetSlice(rawOutputData,0);
-
- delete[] rawOutputData;
-
- mitk::CastToItkImage(curResizeImage, m_FluenceCompResizedItk.at(m_ScatteringCoefficient));
- m_FluenceCompResized.at(m_ScatteringCoefficient) = mitk::GrabItkImageMemory(m_FluenceCompResizedItk.at(m_ScatteringCoefficient));
-
- MITK_INFO << "Resized a fluence image.";
- }
- // actually apply the scattering compensation
- imagePA = ApplyScatteringCompensation(imagePA, m_ScatteringCoefficient);
- ImageReadAccessor inputReadAccessorPA(imagePA, imagePA->GetSliceData(0));
- image->SetSlice(inputReadAccessorPA.GetData(), 0);
- }
- }
- }
-
- //TODO: completely rewrite this mess
-
- imageVector[0] = Image::New();
- unsigned int dim[] = { image->GetDimension(0),image->GetDimension(1),1 };
- imageVector[0]->Initialize(image->GetPixelType(), 3, dim);
- imageVector[0]->SetGeometry(image->GetGeometry());
-
- imageVector[1] = Image::New();
- imageVector[1]->Initialize(image->GetPixelType(), 3, dim);
- imageVector[1]->SetGeometry(image->GetGeometry());
-
- ImageReadAccessor inputReadAccessorCopyPA(image, image->GetSliceData(0));
- imageVector[0]->SetSlice(inputReadAccessorCopyPA.GetData(), 0);
- ImageReadAccessor inputReadAccessorCopyUS(image, image->GetSliceData(1));
- imageVector[1]->SetSlice(inputReadAccessorCopyUS.GetData(), 0);
- }
-}
-
-mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyBmodeFilter(mitk::Image::Pointer image, bool useLogFilter)
-{
- // we use this seperate ApplyBmodeFilter Method for processing of two-dimensional images
-
- // the image needs to be of floating point type for the envelope filter to work; the casting is done automatically by the CastToItkImage
-
- typedef itk::BModeImageFilter < itkFloatImageType, itkFloatImageType > BModeFilterType;
- BModeFilterType::Pointer bModeFilter = BModeFilterType::New(); // LogFilter
-
- typedef itk::PhotoacousticBModeImageFilter < itkFloatImageType, itkFloatImageType > PhotoacousticBModeImageFilter;
- PhotoacousticBModeImageFilter::Pointer photoacousticBModeFilter = PhotoacousticBModeImageFilter::New(); // No LogFilter
-
- itkFloatImageType::Pointer itkImage;
- itkFloatImageType::Pointer bmode;
- mitk::CastToItkImage(image, itkImage);
-
- if (useLogFilter)
- {
- bModeFilter->SetInput(itkImage);
- bModeFilter->SetDirection(1);
- bmode = bModeFilter->GetOutput();
- }
- else
- {
- photoacousticBModeFilter->SetInput(itkImage);
- photoacousticBModeFilter->SetDirection(1);
- bmode = photoacousticBModeFilter->GetOutput();
- }
- return mitk::GrabItkImageMemory(bmode);
-}
-
-mitk::Image::Pointer mitk::USDiPhASImageSource::CutOffTop(mitk::Image::Pointer image, int cutOffSize)
-{
- typedef itk::CropImageFilter < itkFloatImageType, itkFloatImageType > CutImageFilter;
- itkFloatImageType::SizeType cropSize;
- itkFloatImageType::Pointer itkImage;
- mitk::CastToItkImage(image, itkImage);
-
- cropSize[0] = 0;
- if(itkImage->GetLargestPossibleRegion().GetSize()[1] == 2048)
- cropSize[1] = cutOffSize;
- else
- cropSize[1] = 0;
- cropSize[2] = 0;
- CutImageFilter::Pointer cutOffFilter = CutImageFilter::New();
- cutOffFilter->SetInput(itkImage);
- cutOffFilter->SetLowerBoundaryCropSize(cropSize);
- cutOffFilter->UpdateLargestPossibleRegion();
- return mitk::GrabItkImageMemory(cutOffFilter->GetOutput());
-}
-
-mitk::Image::Pointer mitk::USDiPhASImageSource::ResampleOutputVertical(mitk::Image::Pointer image, float verticalSpacing)
-{
- typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter;
- ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New();
-
- itkFloatImageType::Pointer itkImage;
-
- mitk::CastToItkImage(image, itkImage);
- itkFloatImageType::SpacingType outputSpacing;
- itkFloatImageType::SizeType inputSize = itkImage->GetLargestPossibleRegion().GetSize();
- itkFloatImageType::SizeType outputSize = inputSize;
-
- outputSpacing[0] = itkImage->GetSpacing()[0] * (static_cast<double>(inputSize[0]) / static_cast<double>(outputSize[0]));
- outputSpacing[1] = verticalSpacing;
- outputSpacing[2] = itkImage->GetSpacing()[2];
-
- outputSize[1] = inputSize[1] * itkImage->GetSpacing()[1] / outputSpacing[1];
-
- typedef itk::IdentityTransform<double, 3> TransformType;
- resampleImageFilter->SetInput(itkImage);
- resampleImageFilter->SetSize(outputSize);
- resampleImageFilter->SetOutputSpacing(outputSpacing);
- resampleImageFilter->SetTransform(TransformType::New());
-
- resampleImageFilter->UpdateLargestPossibleRegion();
- return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput());
-}
-
-mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scattering)
-{
- typedef itk::MultiplyImageFilter <itkFloatImageType, itkFloatImageType > MultiplyImageFilterType;
-
- itkFloatImageType::Pointer itkImage;
- mitk::CastToItkImage(inputImage, itkImage);
-
- MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New();
- multiplyFilter->SetInput1(itkImage);
- multiplyFilter->SetInput2(m_FluenceCompResizedItk.at(m_ScatteringCoefficient));
-
- return mitk::GrabItkImageMemory(multiplyFilter->GetOutput());
-}
-
-mitk::Image::Pointer mitk::USDiPhASImageSource::ApplyResampling(mitk::Image::Pointer inputImage, mitk::Vector3D outputSpacing, unsigned int outputSize[3])
-{
- typedef itk::ResampleImageFilter < itkFloatImageType, itkFloatImageType > ResampleImageFilter;
- ResampleImageFilter::Pointer resampleImageFilter = ResampleImageFilter::New();
-
- itkFloatImageType::Pointer itkImage;
-
- mitk::CastToItkImage(inputImage, itkImage);
-
- itkFloatImageType::SpacingType outputSpacingItk;
- itkFloatImageType::SizeType inputSizeItk = itkImage->GetLargestPossibleRegion().GetSize();
- itkFloatImageType::SizeType outputSizeItk = inputSizeItk;
- itkFloatImageType::SpacingType inputSpacing = itkImage->GetSpacing();
-
- outputSizeItk[0] = outputSize[0];
- outputSizeItk[1] = 10*(inputSpacing[1] * inputSizeItk[1]) / (outputSpacing[1]);
- outputSizeItk[2] = 1;
-
- outputSpacingItk[0] = 0.996 * inputSpacing[0] * (static_cast<double>(inputSizeItk[0]) / static_cast<double>(outputSizeItk[0])); // TODO: find out why the spacing is not correct, so we need that factor; ?!?!
- outputSpacingItk[1] = inputSpacing[1] * (static_cast<double>(inputSizeItk[1]) / static_cast<double>(outputSizeItk[1]));
- outputSpacingItk[2] = outputSpacing[2];
-
- typedef itk::IdentityTransform<double, 3> TransformType;
- resampleImageFilter->SetInput(itkImage);
- resampleImageFilter->SetSize(outputSizeItk);
- resampleImageFilter->SetOutputSpacing(outputSpacingItk);
- resampleImageFilter->SetTransform(TransformType::New());
-
- resampleImageFilter->UpdateLargestPossibleRegion();
- return mitk::GrabItkImageMemory(resampleImageFilter->GetOutput());
-}
-
-mitk::Image::Pointer mitk::USDiPhASImageSource::MultiplyImage(mitk::Image::Pointer inputImage, double value)
-{
- typedef itk::MultiplyImageFilter <itkFloatImageType, itkFloatImageType > MultiplyImageFilterType;
-
- itkFloatImageType::Pointer itkImage;
- mitk::CastToItkImage(inputImage, itkImage);
-
- MultiplyImageFilterType::Pointer multiplyFilter = MultiplyImageFilterType::New();
- multiplyFilter->SetInput1(itkImage);
- multiplyFilter->SetConstant(value);
-
- return mitk::GrabItkImageMemory(multiplyFilter->GetOutput());
-}
-
-void mitk::USDiPhASImageSource::ImageDataCallback(
- short* rfDataChannelData,
- int& channelDataChannelsPerDataset,
- int& channelDataSamplesPerChannel,
- int& channelDataTotalDatasets,
-
- short* rfDataArrayBeamformed,
- int& beamformedLines,
- int& beamformedSamples,
- int& beamformedTotalDatasets,
-
- unsigned char* imageData,
- int& imageWidth,
- int& imageHeight,
- int& imageBytesPerPixel,
- int& imageSetsTotal,
-
- double& timeStamp)
-{
- if (m_DataTypeModified)
- return;
-
- if (!m_PyroConnected)
- {
- m_Pyro = mitk::OphirPyro::New();
- MITK_INFO << "[Pyro Debug] OpenConnection: " << m_Pyro->OpenConnection();
- MITK_INFO << "[Pyro Debug] StartDataAcquisition: " << m_Pyro->StartDataAcquisition();
- m_PyroConnected = true;
- }
-
- bool writeImage = ((m_DataType == DataType::Image_uChar) && (imageData != nullptr)) || ((m_DataType == DataType::Beamformed_Short) && (rfDataArrayBeamformed != nullptr));
- if (writeImage)
- {
- //get the timestamp we might save later on
- m_CurrentImageTimestamp = std::chrono::high_resolution_clock::now().time_since_epoch().count();
-
- // create a new image and initialize it
- mitk::Image::Pointer image = mitk::Image::New();
-
- switch (m_DataType)
- {
- case DataType::Image_uChar: {
- m_ImageDimensions[0] = imageWidth;
- m_ImageDimensions[1] = imageHeight;
- m_ImageDimensions[2] = imageSetsTotal;
- image->Initialize(mitk::MakeScalarPixelType<unsigned char>(), 3, m_ImageDimensions);
- break;
- }
- case DataType::Beamformed_Short: {
- m_ImageDimensions[0] = beamformedLines;
- m_ImageDimensions[1] = beamformedSamples;
- m_ImageDimensions[2] = beamformedTotalDatasets;
- image->Initialize(mitk::MakeScalarPixelType<short>(), 3, m_ImageDimensions);
- break;
- }
- }
- image->GetGeometry()->SetSpacing(m_ImageSpacing);
- image->GetGeometry()->Modified();
-
- // write the given buffer into the image
- switch (m_DataType)
- {
- case DataType::Image_uChar: {
- for (unsigned char i = 0; i < imageSetsTotal; i++) {
- image->SetSlice(&imageData[i*imageHeight*imageWidth], i);
- }
- break;
- }
-
- case DataType::Beamformed_Short: {
- short* flipme = new short[beamformedLines*beamformedSamples*beamformedTotalDatasets];
- int pixelsPerImage = beamformedLines*beamformedSamples;
-
- for (unsigned char currentSet = 0; currentSet < beamformedTotalDatasets; currentSet++)
- {
- for (unsigned short sample = 0; sample < beamformedSamples; sample++)
- {
- for (unsigned short line = 0; line < beamformedLines; line++)
- {
- flipme[sample*beamformedLines + line + pixelsPerImage*currentSet]
- = rfDataArrayBeamformed[line*beamformedSamples + sample + pixelsPerImage*currentSet];
- }
- } // the beamformed pa image is flipped by 90 degrees; we need to flip it manually
- }
-
- for (unsigned char i = 0; i < beamformedTotalDatasets; i++) {
- image->SetSlice(&flipme[i*beamformedLines*beamformedSamples], i);
- // set every image to a different slice
- }
-
- delete[] flipme;
- break;
- }
- }
-
- if (m_SavingSettings.saveRaw && m_CurrentlyRecording && rfDataChannelData != nullptr)
- {
- unsigned int dim[3];
- dim[0] = channelDataChannelsPerDataset;
- dim[1] = channelDataSamplesPerChannel;
- dim[2] = 1;
- short offset = m_Device->GetScanMode().accumulation * 2048;
-
- short* noOffset = new short[channelDataChannelsPerDataset*channelDataSamplesPerChannel*channelDataTotalDatasets];
- for (unsigned char set = 0; set < 1; ++set)// channelDataTotalDatasets; ++set) // we ignore the raw US images for now
- {
- for (unsigned short sam = 0; sam < channelDataSamplesPerChannel; ++sam)
- {
- for (unsigned short chan = 0; chan < channelDataChannelsPerDataset; ++chan)
- {
- noOffset[set*channelDataSamplesPerChannel*channelDataChannelsPerDataset + sam * channelDataChannelsPerDataset + chan] =
- rfDataChannelData[set*channelDataSamplesPerChannel*channelDataChannelsPerDataset + sam * channelDataChannelsPerDataset + chan] - offset; // this offset in the raw Images is given by the API...
- }
- }
- }
-
- // save the raw images when recording
- for (unsigned char i = 0; i < 1; ++i)// channelDataTotalDatasets; ++i) // we ignore the raw US images for now
- {
- mitk::Image::Pointer rawImage = mitk::Image::New();
- rawImage->Initialize(mitk::MakeScalarPixelType<short>(), 3, dim);
-
- rawImage->SetSlice(&noOffset[i*channelDataChannelsPerDataset*channelDataSamplesPerChannel]);
-
- float& recordTime = m_Device->GetScanMode().receivePhaseLengthSeconds;
- int& speedOfSound = m_Device->GetScanMode().averageSpeedOfSound;
-
- mitk::Vector3D rawSpacing;
- rawSpacing[0] = m_Device->GetScanMode().transducerPitchMeter * 1000; // save in mm
- rawSpacing[1] = recordTime / channelDataSamplesPerChannel * 1000000; // save in us
- rawSpacing[2] = 1;
-
- rawImage->GetGeometry()->SetSpacing(rawSpacing);
- rawImage->GetGeometry()->Modified();
-
- m_RawRecordedImages.push_back(rawImage);
- }
-
- delete[] noOffset;
- }
-
- itk::Index<3> pixel = { {
- (itk::Index<3>::IndexValueType)(image->GetDimension(0) / 2),
- (itk::Index<3>::IndexValueType)(22.0/532.0*m_Device->GetScanMode().reconstructionSamplesPerLine),
- 0 } }; //22/532*2048 = 84
- if (!m_Pyro->IsSyncDelaySet() &&(image->GetPixelValueByIndex(pixel) < -30)) // #MagicNumber
- {
- MITK_INFO << "Setting SyncDelay now";
- m_Pyro->SetSyncDelay(m_CurrentImageTimestamp);
- }
-
- m_ImageTimestampBuffer[(m_LastWrittenImage + 1) % m_BufferSize] = m_CurrentImageTimestamp;
- m_ImageBuffer[(m_LastWrittenImage + 1) % m_BufferSize] = image;
- m_LastWrittenImage = (m_LastWrittenImage + 1) % m_BufferSize;
-
- // if the user decides to start recording, we feed the vector the generated images
- if (m_CurrentlyRecording) {
- for (unsigned char index = 0; index < image->GetDimension(2); ++index)
- {
- if (image->IsSliceSet(index))
- {
- m_RecordedImages.push_back(Image::New());
- unsigned int dim[] = { image ->GetDimension(0), image->GetDimension(1), 1};
- m_RecordedImages.back()->Initialize(image->GetPixelType(), 3, dim);
- m_RecordedImages.back()->SetGeometry(image->GetGeometry());
-
- mitk::ImageReadAccessor inputReadAccessor(image, image->GetSliceData(index));
- m_RecordedImages.back()->SetSlice(inputReadAccessor.GetData(),0);
- }
- }
- m_ImageTimestampRecord.push_back(m_CurrentImageTimestamp);
- // save timestamps for each laser image!
- }
- }
-}
-
-void mitk::USDiPhASImageSource::UpdateImageGeometry()
-{
- MITK_INFO << "Retreaving Image Geometry Information for Spacing...";
- float& recordTime = m_Device->GetScanMode().receivePhaseLengthSeconds;
- int& speedOfSound = m_Device->GetScanMode().averageSpeedOfSound;
- float& pitch = m_Device->GetScanMode().reconstructedLinePitchMmOrAngleDegree;
- int& reconstructionLines = m_Device->GetScanMode().reconstructionLines;
-
- switch (m_DataType)
- {
- case DataType::Image_uChar : {
- int& imageWidth = m_Device->GetScanMode().imageWidth;
- int& imageHeight = m_Device->GetScanMode().imageHeight;
- m_ImageSpacing[0] = pitch * reconstructionLines / imageWidth;
- m_ImageSpacing[1] = recordTime * speedOfSound / 2 * 1000 / imageHeight;
- break;
- }
- case DataType::Beamformed_Short : {
- int& imageWidth = reconstructionLines;
- int& imageHeight = m_Device->GetScanMode().reconstructionSamplesPerLine;
- m_ImageSpacing[0] = pitch;
- m_ImageSpacing[1] = recordTime * speedOfSound / 2 * 1000 / imageHeight;
- break;
- }
- }
- m_ImageSpacing[2] = 1;
-
- MITK_INFO << "Retreaving Image Geometry Information for Spacing " << m_ImageSpacing[0] << " ... " << m_ImageSpacing[1] << " ... " << m_ImageSpacing[2] << " ...[DONE]";
-}
-
-void mitk::USDiPhASImageSource::ModifyDataType(DataType dataT)
-{
- m_DataTypeModified = true;
- m_DataTypeNext = dataT;
-}
-
-void mitk::USDiPhASImageSource::ModifyUseBModeFilter(bool isSet)
-{
- m_UseBModeFilterModified = true;
- m_UseBModeFilterNext = isSet;
-}
-
-void mitk::USDiPhASImageSource::ModifyScatteringCoefficient(int coeff)
-{
- m_ScatteringCoefficientNext = coeff;
- m_ScatteringCoefficientModified = true;
-}
-
-void mitk::USDiPhASImageSource::ModifyCompensateForScattering(bool useIt)
-{
- m_CompensateForScatteringNext = useIt;
- m_CompensateForScatteringModified = true;
-}
-
-void mitk::USDiPhASImageSource::ModifyEnergyCompensation(bool compensate)
-{
- m_CompensateEnergyNext = compensate;
- m_CompensateEnergyModified = true;
-}
-
-void mitk::USDiPhASImageSource::SetDataType(DataType dataT)
-{
- if (dataT != m_DataType)
- {
- m_DataType = dataT;
- MITK_INFO << "Setting new DataType..." << dataT;
- switch (m_DataType)
- {
- case DataType::Image_uChar :
- MITK_INFO << "height: " << m_Device->GetScanMode().imageHeight << " width: " << m_Device->GetScanMode().imageWidth;
- break;
- case DataType::Beamformed_Short :
- MITK_INFO << "samples: " << m_Device->GetScanMode().reconstructionSamplesPerLine << " lines: " << m_Device->GetScanMode().reconstructionLines;
- break;
- }
- }
-}
-
-void mitk::USDiPhASImageSource::SetGUIOutput(std::function<void(QString)> out)
-{
- USDiPhASImageSource::m_GUIOutput = out;
- m_StartTime = ((float)std::clock()) / CLOCKS_PER_SEC; //wait till the callback is available again
- m_UseGUIOutPut = false;
-}
-
-void mitk::USDiPhASImageSource::SetUseBModeFilter(bool isSet)
-{
- m_UseBModeFilter = isSet;
-}
-
-void mitk::USDiPhASImageSource::SetVerticalSpacing(float mm)
-{
- m_VerticalSpacingNext = mm;
- m_VerticalSpacingModified = true;
-}
-
-void mitk::USDiPhASImageSource::SetSavingSettings(SavingSettings settings)
-{
- m_SavingSettings = settings;
-}
-
-// this is just a little function to set the filenames below right
-inline void replaceAll(std::string& str, const std::string& from, const std::string& to) {
- if (from.empty())
- return;
- size_t start_pos = 0;
- while ((start_pos = str.find(from, start_pos)) != std::string::npos) {
- str.replace(start_pos, from.length(), to);
- start_pos += to.length(); // In case 'to' contains 'from', like replacing 'x' with 'yx'
- }
-}
-
-void mitk::USDiPhASImageSource::SetRecordingStatus(bool record)
-{
- // start the recording process
- if (record)
- {
- m_RecordedImages.clear();
- m_RawRecordedImages.clear(); // we make sure there are no leftovers
- m_ImageTimestampRecord.clear(); // also for the timestamps
- m_PixelValues.clear(); // aaaand for the pixel values
-
- if (m_SavingSettings.saveRaw)
- {
- m_Device->GetScanMode().transferChannelData = true;
- m_Device->UpdateScanmode();
- // set the raw Data to be transfered
- }
-
- // tell the callback to start recording images
- m_CurrentlyRecording = true;
- }
- // save images, end recording, and clean up
- else
- {
- m_CurrentlyRecording = false;
-
- m_Device->GetScanMode().transferChannelData = false; // make sure raw Channel Data is not transferred anymore!
- m_Device->UpdateScanmode();
-
- // get the time and date, put them into a nice string and create a folder for the images
- time_t time = std::time(nullptr);
- time_t* timeptr = &time;
- std::string currentDate = std::ctime(timeptr);
- replaceAll(currentDate, ":", "-");
- currentDate.pop_back();
- //std::string MakeFolder = "mkdir \"c:/DiPhASImageData/" + currentDate + "\"";
- //system(MakeFolder.c_str());
-
- // initialize file paths and the images
- Image::Pointer PAImage = Image::New();
- Image::Pointer USImage = Image::New();
- std::string pathPA = "c:\\ImageData\\" + currentDate + "-" + "PAbeamformed" + ".nrrd";
- std::string pathUS = "c:\\ImageData\\" + currentDate + "-" + "USImages" + ".nrrd";
- std::string pathTS = "c:\\ImageData\\" + currentDate + "-" + "ts" + ".csv";
- std::string pathS = "c:\\ImageData\\" + currentDate + "-" + "Settings" + ".txt";
-
- // idon't forget the raw Images (if chosen to be saved)
- Image::Pointer PAImageRaw = Image::New();
- Image::Pointer USImageRaw = Image::New();
- std::string pathPARaw = "c:\\ImageData\\" + currentDate + "-" + "PAraw" + ".nrrd";
- std::string pathUSRaw = "c:\\ImageData\\" + currentDate + "-" + "USImagesRaw" + ".nrrd";
-
- if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::Interleaved_OA_US) // save a PAImage if we used interleaved mode
- {
- // first, save the data, so the pyro does not aquire more unneccessary timestamps
- m_Pyro->SaveData();
-
- // now order the images and save them
- // the beamformed ones...
- if (m_SavingSettings.saveBeamformed)
- {
- OrderImagesInterleaved(PAImage, USImage, m_RecordedImages, false);
- mitk::IOUtil::Save(USImage, pathUS);
- mitk::IOUtil::Save(PAImage, pathPA);
- }
-
- // ...and the raw images
- if (m_SavingSettings.saveRaw)
- {
- OrderImagesInterleaved(PAImageRaw, USImageRaw, m_RawRecordedImages, true);
- // mitk::IOUtil::Save(USImageRaw, pathUSRaw);
- mitk::IOUtil::Save(PAImageRaw, pathPARaw);
- }
-
- // read the pixelvalues of the enveloped images at this position
-
- itk::Index<3> pixel = { {
- (itk::Index<3>::IndexValueType)(m_RecordedImages.at(0)->GetDimension(0) / 2),
- (itk::Index<3>::IndexValueType)(22.0 / 532.0*m_Device->GetScanMode().reconstructionSamplesPerLine),
- 0 } }; //22/532*2048 = 84
-
- GetPixelValues(pixel, m_PixelValues); // write the Pixelvalues to m_PixelValues
-
- // save the timestamps!
- ofstream timestampFile;
-
- timestampFile.open(pathTS);
- timestampFile << ",timestamp,pixelvalue"; // write the header
-
- for (int index = 0; index < m_ImageTimestampRecord.size(); ++index)
- {
- timestampFile << "\n" << index << "," << m_ImageTimestampRecord.at(index) << "," << m_PixelValues.at(index);
- }
- timestampFile.close();
-
- //save the settings!
-
- ofstream settingsFile;
-
- settingsFile.open(pathS);
- auto& sM = m_Device->GetScanMode();
-
- settingsFile << "[General Parameters]\n";
- settingsFile << "Scan Depth [mm] = " << sM.receivePhaseLengthSeconds * sM.averageSpeedOfSound / 2 * 1000 << "\n";
- settingsFile << "Speed of Sound [m/s] = " << sM.averageSpeedOfSound << "\n";
- settingsFile << "Excitation Frequency [MHz] = " << sM.transducerFrequencyHz/1000000 << "\n";
- settingsFile << "Voltage [V] = " << sM.voltageV << "\n";
- settingsFile << "TGC min = " << (int)sM.tgcdB[0] << " max = " << (int)sM.tgcdB[7] << "\n";
-
- settingsFile << "[Beamforming Parameters]\n";
- settingsFile << "Reconstructed Lines = " << sM.reconstructionLines << "\n";
- settingsFile << "Samples per Line = " << sM.reconstructionSamplesPerLine << "\n";
-
- settingsFile.close();
- }
- else if (m_Device->GetScanMode().beamformingAlgorithm == (int)Beamforming::PlaneWaveCompound) // save no PAImage if we used US only mode
- {
- OrderImagesUltrasound(USImage, m_RecordedImages);
- mitk::IOUtil::Save(USImage, pathUS);
- }
-
- m_PixelValues.clear();
- m_RawRecordedImages.clear(); // clean up the pixel values
- m_RecordedImages.clear(); // clean up the images
- m_ImageTimestampRecord.clear(); // clean up the timestamps
- }
-}
-
-void mitk::USDiPhASImageSource::GetPixelValues(itk::Index<3> pixel, std::vector<float>& values)
-{
- unsigned int events = 2;
- for (int index = 0; index < m_RecordedImages.size(); index += events) // omit sound images
- {
- Image::Pointer image = m_RecordedImages.at(index);
- image = ApplyBmodeFilter(image);
- values.push_back(image.GetPointer()->GetPixelValueByIndex(pixel));
- }
-}
-
-void mitk::USDiPhASImageSource::OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector<Image::Pointer> recordedList, bool raw)
-{
- unsigned int width = 32;
- unsigned int height = 32;
- unsigned int events = m_Device->GetScanMode().transmitEventsCount + 1; // the PA event is not included in the transmitEvents, so we add 1 here
- if (!raw)
- events = 2; // the beamformed image array contains only the resulting image of multiple events
-
- if (raw)
- {
- width = recordedList.at(0)->GetDimension(0);
- height = recordedList.at(0)->GetDimension(1);
- }
- else if (m_DataType == DataType::Beamformed_Short)
- {
- width = m_Device->GetScanMode().reconstructionLines;
- height = m_Device->GetScanMode().reconstructionSamplesPerLine;
- }
- else if (m_DataType == DataType::Image_uChar)
- {
- width = m_Device->GetScanMode().imageWidth;
- height = m_Device->GetScanMode().imageHeight;
- }
-
- unsigned int dimLaser[] = { (unsigned int)width, (unsigned int)height, (unsigned int)(recordedList.size() / events)};
- unsigned int dimSound[] = { (unsigned int)width, (unsigned int)height, (unsigned int)(recordedList.size() / events * (events-1))};
-
- PAImage->Initialize(recordedList.back()->GetPixelType(), 3, dimLaser);
- PAImage->SetGeometry(recordedList.back()->GetGeometry());
- USImage->Initialize(recordedList.back()->GetPixelType(), 3, dimSound);
- USImage->SetGeometry(recordedList.back()->GetGeometry());
-
- for (int index = 0; index < recordedList.size(); ++index)
- {
- mitk::ImageReadAccessor inputReadAccessor(recordedList.at(index));
-
- if (index % events == 0)
- {
- PAImage->SetSlice(inputReadAccessor.GetData(), index / events);
- }
- else
- {
- if(!raw)
- USImage->SetSlice(inputReadAccessor.GetData(), ((index - (index % events)) / events) + (index % events)-1);
- }
- }
-}
-
-void mitk::USDiPhASImageSource::OrderImagesUltrasound(Image::Pointer USImage, std::vector<Image::Pointer> recordedList)
-{
- unsigned int width = 32;
- unsigned int height = 32;
- unsigned int events = m_Device->GetScanMode().transmitEventsCount;
-
- if (m_DataType == DataType::Beamformed_Short)
- {
- width = (unsigned int)m_Device->GetScanMode().reconstructionLines;
- height = (unsigned int)m_Device->GetScanMode().reconstructionSamplesPerLine;
- }
- else if (m_DataType == DataType::Image_uChar)
- {
- width = (unsigned int)m_Device->GetScanMode().imageWidth;
- height = (unsigned int)m_Device->GetScanMode().imageHeight;
- }
-
- unsigned int dimSound[] = { (unsigned int)width, (unsigned int)height, (unsigned int)recordedList.size()};
-
- USImage->Initialize(recordedList.back()->GetPixelType(), 3, dimSound);
- USImage->SetGeometry(recordedList.back()->GetGeometry());
-
- for (int index = 0; index < recordedList.size(); ++index)
- {
- mitk::ImageReadAccessor inputReadAccessor(recordedList.at(index));
- USImage->SetSlice(inputReadAccessor.GetData(), index);
- }
-}
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.h
deleted file mode 100644
index 428b8e6b32..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASImageSource.h
+++ /dev/null
@@ -1,189 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKUSDiPhASImageSource_H_HEADER_INCLUDED_
-#define MITKUSDiPhASImageSource_H_HEADER_INCLUDED_
-
-
-#include "mitkUSImageSource.h"
-#include "mitkUSDiPhASCustomControls.h"
-
-#include "Framework.IBMT.US.CWrapper.h"
-
-#include "mitkImageReadAccessor.h"
-#include "itkFastMutexLock.h"
-#include <functional>
-#include <qstring.h>
-#include <ctime>
-#include <string>
-#include <mutex>
-#include <iostream>
-#include <fstream>
-#include <mitkOphirPyro.h>
-
-
-namespace mitk {
-
-class USDiPhASDevice;
-/**
- * \brief Implementation of mitk::USImageSource for DiPhAS API devices.
- * The method mitk::USImageSource::GetNextRawImage() is implemented for
- * getting images from the DiPhAS API.
- *
- * The image data is given to this class from the DiPhAS API by calling
- * a callback method that writes the image data to an mitk::image
- */
-class USDiPhASImageSource : public USImageSource
-{
-
-public:
- mitkClassMacro(USDiPhASImageSource, USImageSource);
- mitkNewMacro1Param(Self, mitk::USDiPhASDevice*);
- itkCloneMacro(Self);
-
- typedef itk::Image< float, 3 > itkFloatImageType;
- typedef mitk::USDiPhASDeviceCustomControls::DataType DataType;
- typedef mitk::USDiPhASDeviceCustomControls::SavingSettings SavingSettings;
-
- /**
- * Implementation of the superclass method. Returns the pointer
- * to the mitk::Image filled by DiPhAS API callback.
- */
- virtual void GetNextRawImage( std::vector<mitk::Image::Pointer>& ) override;
-
- /**
- * The API calls this function to pass the image data to the
- * user; here the m_Image is updated
- */
- void mitk::USDiPhASImageSource::ImageDataCallback(
- short* rfDataChannelData,
- int& channelDataChannelsPerDataset,
- int& channelDataSamplesPerChannel,
- int& channelDataTotalDatasets,
-
- short* rfDataArrayBeamformed,
- int& beamformedLines,
- int& beamformedSamples,
- int& beamformedTotalDatasets,
-
- unsigned char* imageData,
- int& imageWidth,
- int& imageHeight,
- int& imagePixelFormat,
- int& imageSetsTotal,
-
- double& timeStamp);
-
- void SetGUIOutput(std::function<void(QString)> out);
-
- /** This starts or ends the recording session*/
- void SetRecordingStatus(bool record);
- void SetSavingSettings(SavingSettings settings);
- void SetVerticalSpacing(float mm);
-
- void ModifyDataType(DataType dataT);
- void ModifyUseBModeFilter(bool isSet);
- void ModifyScatteringCoefficient(int coeff);
- void ModifyCompensateForScattering(bool useIt);
- void ModifyEnergyCompensation(bool compensate);
-
- /**
- * Sets the spacing used in the image based on the informations of the ScanMode in USDiPhAS Device
- */
- void UpdateImageGeometry();
-
-protected:
- void SetDataType(DataType dataT);
- void SetUseBModeFilter(bool isSet);
-
- USDiPhASImageSource(mitk::USDiPhASDevice* device);
- virtual ~USDiPhASImageSource( );
-
- /** This vector holds all the images we record, if recording is set to active. */
- std::vector<mitk::Image::Pointer> m_RecordedImages;
- std::vector<mitk::Image::Pointer> m_RawRecordedImages;
- std::vector<long long> m_ImageTimestampRecord;
- std::vector<long long> m_ImageTimestampBuffer;
- long long m_CurrentImageTimestamp;
- bool m_CurrentlyRecording;
- mitk::OphirPyro::Pointer m_Pyro;
- bool m_PyroConnected;
-
- std::vector<Image::Pointer> m_FluenceCompOriginal;
- std::vector<Image::Pointer> m_FluenceCompResized;
- std::vector<itk::Image<float, 3>::Pointer> m_FluenceCompResizedItk;
-
- std::vector<mitk::Image::Pointer> m_ImageBuffer;
- int m_LastWrittenImage;
- int m_BufferSize;
-
- unsigned int m_ImageDimensions[3];
- mitk::Vector3D m_ImageSpacing;
-
- mitk::Image::Pointer ApplyBmodeFilter(mitk::Image::Pointer image, bool useLogFilter = false);
- mitk::Image::Pointer CutOffTop(mitk::Image::Pointer image, int cutOffSize = 165);
- mitk::Image::Pointer ResampleOutputVertical(mitk::Image::Pointer image, float verticalSpacing = 0.1);
-
- mitk::Image::Pointer ApplyScatteringCompensation(mitk::Image::Pointer inputImage, int scatteringCoefficient);
- mitk::Image::Pointer ApplyResampling(mitk::Image::Pointer inputImage, mitk::Vector3D outputSpacing, unsigned int outputSize[3]);
- mitk::Image::Pointer MultiplyImage(mitk::Image::Pointer inputImage, double value);
-
- void OrderImagesInterleaved(Image::Pointer PAImage, Image::Pointer USImage, std::vector<Image::Pointer> recordedList, bool raw);
- void OrderImagesUltrasound(Image::Pointer USImage, std::vector<Image::Pointer> recordedList);
-
- void GetPixelValues(itk::Index<3> pixel, std::vector<float>& values);
- float GetPixelValue(itk::Index<3> pixel);
- std::vector<float> m_PixelValues;
-
- mitk::USDiPhASDevice* m_Device;
-
- /** This is a callback to pass text data to the GUI. */
- std::function<void(QString)> m_GUIOutput;
-
- /**
- * Variables for management of current state.
- */
- SavingSettings m_SavingSettings;
-
- float m_StartTime;
- bool m_UseGUIOutPut;
-
- BeamformerStateInfoNative m_BeamformerInfos;
- bool m_UseBModeFilter;
-
- bool m_DataTypeModified;
- DataType m_DataTypeNext;
-
- bool m_UseBModeFilterModified;
- bool m_UseBModeFilterNext;
-
- float m_VerticalSpacing;
- float m_VerticalSpacingNext;
- bool m_VerticalSpacingModified;
-
- int m_ScatteringCoefficient;
- int m_ScatteringCoefficientNext;
- bool m_ScatteringCoefficientModified;
-
- bool m_CompensateForScattering;
- bool m_CompensateForScatteringNext;
- bool m_CompensateForScatteringModified;
-
- bool m_CompensateEnergy;
- bool m_CompensateEnergyNext;
- bool m_CompensateEnergyModified;
-
- DataType m_DataType;
-};
-} // namespace mitk
-
-#endif // MITKUSDiPhASImageSource_H
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbe.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbe.cpp
deleted file mode 100644
index afe7d710ff..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbe.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "mitkUSDiPhASProbe.h"
-#include "Framework.IBMT.US.CWrapper.h"
-
-mitk::USDiPhASProbe::USDiPhASProbe(std::string ProbeName)
-{
- SetName(ProbeName);
-}
-
-mitk::USDiPhASProbe::~USDiPhASProbe()
-{
-}
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbe.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbe.h
deleted file mode 100644
index dfb307a928..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbe.h
+++ /dev/null
@@ -1,45 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKUSDiPhASProbe_H_HEADER_INCLUDED_
-#define MITKUSDiPhASProbe_H_HEADER_INCLUDED_
-
-#include "mitkUSProbe.h"
-
-namespace mitk
-{
- /**
- * \brief Specialized mitk::USProbe for handling DiPhAS API probe objects.
- * It encapsulates a probe object from the DiPhAS API.
- *
- * This class should only be instantiated by mitk::USDiPhASProbesControls.
- * Every other object can get instances of mitk::USDiPhASProbe from there.
- */
- class USDiPhASProbe : public USProbe
- {
- public:
- mitkClassMacro(USDiPhASProbe, USProbe);
- mitkNewMacro1Param(Self, std::string);
-
- protected:
- /**
- * Constructs mitk::USDiPhASProbe object.
- *
- * \param ProbeName
- */
- USDiPhASProbe(std::string ProbeName);
- virtual ~USDiPhASProbe();
-
- };
-} // namespace mitk
-
-#endif // MITKUSDiPhASProbe_H_HEADER_INCLUDED_
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbesControls.cpp b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbesControls.cpp
deleted file mode 100644
index 0a7a6f262e..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbesControls.cpp
+++ /dev/null
@@ -1,109 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include <string>
-#include "mitkUSDiPhASProbesControls.h"
-#include "mitkUSDiPhASDevice.h"
-#include <mitkException.h>
-
-mitk::USDiPhASProbesControls::USDiPhASProbesControls(itk::SmartPointer<USDiPhASDevice> device)
- : mitk::USControlInterfaceProbes(device.GetPointer()),
- m_IsActive(false), m_DiPhASDevice(device)
-{
-}
-
-mitk::USDiPhASProbesControls::~USDiPhASProbesControls()
-{
-}
-
-
-void mitk::USDiPhASProbesControls::SetIsActive(bool isActive)
-{
- this->CreateProbesSet();
- m_IsActive = isActive;
-}
-
-bool mitk::USDiPhASProbesControls::GetIsActive()
-{
- return m_IsActive;
-}
-
-std::vector<mitk::USProbe::Pointer> mitk::USDiPhASProbesControls::GetProbeSet()
-{
- // create a new vector of base class (USProbe) objects, because
- // interface wants a vector of this type
- std::vector<mitk::USProbe::Pointer> usProbes(m_ProbesSet.size(), 0);
- for (unsigned int n = 0; n < m_ProbesSet.size(); ++n)
- {
- usProbes.at(n) = m_ProbesSet.at(n).GetPointer();
- }
- return usProbes;
-}
-
-void mitk::USDiPhASProbesControls::OnSelectProbe(unsigned int index)
-{
- if (index >= m_ProbesSet.size())
- {
- MITK_ERROR("USDiPhASProbesControls")("USControlInterfaceProbes")
- << "Cannot select probe with index " << index << ". Maximum possible index is " << m_ProbesSet.size() - 1 << ".";
- mitkThrow() << "Cannot select probe with index " << index <<
- ". Maximum possible index is " << m_ProbesSet.size() - 1 << ".";
- }
-
- m_SelectedProbeIndex = index;
-}
-
-void mitk::USDiPhASProbesControls::OnSelectProbe(mitk::USProbe::Pointer probe)
-{
-}
-
-mitk::USProbe::Pointer mitk::USDiPhASProbesControls::GetSelectedProbe()
-{
- if (m_SelectedProbeIndex >= m_ProbesSet.size())
- {
- MITK_ERROR("USDiPhASProbesControls")("USControlInterfaceProbes")
- << "Cannot get active probe as the current index is" << m_SelectedProbeIndex <<
- ". Maximum possible index is " << m_ProbesSet.size() - 1 << ".";
- mitkThrow() << "Cannot get active probe as the current index is" << m_SelectedProbeIndex <<
- ". Maximum possible index is " << m_ProbesSet.size() - 1 << ".";
- }
-
- return m_ProbesSet.at(m_SelectedProbeIndex).GetPointer();
-}
-
-unsigned int mitk::USDiPhASProbesControls::GetProbesCount() const
-{
- return m_ProbesSet.size();
-}
-
-
-void mitk::USDiPhASProbesControls::ProbeRemoved(unsigned int index)
-{
- MITK_INFO << "Probe removed...";
-
- if (m_ProbesSet.size() > index)
- {
- m_ProbesSet.erase(m_ProbesSet.begin() + index);
- }
-}
-
-void mitk::USDiPhASProbesControls::ProbeAdded(unsigned int index)
-{
- MITK_INFO << "Probe arrived...";
-
- this->CreateProbesSet();
-}
-
-void mitk::USDiPhASProbesControls::CreateProbesSet()
-{
- m_ProbesSet.push_back(mitk::USDiPhASProbe::New( m_DiPhASDevice->GetScanMode().transducerName ));
-}
diff --git a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbesControls.h b/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbesControls.h
deleted file mode 100644
index fb2ddfb0ce..0000000000
--- a/Modules/US/USHardwareDiPhAS/mitkUSDiPhASProbesControls.h
+++ /dev/null
@@ -1,83 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef MITKUSDiPhASProbesControls_H_HEADER_INCLUDED_
-#define MITKUSDiPhASProbesControls_H_HEADER_INCLUDED_
-
-#include "Framework.IBMT.US.CWrapper.h"
-#include "mitkUSDiPhASProbe.h"
-#include "mitkUSControlInterfaceProbes.h"
-
-#include <itkObjectFactory.h>
-
-namespace mitk {
- class USDiPhASDevice;
-
- /**
- * \brief Implementation of mitk::USControlInterfaceProbes for DiPhAS ultrasound devices.
- * See documentation of mitk::USControlInterfaceProbes for a description of the interface methods.
- * This class has to be implemented for the USDevice but the DiPhAS API does not support multiple devices.
- * Therefore there will be just one probe at all times.
- */
- class USDiPhASProbesControls : public USControlInterfaceProbes
- {
- public:
- mitkClassMacro(USDiPhASProbesControls, USControlInterfaceProbes);
- mitkNewMacro1Param(Self, itk::SmartPointer<USDiPhASDevice>);
-
- /**
- * Probe informations are fetched on activation. On deactivation there is nothing done.
- */
- virtual void SetIsActive(bool);
-
- virtual bool GetIsActive();
-
- virtual std::vector<USProbe::Pointer> GetProbeSet();
- virtual void OnSelectProbe(unsigned int index);
- virtual void OnSelectProbe(USProbe::Pointer probe);
- virtual USProbe::Pointer GetSelectedProbe();
- virtual unsigned int GetProbesCount() const;
-
- void ProbeRemoved(unsigned int index);
- void ProbeAdded(unsigned int index);
-
- protected:
- /**
- * Constructs an empty object.
- * DiPhAS device has to be set after constructing by calling
- * mitk::USDiPhASProbesControls::SetDiPhASDevice before the
- * object can be used.
- */
- USDiPhASProbesControls(itk::SmartPointer<USDiPhASDevice> device);
- virtual ~USDiPhASProbesControls();
-
- /**
- * Create collection object (DiPhAS API) for the API device.
- */
- bool CreateProbesCollection();
-
- /**
- * Create vector of mitk::USDiPhASProbe objects from the
- * DiPhAS API probe collection. Hence
- * mitk::USDiPhASProbesControls::CreateProbesCollection has to
- * be called before.
- */
- void CreateProbesSet();
-
- bool m_IsActive;
- unsigned int m_SelectedProbeIndex;
- std::vector<USDiPhASProbe::Pointer> m_ProbesSet;
- itk::SmartPointer<USDiPhASDevice> m_DiPhASDevice;
- };
-}
-
-#endif // MITKUSDiPhASProbesControls_H_HEADER_INCLUDED_
diff --git a/Modules/US/USModel/mitkUSDeviceReaderWriterConstants.cpp b/Modules/US/USModel/mitkUSDeviceReaderWriterConstants.cpp
new file mode 100644
index 0000000000..7eee5038e0
--- /dev/null
+++ b/Modules/US/USModel/mitkUSDeviceReaderWriterConstants.cpp
@@ -0,0 +1,50 @@
+/*============================================================================
+
+The Medical Imaging Interaction Toolkit (MITK)
+
+Copyright (c) German Cancer Research Center (DKFZ)
+All rights reserved.
+
+Use of this source code is governed by a 3-clause BSD license that can be
+found in the LICENSE file.
+
+============================================================================*/
+
+#include "mitkUSDeviceReaderWriterConstants.h"
+
+namespace mitk
+{
+ const char* USDeviceReaderWriterConstants::TAG_ULTRASOUNDDEVICE = "ULTRASOUNDDEVICE";
+ const char* USDeviceReaderWriterConstants::TAG_GENERALSETTINGS = "GENERALSETTINGS";
+ const char* USDeviceReaderWriterConstants::TAG_PROBES = "PROBES";
+ const char* USDeviceReaderWriterConstants::TAG_PROBE = "PROBE";
+ const char* USDeviceReaderWriterConstants::TAG_DEPTHS = "DEPTHS";
+ const char* USDeviceReaderWriterConstants::TAG_DEPTH = "DEPTH";
+ const char* USDeviceReaderWriterConstants::TAG_SPACING = "SPACING";
+ const char* USDeviceReaderWriterConstants::TAG_CROPPING = "CROPPING";
+
+ const char* USDeviceReaderWriterConstants::ATTR_FILEVERS = "filevers";
+ const char* USDeviceReaderWriterConstants::ATTR_TYPE = "type";
+ const char* USDeviceReaderWriterConstants::ATTR_HOST = "host";
+ const char* USDeviceReaderWriterConstants::ATTR_PORT = "port";
+ const char* USDeviceReaderWriterConstants::ATTR_SERVER = "server";
+ const char* USDeviceReaderWriterConstants::ATTR_NAME = "name";
+ const char* USDeviceReaderWriterConstants::ATTR_MANUFACTURER = "manufacturer";
+ const char* USDeviceReaderWriterConstants::ATTR_MODEL = "model";
+ const char* USDeviceReaderWriterConstants::ATTR_COMMENT = "comment";
+ const char* USDeviceReaderWriterConstants::ATTR_IMAGESTREAMS = "imagestreams";
+ const char* USDeviceReaderWriterConstants::ATTR_GREYSCALE = "greyscale";
+ const char* USDeviceReaderWriterConstants::ATTR_RESOLUTIONOVERRIDE = "resolutionOverride";
+ const char* USDeviceReaderWriterConstants::ATTR_RESOLUTIONWIDTH = "resolutionWidth";
+ const char* USDeviceReaderWriterConstants::ATTR_RESOLUTIONHEIGHT = "resolutionHeight";
+ const char* USDeviceReaderWriterConstants::ATTR_SOURCEID = "sourceID";
+ const char* USDeviceReaderWriterConstants::ATTR_FILEPATH = "filepath";
+ const char* USDeviceReaderWriterConstants::ATTR_OPENCVPORT = "opencvPort";
+ const char* USDeviceReaderWriterConstants::ATTR_DEPTH = "depth";
+ const char* USDeviceReaderWriterConstants::ATTR_X = "x";
+ const char* USDeviceReaderWriterConstants::ATTR_Y = "y";
+ const char* USDeviceReaderWriterConstants::ATTR_TOP = "top";
+ const char* USDeviceReaderWriterConstants::ATTR_BOTTOM = "bottom";
+ const char* USDeviceReaderWriterConstants::ATTR_LEFT = "left";
+ const char* USDeviceReaderWriterConstants::ATTR_RIGHT = "right";
+}
diff --git a/Modules/US/USModel/mitkUSDeviceReaderWriterConstants.h b/Modules/US/USModel/mitkUSDeviceReaderWriterConstants.h
index 3c01c2dd6d..7307f04628 100644
--- a/Modules/US/USModel/mitkUSDeviceReaderWriterConstants.h
+++ b/Modules/US/USModel/mitkUSDeviceReaderWriterConstants.h
@@ -1,52 +1,57 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkUSDeviceReaderWriterConstants_H_HEADER_INCLUDED_
#define mitkUSDeviceReaderWriterConstants_H_HEADER_INCLUDED_
-const static char* TAG_ULTRASOUNDDEVICE = "ULTRASOUNDDEVICE";
-const static char* TAG_GENERALSETTINGS = "GENERALSETTINGS";
-const static char* TAG_PROBES = "PROBES";
-const static char* TAG_PROBE = "PROBE";
-const static char* TAG_DEPTHS = "DEPTHS";
-const static char* TAG_DEPTH = "DEPTH";
-const static char* TAG_SPACING = "SPACING";
-const static char* TAG_CROPPING = "CROPPING";
-
-const static char* ATTR_FILEVERS = "filevers";
-const static char* ATTR_TYPE = "type";
-const static char* ATTR_HOST = "host";
-const static char* ATTR_PORT = "port";
-const static char* ATTR_SERVER = "server";
-const static char* ATTR_NAME = "name";
-const static char* ATTR_MANUFACTURER = "manufacturer";
-const static char* ATTR_MODEL = "model";
-const static char* ATTR_COMMENT = "comment";
-const static char* ATTR_IMAGESTREAMS = "imagestreams";
-const static char* ATTR_GREYSCALE = "greyscale";
-const static char* ATTR_RESOLUTIONOVERRIDE = "resolutionOverride";
-const static char* ATTR_RESOLUTIONWIDTH = "resolutionWidth";
-const static char* ATTR_RESOLUTIONHEIGHT = "resolutionHeight";
-const static char* ATTR_SOURCEID = "sourceID";
-const static char* ATTR_FILEPATH = "filepath";
-const static char* ATTR_OPENCVPORT = "opencvPort";
-const static char* ATTR_DEPTH = "depth";
-const static char* ATTR_X = "x";
-const static char* ATTR_Y = "y";
-const static char* ATTR_TOP = "top";
-const static char* ATTR_BOTTOM = "bottom";
-const static char* ATTR_LEFT = "left";
-const static char* ATTR_RIGHT = "right";
-
+namespace mitk
+{
+ struct USDeviceReaderWriterConstants
+ {
+ static const char* TAG_ULTRASOUNDDEVICE;
+ static const char* TAG_GENERALSETTINGS;
+ static const char* TAG_PROBES;
+ static const char* TAG_PROBE;
+ static const char* TAG_DEPTHS;
+ static const char* TAG_DEPTH;
+ static const char* TAG_SPACING;
+ static const char* TAG_CROPPING;
+
+ static const char* ATTR_FILEVERS;
+ static const char* ATTR_TYPE;
+ static const char* ATTR_HOST;
+ static const char* ATTR_PORT;
+ static const char* ATTR_SERVER;
+ static const char* ATTR_NAME;
+ static const char* ATTR_MANUFACTURER;
+ static const char* ATTR_MODEL;
+ static const char* ATTR_COMMENT;
+ static const char* ATTR_IMAGESTREAMS;
+ static const char* ATTR_GREYSCALE;
+ static const char* ATTR_RESOLUTIONOVERRIDE;
+ static const char* ATTR_RESOLUTIONWIDTH;
+ static const char* ATTR_RESOLUTIONHEIGHT;
+ static const char* ATTR_SOURCEID;
+ static const char* ATTR_FILEPATH;
+ static const char* ATTR_OPENCVPORT;
+ static const char* ATTR_DEPTH;
+ static const char* ATTR_X;
+ static const char* ATTR_Y;
+ static const char* ATTR_TOP;
+ static const char* ATTR_BOTTOM;
+ static const char* ATTR_LEFT;
+ static const char* ATTR_RIGHT;
+ };
+}
#endif // mitkUSDeviceReaderWriterConstants_H_HEADER_INCLUDED_
diff --git a/Modules/US/USModel/mitkUSDeviceReaderXML.cpp b/Modules/US/USModel/mitkUSDeviceReaderXML.cpp
index 250b7af835..9c6b2ade02 100644
--- a/Modules/US/USModel/mitkUSDeviceReaderXML.cpp
+++ b/Modules/US/USModel/mitkUSDeviceReaderXML.cpp
@@ -1,204 +1,217 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include "mitkUSDeviceReaderWriterConstants.h"
#include "mitkUSDeviceReaderXML.h"
#include <mitkIGTMimeTypes.h>
#include <mitkLocaleSwitch.h>
#include <mitkUSVideoDevice.h>
// Third Party
#include <itksys/SystemTools.hxx>
#include <fstream>
-#include <tinyxml.h>
+#include <tinyxml2.h>
+
+namespace
+{
+ std::string ReadStringAttribute(const tinyxml2::XMLElement* elem, const char* name)
+ {
+ const char* attrib = elem->Attribute(name);
+
+ return attrib != nullptr
+ ? attrib
+ : "";
+ }
+}
mitk::USDeviceReaderXML::USDeviceReaderXML() : AbstractFileReader(
mitk::IGTMimeTypes::USDEVICEINFORMATIONXML_MIMETYPE(),
"MITK USDevice Reader (XML)"), m_Filename("")
{
RegisterService();
}
mitk::USDeviceReaderXML::~USDeviceReaderXML()
{
}
mitk::USDeviceReaderXML::USDeviceConfigData &mitk::USDeviceReaderXML::GetUSDeviceConfigData()
{
return m_DeviceConfig;
}
mitk::USDeviceReaderXML::USDeviceReaderXML(const mitk::USDeviceReaderXML& other) : AbstractFileReader(other)
{
}
mitk::USDeviceReaderXML* mitk::USDeviceReaderXML::Clone() const
{
return new USDeviceReaderXML(*this);
}
std::vector<itk::SmartPointer<mitk::BaseData>> mitk::USDeviceReaderXML::DoRead()
{
MITK_WARN << "This method is not implemented. \
Please use the method ReadUltrasoundDeviceConfiguration() instead.";
std::vector<mitk::BaseData::Pointer> result;
return result;
}
bool mitk::USDeviceReaderXML::ReadUltrasoundDeviceConfiguration()
{
MITK_INFO << "Try to start reading xml device configuration...";
if (m_Filename == "")
{
MITK_WARN << "Cannot read file - empty filename!";
return false;
}
- TiXmlDocument document(m_Filename);
- if (!document.LoadFile())
+ tinyxml2::XMLDocument document;
+ if (tinyxml2::XML_SUCCESS != document.LoadFile(m_Filename.c_str()))
{
MITK_ERROR << "Error when opening and reading file :" << m_Filename;
return false;
}
- TiXmlHandle documentHandle(&document);
- TiXmlElement* ultrasoundDeviceTag = documentHandle.FirstChildElement(TAG_ULTRASOUNDDEVICE).ToElement();
+ tinyxml2::XMLHandle documentHandle(&document);
+ auto* ultrasoundDeviceTag = documentHandle.FirstChildElement(USDeviceReaderWriterConstants::TAG_ULTRASOUNDDEVICE).ToElement();
if (ultrasoundDeviceTag == nullptr)
{
MITK_ERROR << "Error parsing the file :" << m_Filename << std::endl << "Wrong xml format structure.";
return false;
}
//Extract attribute information of the ULTRASOUNDDEVICE-Tag:
this->ExtractAttributeInformationOfUltrasoundDeviceTag(ultrasoundDeviceTag);
- TiXmlElement* generalSettingsTag = documentHandle.FirstChildElement(TAG_ULTRASOUNDDEVICE).FirstChildElement(TAG_GENERALSETTINGS).ToElement();
+ auto* generalSettingsTag = documentHandle.FirstChildElement(USDeviceReaderWriterConstants::TAG_ULTRASOUNDDEVICE).FirstChildElement(USDeviceReaderWriterConstants::TAG_GENERALSETTINGS).ToElement();
if (generalSettingsTag == nullptr)
{
MITK_ERROR << "Error parsing the GENERALSETTINGS-Tag in the file :" << m_Filename;
return false;
}
//Extract attribute information of the GENERALSETTINGS-Tag:
this->ExtractAttributeInformationOfGeneralSettingsTag(generalSettingsTag);
- TiXmlElement* probesTag = documentHandle.FirstChildElement(TAG_ULTRASOUNDDEVICE).FirstChildElement(TAG_PROBES).ToElement();
+ auto* probesTag = documentHandle.FirstChildElement(USDeviceReaderWriterConstants::TAG_ULTRASOUNDDEVICE).FirstChildElement(USDeviceReaderWriterConstants::TAG_PROBES).ToElement();
if (probesTag == nullptr)
{
MITK_ERROR << "Error: PROBES-Tag was not found in the file :" << m_Filename << "Therefore, creating default probe.";
//Create default ultrasound probe:
mitk::USProbe::Pointer ultrasoundProbeDefault = mitk::USProbe::New();
ultrasoundProbeDefault->SetName("default");
ultrasoundProbeDefault->SetDepth(0);
m_DeviceConfig.probes.push_back(ultrasoundProbeDefault);
return true;
}
//Extract all saved and configured probes of the USDevice:
- for (TiXmlElement* probeTag = probesTag->FirstChildElement(TAG_PROBE);
+ for (auto* probeTag = probesTag->FirstChildElement(USDeviceReaderWriterConstants::TAG_PROBE);
probeTag != nullptr; probeTag = probeTag->NextSiblingElement())
{
this->ExtractProbe(probeTag);
}
return true;
}
void mitk::USDeviceReaderXML::SetFilename(std::string filename)
{
m_Filename = filename;
}
-void mitk::USDeviceReaderXML::ExtractAttributeInformationOfUltrasoundDeviceTag(TiXmlElement *ultrasoundTag)
+void mitk::USDeviceReaderXML::ExtractAttributeInformationOfUltrasoundDeviceTag(const tinyxml2::XMLElement *ultrasoundTag)
{
- ultrasoundTag->QueryDoubleAttribute(ATTR_FILEVERS, &m_DeviceConfig.fileversion);
- ultrasoundTag->QueryStringAttribute(ATTR_TYPE, &m_DeviceConfig.deviceType);
- ultrasoundTag->QueryStringAttribute(ATTR_NAME, &m_DeviceConfig.deviceName);
- ultrasoundTag->QueryStringAttribute(ATTR_MANUFACTURER, &m_DeviceConfig.manufacturer);
- ultrasoundTag->QueryStringAttribute(ATTR_MODEL, &m_DeviceConfig.model);
- ultrasoundTag->QueryStringAttribute(ATTR_COMMENT, &m_DeviceConfig.comment);
- ultrasoundTag->QueryIntAttribute(ATTR_IMAGESTREAMS, &m_DeviceConfig.numberOfImageStreams);
- ultrasoundTag->QueryStringAttribute(ATTR_HOST, &m_DeviceConfig.host);
- ultrasoundTag->QueryIntAttribute(ATTR_PORT, &m_DeviceConfig.port);
- ultrasoundTag->QueryBoolAttribute(ATTR_SERVER, &m_DeviceConfig.server);
+ ultrasoundTag->QueryDoubleAttribute(USDeviceReaderWriterConstants::ATTR_FILEVERS, &m_DeviceConfig.fileversion);
+ ultrasoundTag->QueryIntAttribute(USDeviceReaderWriterConstants::ATTR_IMAGESTREAMS, &m_DeviceConfig.numberOfImageStreams);
+ ultrasoundTag->QueryIntAttribute(USDeviceReaderWriterConstants::ATTR_PORT, &m_DeviceConfig.port);
+ ultrasoundTag->QueryBoolAttribute(USDeviceReaderWriterConstants::ATTR_SERVER, &m_DeviceConfig.server);
+
+ m_DeviceConfig.deviceType = ReadStringAttribute(ultrasoundTag, USDeviceReaderWriterConstants::ATTR_TYPE);
+ m_DeviceConfig.deviceName = ReadStringAttribute(ultrasoundTag, USDeviceReaderWriterConstants::ATTR_TYPE);
+ m_DeviceConfig.manufacturer = ReadStringAttribute(ultrasoundTag, USDeviceReaderWriterConstants::ATTR_TYPE);
+ m_DeviceConfig.model = ReadStringAttribute(ultrasoundTag, USDeviceReaderWriterConstants::ATTR_TYPE);
+ m_DeviceConfig.comment = ReadStringAttribute(ultrasoundTag, USDeviceReaderWriterConstants::ATTR_TYPE);
+ m_DeviceConfig.host = ReadStringAttribute(ultrasoundTag, USDeviceReaderWriterConstants::ATTR_HOST);
}
-void mitk::USDeviceReaderXML::ExtractAttributeInformationOfGeneralSettingsTag(TiXmlElement *generalSettingsTag)
+void mitk::USDeviceReaderXML::ExtractAttributeInformationOfGeneralSettingsTag(const tinyxml2::XMLElement *generalSettingsTag)
{
- generalSettingsTag->QueryBoolAttribute(ATTR_GREYSCALE, &m_DeviceConfig.useGreyscale);
- generalSettingsTag->QueryBoolAttribute(ATTR_RESOLUTIONOVERRIDE, &m_DeviceConfig.useResolutionOverride);
- generalSettingsTag->QueryIntAttribute(ATTR_RESOLUTIONHEIGHT, &m_DeviceConfig.resolutionHeight);
- generalSettingsTag->QueryIntAttribute(ATTR_RESOLUTIONWIDTH, &m_DeviceConfig.resolutionWidth);
- generalSettingsTag->QueryIntAttribute(ATTR_SOURCEID, &m_DeviceConfig.sourceID);
- generalSettingsTag->QueryStringAttribute(ATTR_FILEPATH, &m_DeviceConfig.filepathVideoSource);
- generalSettingsTag->QueryIntAttribute(ATTR_OPENCVPORT, &m_DeviceConfig.opencvPort);
+ generalSettingsTag->QueryBoolAttribute(USDeviceReaderWriterConstants::ATTR_GREYSCALE, &m_DeviceConfig.useGreyscale);
+ generalSettingsTag->QueryBoolAttribute(USDeviceReaderWriterConstants::ATTR_RESOLUTIONOVERRIDE, &m_DeviceConfig.useResolutionOverride);
+ generalSettingsTag->QueryIntAttribute(USDeviceReaderWriterConstants::ATTR_RESOLUTIONHEIGHT, &m_DeviceConfig.resolutionHeight);
+ generalSettingsTag->QueryIntAttribute(USDeviceReaderWriterConstants::ATTR_RESOLUTIONWIDTH, &m_DeviceConfig.resolutionWidth);
+ generalSettingsTag->QueryIntAttribute(USDeviceReaderWriterConstants::ATTR_SOURCEID, &m_DeviceConfig.sourceID);
+ generalSettingsTag->QueryIntAttribute(USDeviceReaderWriterConstants::ATTR_OPENCVPORT, &m_DeviceConfig.opencvPort);
+
+ m_DeviceConfig.filepathVideoSource = ReadStringAttribute(generalSettingsTag, USDeviceReaderWriterConstants::ATTR_FILEPATH);
}
-void mitk::USDeviceReaderXML::ExtractProbe(TiXmlElement *probeTag)
+void mitk::USDeviceReaderXML::ExtractProbe(const tinyxml2::XMLElement *probeTag)
{
mitk::USProbe::Pointer ultrasoundProbe = mitk::USProbe::New();
- std::string probeName;
- probeTag->QueryStringAttribute(ATTR_NAME, &probeName);
+ auto probeName = ReadStringAttribute(probeTag, USDeviceReaderWriterConstants::ATTR_NAME);
ultrasoundProbe->SetName(probeName);
- TiXmlElement* depthsTag = probeTag->FirstChildElement(TAG_DEPTHS);
+ auto* depthsTag = probeTag->FirstChildElement(USDeviceReaderWriterConstants::TAG_DEPTHS);
if (depthsTag != nullptr)
{
- for (TiXmlElement* depthTag = depthsTag->FirstChildElement(TAG_DEPTH);
+ for (auto* depthTag = depthsTag->FirstChildElement(USDeviceReaderWriterConstants::TAG_DEPTH);
depthTag != nullptr; depthTag = depthTag->NextSiblingElement())
{
int depth = 0;
mitk::Vector3D spacing;
spacing[0] = 1;
spacing[1] = 1;
spacing[2] = 1;
- depthTag->QueryIntAttribute(ATTR_DEPTH, &depth);
+ depthTag->QueryIntAttribute(USDeviceReaderWriterConstants::ATTR_DEPTH, &depth);
- TiXmlElement* spacingTag = depthTag->FirstChildElement(TAG_SPACING);
+ auto* spacingTag = depthTag->FirstChildElement(USDeviceReaderWriterConstants::TAG_SPACING);
if (spacingTag != nullptr)
{
- spacingTag->QueryDoubleAttribute(ATTR_X, &spacing[0]);
- spacingTag->QueryDoubleAttribute(ATTR_Y, &spacing[1]);
+ spacingTag->QueryDoubleAttribute(USDeviceReaderWriterConstants::ATTR_X, &spacing[0]);
+ spacingTag->QueryDoubleAttribute(USDeviceReaderWriterConstants::ATTR_Y, &spacing[1]);
}
ultrasoundProbe->SetDepthAndSpacing(depth, spacing);
}
}
else
{
MITK_ERROR << "Error: DEPTHS-Tag was not found in the file :" << m_Filename
<< "Therefore, creating default depth [0] and spacing [1,1,1] for the probe.";
ultrasoundProbe->SetDepth(0);
}
unsigned int croppingTop = 0;
unsigned int croppingBottom = 0;
unsigned int croppingLeft = 0;
unsigned int croppingRight = 0;
- TiXmlElement* croppingTag = probeTag->FirstChildElement(TAG_CROPPING);
+ auto* croppingTag = probeTag->FirstChildElement(USDeviceReaderWriterConstants::TAG_CROPPING);
if (croppingTag != nullptr)
{
- croppingTag->QueryUnsignedAttribute(ATTR_TOP, &croppingTop);
- croppingTag->QueryUnsignedAttribute(ATTR_BOTTOM, &croppingBottom);
- croppingTag->QueryUnsignedAttribute(ATTR_LEFT, &croppingLeft);
- croppingTag->QueryUnsignedAttribute(ATTR_RIGHT, &croppingRight);
+ croppingTag->QueryUnsignedAttribute(USDeviceReaderWriterConstants::ATTR_TOP, &croppingTop);
+ croppingTag->QueryUnsignedAttribute(USDeviceReaderWriterConstants::ATTR_BOTTOM, &croppingBottom);
+ croppingTag->QueryUnsignedAttribute(USDeviceReaderWriterConstants::ATTR_LEFT, &croppingLeft);
+ croppingTag->QueryUnsignedAttribute(USDeviceReaderWriterConstants::ATTR_RIGHT, &croppingRight);
}
ultrasoundProbe->SetProbeCropping(croppingTop, croppingBottom, croppingLeft, croppingRight);
m_DeviceConfig.probes.push_back(ultrasoundProbe);
}
diff --git a/Modules/US/USModel/mitkUSDeviceReaderXML.h b/Modules/US/USModel/mitkUSDeviceReaderXML.h
index a81663d7c2..ca168add34 100644
--- a/Modules/US/USModel/mitkUSDeviceReaderXML.h
+++ b/Modules/US/USModel/mitkUSDeviceReaderXML.h
@@ -1,103 +1,104 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkUSDeviceReaderXML_H_HEADER_INCLUDED_
#define mitkUSDeviceReaderXML_H_HEADER_INCLUDED_
#include <MitkUSExports.h>
#include <mitkAbstractFileReader.h>
#include <mitkUSProbe.h>
-class TiXmlElement;
-class TiXmlNode;
+namespace tinyxml2 {
+ class XMLElement;
+}
namespace mitk {
class MITKUS_EXPORT USDeviceReaderXML : public AbstractFileReader
{
public:
USDeviceReaderXML();
~USDeviceReaderXML() override;
using AbstractFileReader::Read;
bool ReadUltrasoundDeviceConfiguration();
void SetFilename(std::string filename);
typedef struct USDeviceConfigData_
{
double fileversion;
std::string deviceType;
std::string deviceName;
std::string manufacturer;
std::string model;
std::string comment;
std::string host;
int port;
bool server;
int numberOfImageStreams;
bool useGreyscale;
bool useResolutionOverride;
int resolutionWidth;
int resolutionHeight;
int sourceID;
std::string filepathVideoSource;
int opencvPort;
std::vector <mitk::USProbe::Pointer> probes;
USDeviceConfigData_()
: fileversion(0), deviceType("Unknown"), deviceName("Unknown"),
manufacturer("Unknown"), comment(""), host("localhost"),
port(18944), server(false), numberOfImageStreams(1),
useGreyscale(true), useResolutionOverride(true),
resolutionWidth(640), resolutionHeight(480), sourceID(0),
filepathVideoSource(""), opencvPort(0)
{ };
}USDeviceConfigData;
USDeviceConfigData &GetUSDeviceConfigData();
protected:
std::vector<itk::SmartPointer<BaseData>> DoRead() override;
USDeviceReaderXML(const USDeviceReaderXML& other);
mitk::USDeviceReaderXML* Clone() const override;
/**
* \brief Extracts all stored attribute information of the ULTRASOUNDDEVICE-Tag.
*/
- void ExtractAttributeInformationOfUltrasoundDeviceTag(TiXmlElement *element);
+ void ExtractAttributeInformationOfUltrasoundDeviceTag(const tinyxml2::XMLElement *element);
/**
* \brief Extracts all stored attribute information of the GENERALSETTINGS-Tag.
*/
- void ExtractAttributeInformationOfGeneralSettingsTag(TiXmlElement *element);
+ void ExtractAttributeInformationOfGeneralSettingsTag(const tinyxml2::XMLElement *element);
/**
* \brief Extracts all stored information of a single ultrasound probe.
*/
- void ExtractProbe(TiXmlElement *element);
+ void ExtractProbe(const tinyxml2::XMLElement *element);
private:
std::string m_Filename;
USDeviceConfigData m_DeviceConfig;
};
} // namespace mitk
#endif // mitkUSDeviceReaderXML_H_HEADER_INCLUDED_
diff --git a/Modules/US/USModel/mitkUSDeviceWriterXML.cpp b/Modules/US/USModel/mitkUSDeviceWriterXML.cpp
index d0be517a1e..6d56cc163c 100644
--- a/Modules/US/USModel/mitkUSDeviceWriterXML.cpp
+++ b/Modules/US/USModel/mitkUSDeviceWriterXML.cpp
@@ -1,161 +1,157 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
// MITK
#include "mitkUSDeviceReaderWriterConstants.h"
#include "mitkUSDeviceWriterXML.h"
#include <mitkIGTMimeTypes.h>
#include <mitkLocaleSwitch.h>
#include <mitkUSDevice.h>
// Third Party
-#include <tinyxml.h>
+#include <tinyxml2.h>
#include <itksys/SystemTools.hxx>
#include <fstream>
#include <iostream>
mitk::USDeviceWriterXML::USDeviceWriterXML() : AbstractFileWriter(USDevice::GetStaticNameOfClass(),
mitk::IGTMimeTypes::USDEVICEINFORMATIONXML_MIMETYPE(),
"MITK USDevice Writer (XML)"), m_Filename("")
{
RegisterService();
}
mitk::USDeviceWriterXML::USDeviceWriterXML(const mitk::USDeviceWriterXML& other) : AbstractFileWriter(other)
{
}
mitk::USDeviceWriterXML::~USDeviceWriterXML()
{
}
mitk::USDeviceWriterXML* mitk::USDeviceWriterXML::Clone() const
{
return new USDeviceWriterXML(*this);
}
void mitk::USDeviceWriterXML::Write()
{
if (m_Filename == "")
{
MITK_WARN << "Cannot write to file - empty filename!";
return;
}
}
void mitk::USDeviceWriterXML::SetFilename(std::string filename)
{
m_Filename = filename;
}
bool mitk::USDeviceWriterXML::WriteUltrasoundDeviceConfiguration(mitk::USDeviceReaderXML::USDeviceConfigData & config)
{
- TiXmlDocument document;
- TiXmlDeclaration* xmlDeclaration = new TiXmlDeclaration("1.0", "", "");
- document.LinkEndChild(xmlDeclaration);
-
+ tinyxml2::XMLDocument document;
+ document.InsertEndChild(document.NewDeclaration());
//Create the xml information of the ULTRASOUNDDEVICE-Tag:
- TiXmlElement *ultrasoundDeviceTag = new TiXmlElement(TAG_ULTRASOUNDDEVICE);
+ auto *ultrasoundDeviceTag = document.NewElement(USDeviceReaderWriterConstants::TAG_ULTRASOUNDDEVICE);
this->CreateXmlInformationOfUltrasoundDeviceTag(document, ultrasoundDeviceTag, config);
//Create the xml information of the GENERALSETTINGS-Tag:
- TiXmlElement *generalSettingsTag = new TiXmlElement(TAG_GENERALSETTINGS);
+ auto *generalSettingsTag = document.NewElement(USDeviceReaderWriterConstants::TAG_GENERALSETTINGS);
this->CreateXmlInformationOfGeneralSettingsTag(ultrasoundDeviceTag, generalSettingsTag, config);
//Create the xml information of the PROBES-Tag:
this->CreateXmlInformationOfProbesTag(ultrasoundDeviceTag, config);
- return document.SaveFile(m_Filename);
+ return document.SaveFile(m_Filename.c_str()) == tinyxml2::XML_SUCCESS;
}
void mitk::USDeviceWriterXML::CreateXmlInformationOfUltrasoundDeviceTag(
- TiXmlDocument &document, TiXmlElement * ultrasoundDeviceTag,
+ tinyxml2::XMLDocument &document, tinyxml2::XMLElement* ultrasoundDeviceTag,
mitk::USDeviceReaderXML::USDeviceConfigData &config)
{
- ultrasoundDeviceTag->SetAttribute(ATTR_FILEVERS, config.fileversion);
- ultrasoundDeviceTag->SetAttribute(ATTR_TYPE, config.deviceType);
- ultrasoundDeviceTag->SetAttribute(ATTR_NAME, config.deviceName);
- ultrasoundDeviceTag->SetAttribute(ATTR_MANUFACTURER, config.manufacturer);
- ultrasoundDeviceTag->SetAttribute(ATTR_MODEL, config.model);
- ultrasoundDeviceTag->SetAttribute(ATTR_COMMENT, config.comment);
- ultrasoundDeviceTag->SetAttribute(ATTR_IMAGESTREAMS, config.numberOfImageStreams);
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_FILEVERS, config.fileversion);
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_TYPE, config.deviceType.c_str());
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_NAME, config.deviceName.c_str());
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_MANUFACTURER, config.manufacturer.c_str());
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_MODEL, config.model.c_str());
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_COMMENT, config.comment.c_str());
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_IMAGESTREAMS, config.numberOfImageStreams);
if (config.deviceType.compare("oigtl") == 0)
{
- ultrasoundDeviceTag->SetAttribute(ATTR_HOST, config.host);
- ultrasoundDeviceTag->SetAttribute(ATTR_PORT, config.port);
- std::string value = config.server ? "true" : "false";
- ultrasoundDeviceTag->SetAttribute(ATTR_SERVER, value);
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_HOST, config.host.c_str());
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_PORT, config.port);
+ ultrasoundDeviceTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_SERVER, config.server);
}
- document.LinkEndChild(ultrasoundDeviceTag);
+ document.InsertEndChild(ultrasoundDeviceTag);
}
-void mitk::USDeviceWriterXML::CreateXmlInformationOfGeneralSettingsTag(TiXmlElement *parentTag, TiXmlElement *generalSettingsTag, mitk::USDeviceReaderXML::USDeviceConfigData & config)
+void mitk::USDeviceWriterXML::CreateXmlInformationOfGeneralSettingsTag(tinyxml2::XMLElement *parentTag, tinyxml2::XMLElement *generalSettingsTag, mitk::USDeviceReaderXML::USDeviceConfigData & config)
{
- std::string value = config.useGreyscale ? "true" : "false";
- generalSettingsTag->SetAttribute(ATTR_GREYSCALE, value);
- value = config.useResolutionOverride ? "true" : "false";
- generalSettingsTag->SetAttribute(ATTR_RESOLUTIONOVERRIDE, value);
- generalSettingsTag->SetAttribute(ATTR_RESOLUTIONWIDTH, config.resolutionWidth);
- generalSettingsTag->SetAttribute(ATTR_RESOLUTIONHEIGHT, config.resolutionHeight);
-
- generalSettingsTag->SetAttribute(ATTR_SOURCEID, config.sourceID);
- generalSettingsTag->SetAttribute(ATTR_FILEPATH, config.filepathVideoSource);
- generalSettingsTag->SetAttribute(ATTR_OPENCVPORT, config.opencvPort);
-
- parentTag->LinkEndChild(generalSettingsTag);
+ generalSettingsTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_GREYSCALE, config.useGreyscale);
+ generalSettingsTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_RESOLUTIONOVERRIDE, config.useResolutionOverride);
+ generalSettingsTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_RESOLUTIONWIDTH, config.resolutionWidth);
+ generalSettingsTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_RESOLUTIONHEIGHT, config.resolutionHeight);
+
+ generalSettingsTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_SOURCEID, config.sourceID);
+ generalSettingsTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_FILEPATH, config.filepathVideoSource.c_str());
+ generalSettingsTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_OPENCVPORT, config.opencvPort);
+
+ parentTag->InsertEndChild(generalSettingsTag);
}
-void mitk::USDeviceWriterXML::CreateXmlInformationOfProbesTag(TiXmlElement * parentTag, mitk::USDeviceReaderXML::USDeviceConfigData & config)
+void mitk::USDeviceWriterXML::CreateXmlInformationOfProbesTag(tinyxml2::XMLElement *parentTag, mitk::USDeviceReaderXML::USDeviceConfigData & config)
{
if (config.probes.size() != 0)
{
- TiXmlElement *probesTag = new TiXmlElement(TAG_PROBES);
- parentTag->LinkEndChild(probesTag);
+ auto* doc = parentTag->GetDocument();
+ auto *probesTag = doc->NewElement(USDeviceReaderWriterConstants::TAG_PROBES);
+ parentTag->InsertEndChild(probesTag);
for (size_t index = 0; index < config.probes.size(); ++index)
{
- TiXmlElement *probeTag = new TiXmlElement(TAG_PROBE);
- probesTag->LinkEndChild(probeTag);
+ auto *probeTag = doc->NewElement(USDeviceReaderWriterConstants::TAG_PROBE);
+ probesTag->InsertEndChild(probeTag);
mitk::USProbe::Pointer probe = config.probes.at(index);
- probeTag->SetAttribute(ATTR_NAME, probe->GetName());
+ probeTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_NAME, probe->GetName().c_str());
std::map<int, mitk::Vector3D> depthsAndSpacing = probe->GetDepthsAndSpacing();
if (depthsAndSpacing.size() != 0)
{
- TiXmlElement *depthsTag = new TiXmlElement(TAG_DEPTHS);
- probeTag->LinkEndChild(depthsTag);
+ auto *depthsTag = doc->NewElement(USDeviceReaderWriterConstants::TAG_DEPTHS);
+ probeTag->InsertEndChild(depthsTag);
for (std::map<int, mitk::Vector3D>::iterator it = depthsAndSpacing.begin(); it != depthsAndSpacing.end(); it++)
{
- TiXmlElement *depthTag = new TiXmlElement(TAG_DEPTH);
- depthTag->SetAttribute(ATTR_DEPTH, it->first);
- depthsTag->LinkEndChild(depthTag);
-
- TiXmlElement *spacingTag = new TiXmlElement(TAG_SPACING);
- spacingTag->SetDoubleAttribute(ATTR_X, it->second[0], 6);
- spacingTag->SetDoubleAttribute(ATTR_Y, it->second[1], 6);
- depthTag->LinkEndChild(spacingTag);
+ auto *depthTag = doc->NewElement(USDeviceReaderWriterConstants::TAG_DEPTH);
+ depthTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_DEPTH, it->first);
+ depthsTag->InsertEndChild(depthTag);
+
+ auto *spacingTag = doc->NewElement(USDeviceReaderWriterConstants::TAG_SPACING);
+ spacingTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_X, it->second[0]);
+ spacingTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_Y, it->second[1]);
+ depthTag->InsertEndChild(spacingTag);
}
- TiXmlElement *croppingTag = new TiXmlElement(TAG_CROPPING);
- probeTag->LinkEndChild(croppingTag);
- croppingTag->SetAttribute(ATTR_TOP, probe->GetProbeCropping().top);
- croppingTag->SetAttribute(ATTR_BOTTOM, probe->GetProbeCropping().bottom);
- croppingTag->SetAttribute(ATTR_LEFT, probe->GetProbeCropping().left);
- croppingTag->SetAttribute(ATTR_RIGHT, probe->GetProbeCropping().right);
+ auto *croppingTag = doc->NewElement(USDeviceReaderWriterConstants::TAG_CROPPING);
+ probeTag->InsertEndChild(croppingTag);
+ croppingTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_TOP, probe->GetProbeCropping().top);
+ croppingTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_BOTTOM, probe->GetProbeCropping().bottom);
+ croppingTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_LEFT, probe->GetProbeCropping().left);
+ croppingTag->SetAttribute(USDeviceReaderWriterConstants::ATTR_RIGHT, probe->GetProbeCropping().right);
}
}
}
}
diff --git a/Modules/US/USModel/mitkUSDeviceWriterXML.h b/Modules/US/USModel/mitkUSDeviceWriterXML.h
index 657f07d25c..1177b144e3 100644
--- a/Modules/US/USModel/mitkUSDeviceWriterXML.h
+++ b/Modules/US/USModel/mitkUSDeviceWriterXML.h
@@ -1,88 +1,91 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef mitkUSDeviceWriterXML_H_Header_INCLUDED_
#define mitkUSDeviceWriterXML_H_Header_INCLUDED_
#include <MitkUSExports.h>
#include <mitkAbstractFileWriter.h>
#include <mitkUSDeviceReaderXML.h>
-class TiXmlDocument;
-class TiXmlElement;
+namespace tinyxml2
+{
+ class XMLDocument;
+ class XMLElement;
+}
namespace mitk {
class MITKUS_EXPORT USDeviceWriterXML : public AbstractFileWriter
{
public:
USDeviceWriterXML();
~USDeviceWriterXML() override;
using AbstractFileWriter::Write;
void Write() override;
/**
* \brief Sets the filename of the ultrasound device configuration file which should be created.
*/
void SetFilename(std::string filename);
/**
* \brief Writes the configuration settings of an ultrasound device to a xml-file.
* \param config The struct containing all information of the ultrasound device.
*/
bool WriteUltrasoundDeviceConfiguration(mitk::USDeviceReaderXML::USDeviceConfigData &config);
protected:
USDeviceWriterXML(const USDeviceWriterXML& other);
mitk::USDeviceWriterXML* Clone() const override;
/**
* \brief Creates the xml ULTRASOUNDDEVICE-Tag entry of the ultrasound video device configuration file.
* \param document A reference to the xml document.
* \param ultrasoundDeviceTag The ULTRASOUNDDEVICETAG which should be created.
* \param config The struct containing all information of the ultrasound device.
*/
- void CreateXmlInformationOfUltrasoundDeviceTag( TiXmlDocument &document,
- TiXmlElement *ultrasoundDeviceTag,
+ void CreateXmlInformationOfUltrasoundDeviceTag( tinyxml2::XMLDocument &document,
+ tinyxml2::XMLElement *ultrasoundDeviceTag,
mitk::USDeviceReaderXML::USDeviceConfigData &config);
/**
* \brief Creates the xml GENERALSETTINGS-Tag entry of the ultrasound video device configuration file.
* \param parentTag The xml parent tag of the GENERALSETTINGS-Tag. This is the ULTRASOUNDDEVICE-Tag.
* \param generalSettingsTag The GENERALSETTINGS-Tag which should be created.
* \param config The struct containing all information of the ultrasound device.
*/
- void CreateXmlInformationOfGeneralSettingsTag( TiXmlElement *parentTag,
- TiXmlElement *generalSettingsTag,
+ void CreateXmlInformationOfGeneralSettingsTag( tinyxml2::XMLElement *parentTag,
+ tinyxml2::XMLElement *generalSettingsTag,
mitk::USDeviceReaderXML::USDeviceConfigData &config);
/**
* \brief Creates the xml PROBES-Tag entry of the ultrasound video device configuration file. All information
* of all configured probes is extracted and then stored in the xml file.
* \param parentTag The xml parent tag of the GENERALSETTINGS-Tag. This is the ULTRASOUNDDEVICE-Tag.
* \param config The struct containing all information of the ultrasound device.
*/
- void CreateXmlInformationOfProbesTag( TiXmlElement *parentTag,
+ void CreateXmlInformationOfProbesTag( tinyxml2::XMLElement*parentTag,
mitk::USDeviceReaderXML::USDeviceConfigData &config);
private:
/**
* \brief The filename of the ultrasound device configuration file which should be created.
*/
std::string m_Filename;
};
}
#endif // mitkUSDeviceWriterXML_H_Header_INCLUDED_
diff --git a/Modules/US/USNavigation/Testing/mitkCombinedModalityTest.cpp b/Modules/US/USNavigation/Testing/mitkCombinedModalityTest.cpp
index e12ebc1b21..87465cbbd8 100644
--- a/Modules/US/USNavigation/Testing/mitkCombinedModalityTest.cpp
+++ b/Modules/US/USNavigation/Testing/mitkCombinedModalityTest.cpp
@@ -1,176 +1,171 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkUSCombinedModality.h"
#include <mitkVirtualTrackingDevice.h>
#include <mitkUSVideoDevice.h>
#include <mitkTestingMacros.h>
#include <mitkTrackingDeviceSource.h>
class mitkCombinedModalityTestClass
{
public:
- /*
- * \brief Returns a reference string for serialized calibrations.
- */
-
- static std::string GetSerializedReference()
- {
-
- return std::string("<calibrations>\n<") + mitk::USCombinedModality::DefaultProbeIdentifier + mitk::USCombinedModality::ProbeAndDepthSeperator
- + "0 M00=\"1.1234\" M01=\"1.2234\" M02=\"1.3234\" M10=\"1.4234\" M11=\"1.5234\" M12=\"1.6234\" M20=\"1.7234\" M21=\"1.8234\" M22=\"1.9234\" T0=\"2.1234\" T1=\"2.2234\" T2=\"2.3234\" />\n</calibrations>\n";
- }
-
static bool CompareDoubles (double A, double B)
{
- float diff = A - B;
- return (diff < 0.0001) && (-diff < 0.0001);
+ return std::abs(A - B) < 0.0001;
}
/*
* \brief Creates a dummy combined modality.
*/
static mitk::USCombinedModality::Pointer CreateModality()
{
mitk::USVideoDevice::Pointer usDevice = mitk::USVideoDevice::New("IllegalPath", "Manufacturer", "Model");
mitk::VirtualTrackingDevice::Pointer tracker = mitk::VirtualTrackingDevice::New();
tracker->AddTool("tool1");
tracker->AddTool("tool2");
mitk::TrackingDeviceSource::Pointer source = mitk::TrackingDeviceSource::New();
source->SetTrackingDevice(tracker);
source->Connect();
source->StartTracking();
return mitk::USCombinedModality::New(usDevice.GetPointer(), source.GetPointer(), false);
}
static void TestInstantiation()
{
mitk::USCombinedModality::Pointer combinedModality = CreateModality();
MITK_TEST_CONDITION_REQUIRED(combinedModality.IsNotNull(), "CombinedModality should not be null after instantiation");
}
static void TestSerialization()
{
- mitk::USCombinedModality::Pointer modality = CreateModality();
+ auto modality = CreateModality();
mitk::AffineTransform3D::MatrixType matrix;
matrix[0][0] = 1.1234;
matrix[0][1] = 1.2234;
matrix[0][2] = 1.3234;
matrix[1][0] = 1.4234;
matrix[1][1] = 1.5234;
matrix[1][2] = 1.6234;
matrix[2][0] = 1.7234;
matrix[2][1] = 1.8234;
matrix[2][2] = 1.9234;
mitk::AffineTransform3D::OffsetType offset;
offset[0] = 2.1234;
offset[1] = 2.2234;
offset[2] = 2.3234;
mitk::AffineTransform3D::Pointer transform = mitk::AffineTransform3D::New();
transform->SetMatrix(matrix);
transform->SetOffset(offset);
modality->SetCalibration(transform);
- MITK_TEST_CONDITION_REQUIRED(modality->SerializeCalibration() == GetSerializedReference(), "Testing correct Serialization...");
- }
-
- static void TestDeserialization()
- {
- mitk::USCombinedModality::Pointer modality = CreateModality();
- modality->DeserializeCalibration(GetSerializedReference());
- mitk::AffineTransform3D::Pointer transform = modality->GetCalibration();
-
- mitk::AffineTransform3D::MatrixType matrix = transform->GetMatrix();
- mitk::AffineTransform3D::OffsetType offset = transform->GetOffset();;
+ const auto xmlString = modality->SerializeCalibration();
+ auto otherModality = CreateModality();
+ otherModality->DeserializeCalibration(xmlString);
+ auto calibration = otherModality->GetCalibration();
+ const auto& otherMatrix = calibration->GetMatrix();
+ const auto& otherOffset = calibration->GetOffset();
bool identical = true;
- if (! CompareDoubles(matrix[0][0], 1.1234)) identical = false;
- if (! CompareDoubles(matrix[0][1], 1.2234)) identical = false;
- if (! CompareDoubles(matrix[0][2], 1.3234)) identical = false;
- if (! CompareDoubles(matrix[1][0], 1.4234)) identical = false;
- if (! CompareDoubles(matrix[1][1], 1.5234)) identical = false;
- if (! CompareDoubles(matrix[1][2], 1.6234)) identical = false;
- if (! CompareDoubles(matrix[2][0], 1.7234)) identical = false;
- if (! CompareDoubles(matrix[2][1], 1.8234)) identical = false;
- if (! CompareDoubles(matrix[2][2], 1.9234)) identical = false;
-
- if (! CompareDoubles(offset[0], 2.1234)) identical = false;
- if (! CompareDoubles(offset[1], 2.2234)) identical = false;
- if (! CompareDoubles(offset[2], 2.3234)) identical = false;
+ for (size_t i = 0; i < 3; ++i)
+ {
+ for (size_t j = 0; j < 3; ++j)
+ {
+ if (!CompareDoubles(matrix[i][j], otherMatrix[i][j]))
+ {
+ identical = false;
+ break;
+ }
+ }
+
+ if (!identical)
+ break;
+ }
+
+ if (identical)
+ {
+ for (size_t i = 0; i < 3; ++i)
+ {
+ if (!CompareDoubles(offset[i], otherOffset[i]))
+ {
+ identical = false;
+ break;
+ }
+ }
+ }
MITK_TEST_CONDITION_REQUIRED(identical, "Testing if deserialized calibration is identical to serialized one...");
// test if invalid strings cause exceptions
MITK_TEST_FOR_EXCEPTION(mitk::Exception, modality->DeserializeCalibration("invalid-string"));
MITK_TEST_FOR_EXCEPTION(mitk::Exception, modality->DeserializeCalibration("<xml><test></xml>", false));
}
static void TestFilterPipeline()
{
/*mitk::USCombinedModality::Pointer combinedModality = mitkCombinedModalityTestClass::CreateModality();
MITK_INFO << combinedModality->GetNavigationDataSource()->GetNameOfClass();
MITK_TEST_CONDITION(strcmp(combinedModality->GetNavigationDataSource()->GetNameOfClass(), "TrackingDeviceSource") == 0,
"")*/
mitk::USVideoDevice::Pointer usDevice = mitk::USVideoDevice::New("IllegalPath", "Manufacturer", "Model");
mitk::VirtualTrackingDevice::Pointer tracker = mitk::VirtualTrackingDevice::New();
tracker->AddTool("tool1");
tracker->AddTool("tool2");
mitk::TrackingDeviceSource::Pointer source = mitk::TrackingDeviceSource::New();
source->SetTrackingDevice(tracker);
source->Connect();
source->StartTracking();
mitk::USCombinedModality::Pointer modality = mitk::USCombinedModality::New(usDevice.GetPointer(), source.GetPointer(), false);
MITK_TEST_CONDITION(source->GetOutput(0) == modality->GetNavigationDataSource()->GetOutput(0),
"Navigation data output of the Combined Modality should be the same as the source output as no filters are active.")
modality->SetNumberOfSmoothingValues(2);
mitk::NavigationDataSource::Pointer smoothingFilter = modality->GetNavigationDataSource();
MITK_TEST_CONDITION(source->GetOutput(0) != smoothingFilter->GetOutput(0),
"Navigation data output of the Combined Modality should be different to the source output as smoothing filter is active.")
modality->SetNumberOfSmoothingValues(0);
MITK_TEST_CONDITION(source->GetOutput(0) == modality->GetNavigationDataSource()->GetOutput(0),
"Navigation data output of the Combined Modality should be the same as the source output again.")
modality->SetDelayCount(5);
MITK_TEST_CONDITION(source->GetOutput(0) != smoothingFilter->GetOutput(0),
"Navigation data output of the Combined Modality should be different to the source output as delay filter is active.")
modality->SetDelayCount(0);
MITK_TEST_CONDITION(source->GetOutput(0) == modality->GetNavigationDataSource()->GetOutput(0),
"Navigation data output of the Combined Modality should be the same as the source output again.")
}
};
/**
* This function is testing methods of the class USDevice.
*/
int mitkCombinedModalityTest(int /* argc */, char* /*argv*/[])
{
MITK_TEST_BEGIN("mitkCombinedModalityTest");
mitkCombinedModalityTestClass::TestInstantiation();
mitkCombinedModalityTestClass::TestSerialization();
- mitkCombinedModalityTestClass::TestDeserialization();
mitkCombinedModalityTestClass::TestFilterPipeline();
MITK_TEST_END();
}
diff --git a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp
index 7c64a04970..0f9e821238 100644
--- a/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp
+++ b/Modules/US/USNavigation/mitkAbstractUltrasoundTrackerDevice.cpp
@@ -1,491 +1,495 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkAbstractUltrasoundTrackerDevice.h"
#include "mitkImageReadAccessor.h"
#include "mitkNavigationDataDelayFilter.h"
#include "mitkNavigationDataDisplacementFilter.h"
#include "mitkNavigationDataSmoothingFilter.h"
#include "mitkTrackingDeviceSource.h"
// US Control Interfaces
#include "mitkUSControlInterfaceBMode.h"
#include "mitkUSControlInterfaceDoppler.h"
#include "mitkUSControlInterfaceProbes.h"
// Microservices
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usServiceProperties.h>
#include <algorithm>
// TempIncludes
-#include <tinyxml.h>
+#include <tinyxml2.h>
const std::string mitk::AbstractUltrasoundTrackerDevice::DeviceClassIdentifier =
"org.mitk.modules.us.AbstractUltrasoundTrackerDevice";
const char *mitk::AbstractUltrasoundTrackerDevice::DefaultProbeIdentifier = "default";
const char *mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator = "_";
const std::string mitk::AbstractUltrasoundTrackerDevice::US_INTERFACE_NAME =
"org.mitk.services.AbstractUltrasoundTrackerDevice";
const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_DEVICENAME = US_INTERFACE_NAME + ".devicename";
const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_CLASS = US_INTERFACE_NAME + ".class";
const std::string mitk::AbstractUltrasoundTrackerDevice::US_PROPKEY_ID = US_INTERFACE_NAME + ".id";
//____
mitk::AbstractUltrasoundTrackerDevice::AbstractUltrasoundTrackerDevice(USDevice::Pointer usDevice,
NavigationDataSource::Pointer trackingDevice,
bool trackedUltrasoundActive)
: m_UltrasoundDevice(usDevice),
m_TrackingDeviceDataSource(trackingDevice),
m_SmoothingFilter(mitk::NavigationDataSmoothingFilter::New()),
m_DelayFilter(mitk::NavigationDataDelayFilter::New(0)),
m_DisplacementFilter(mitk::NavigationDataDisplacementFilter::New()),
m_LastFilterOfIGTPipeline(nullptr),
m_NumberOfSmoothingValues(0),
m_DelayCount(0),
m_IsTrackedUltrasoundActive(trackedUltrasoundActive)
{
m_DisplacementFilter->SetTransform6DOF(true);
this->RebuildFilterPipeline();
// create a new output (for the image data)
//___ mitk::Image::Pointer newOutput = mitk::Image::New();
//___ this->SetNthOutput(0, newOutput);
// Combined Modality should not spawn an own acquire thread, because
// image acquiring is done by the included us device
//___ m_UltrasoundDevice->SetSpawnAcquireThread(false);
}
mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetUSPlaneTransform()
{
return mitk::AffineTransform3D::New();
}
void mitk::AbstractUltrasoundTrackerDevice::SetIsFreezed(bool freeze)
{
if (m_UltrasoundDevice.IsNull() || m_TrackingDeviceDataSource.IsNull())
{
MITK_WARN << "Combined modality not correctly initialized, aborting!";
return;
}
if (!m_UltrasoundDevice->GetIsActive())
{
MITK_WARN("mitkUSDevice")
<< "Cannot freeze or unfreeze if device is not active.";
return;
}
this->OnFreeze(freeze);
if (freeze)
{
m_IsFreezed = true;
}
else
{
m_IsFreezed = false;
}
}
bool mitk::AbstractUltrasoundTrackerDevice::GetIsFreezed()
{
return m_IsFreezed;
}
mitk::AbstractUltrasoundTrackerDevice::~AbstractUltrasoundTrackerDevice()
{
if (m_ServiceRegistration != nullptr)
{
m_ServiceRegistration.Unregister();
}
m_ServiceRegistration = 0;
}
mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration()
{
return this->GetCalibration(this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe());
}
mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration(std::string depth)
{
return this->GetCalibration(depth, this->GetIdentifierForCurrentProbe());
}
mitk::AffineTransform3D::Pointer mitk::AbstractUltrasoundTrackerDevice::GetCalibration(std::string depth,
std::string probe)
{
// make sure that there is no '/' which would cause problems for TinyXML
std::replace(probe.begin(), probe.end(), '/', '-');
// create identifier for calibration from probe and depth
std::string calibrationKey = probe + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + depth;
// find calibration for combination of probe identifier and depth
std::map<std::string, mitk::AffineTransform3D::Pointer>::iterator calibrationIterator =
m_Calibrations.find(calibrationKey);
if (calibrationIterator == m_Calibrations.end())
{
return nullptr;
}
return calibrationIterator->second;
}
void mitk::AbstractUltrasoundTrackerDevice::SetCalibration(mitk::AffineTransform3D::Pointer calibration)
{
if (calibration.IsNull())
{
MITK_WARN << "Null pointer passed to SetCalibration of mitk::USDevice. Ignoring call.";
return;
}
std::string calibrationKey = this->GetIdentifierForCurrentCalibration();
if (calibrationKey.empty())
{
MITK_WARN << "Could not get a key for the calibration -> Calibration cannot be set.";
return;
}
m_Calibrations[calibrationKey] = calibration;
}
bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration()
{
return this->RemoveCalibration(this->GetCurrentDepthValue(), this->GetIdentifierForCurrentProbe());
}
bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration(std::string depth)
{
return this->RemoveCalibration(depth, this->GetIdentifierForCurrentProbe());
}
bool mitk::AbstractUltrasoundTrackerDevice::RemoveCalibration(std::string depth, std::string probe)
{
// make sure that there is no '/' which would cause problems for TinyXML
std::replace(probe.begin(), probe.end(), '/', '-');
// create identifier for calibration from probe and depth
std::string calibrationKey = probe + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator + depth;
return m_Calibrations.erase(calibrationKey) > 0;
}
std::string mitk::AbstractUltrasoundTrackerDevice::GetDeviceClass()
{
return DeviceClassIdentifier;
}
mitk::USImageSource::Pointer mitk::AbstractUltrasoundTrackerDevice::GetUSImageSource()
{
if (m_UltrasoundDevice.IsNull())
{
MITK_ERROR("AbstractUltrasoundTrackerDevice")("USDevice") << "UltrasoundDevice must not be null.";
mitkThrow() << "UltrasoundDevice must not be null.";
}
return m_UltrasoundDevice->GetUSImageSource();
}
mitk::NavigationDataSource::Pointer mitk::AbstractUltrasoundTrackerDevice::GetNavigationDataSource()
{
if (m_LastFilterOfIGTPipeline.IsNull())
{
this->RebuildFilterPipeline();
}
m_LastFilterOfIGTPipeline->SetToolMetaDataCollection(this->m_TrackingDeviceDataSource->GetToolMetaDataCollection());
return m_LastFilterOfIGTPipeline;
}
bool mitk::AbstractUltrasoundTrackerDevice::GetIsCalibratedForCurrentStatus()
{
return m_Calibrations.find(this->GetIdentifierForCurrentCalibration()) != m_Calibrations.end();
}
bool mitk::AbstractUltrasoundTrackerDevice::GetContainsAtLeastOneCalibration()
{
return !m_Calibrations.empty();
}
std::string mitk::AbstractUltrasoundTrackerDevice::SerializeCalibration()
{
- std::stringstream result;
- result << "<calibrations>" << std::endl;
+ tinyxml2::XMLDocument doc;
+ auto* calibrations = doc.NewElement("calibrations");
+ doc.InsertEndChild(calibrations);
+
// For each calibration in the set
for (std::map<std::string, mitk::AffineTransform3D::Pointer>::iterator it = m_Calibrations.begin();
it != m_Calibrations.end();
it++)
{
mitk::AffineTransform3D::MatrixType matrix = it->second->GetMatrix();
mitk::AffineTransform3D::TranslationType translation = it->second->GetTranslation();
- TiXmlElement elem(it->first);
+ auto *elem = doc.NewElement(it->first.c_str());
// Serialize Matrix
- elem.SetDoubleAttribute("M00", matrix[0][0]);
- elem.SetDoubleAttribute("M01", matrix[0][1]);
- elem.SetDoubleAttribute("M02", matrix[0][2]);
- elem.SetDoubleAttribute("M10", matrix[1][0]);
- elem.SetDoubleAttribute("M11", matrix[1][1]);
- elem.SetDoubleAttribute("M12", matrix[1][2]);
- elem.SetDoubleAttribute("M20", matrix[2][0]);
- elem.SetDoubleAttribute("M21", matrix[2][1]);
- elem.SetDoubleAttribute("M22", matrix[2][2]);
+ elem->SetAttribute("M00", matrix[0][0]);
+ elem->SetAttribute("M01", matrix[0][1]);
+ elem->SetAttribute("M02", matrix[0][2]);
+ elem->SetAttribute("M10", matrix[1][0]);
+ elem->SetAttribute("M11", matrix[1][1]);
+ elem->SetAttribute("M12", matrix[1][2]);
+ elem->SetAttribute("M20", matrix[2][0]);
+ elem->SetAttribute("M21", matrix[2][1]);
+ elem->SetAttribute("M22", matrix[2][2]);
// Serialize Offset
- elem.SetDoubleAttribute("T0", translation[0]);
- elem.SetDoubleAttribute("T1", translation[1]);
- elem.SetDoubleAttribute("T2", translation[2]);
+ elem->SetAttribute("T0", translation[0]);
+ elem->SetAttribute("T1", translation[1]);
+ elem->SetAttribute("T2", translation[2]);
- result << elem << std::endl;
+ calibrations->InsertEndChild(elem);
}
- result << "</calibrations>" << std::endl;
- return result.str();
+ tinyxml2::XMLPrinter printer;
+ doc.Print(&printer);
+
+ return printer.CStr();
}
void mitk::AbstractUltrasoundTrackerDevice::DeserializeCalibration(const std::string &xmlString,
bool clearPreviousCalibrations)
{
// Sanitize Input
if (xmlString == "")
{
MITK_ERROR << "Empty string passed to Deserialize() method of CombinedModality. Aborting...";
mitkThrow() << "Empty string passed to Deserialize() method of CombinedModality. Aborting...";
return;
}
// Clear previous calibrations if necessary
if (clearPreviousCalibrations)
m_Calibrations.clear();
// Parse Input
- TiXmlDocument doc;
- if (!doc.Parse(xmlString.c_str()))
+ tinyxml2::XMLDocument doc;
+ if (tinyxml2::XML_SUCCESS != doc.Parse(xmlString.c_str()))
{
- MITK_ERROR << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorDesc();
- mitkThrow() << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorDesc();
+ MITK_ERROR << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorStr();
+ mitkThrow() << "Unable to deserialize calibrations in CombinedModality. Error was: " << doc.ErrorStr();
return;
}
- TiXmlElement *root = doc.FirstChildElement();
+ auto *root = doc.FirstChildElement();
if (root == nullptr)
{
MITK_ERROR << "Unable to deserialize calibrations in CombinedModality. String contained no root element.";
mitkThrow() << "Unable to deserialize calibrations in CombinedModality. String contained no root element.";
return;
}
// Read Calibrations
- for (TiXmlElement *elem = root->FirstChildElement(); elem != nullptr; elem = elem->NextSiblingElement())
+ for (auto *elem = root->FirstChildElement(); elem != nullptr; elem = elem->NextSiblingElement())
{
mitk::AffineTransform3D::MatrixType matrix;
mitk::AffineTransform3D::OffsetType translation;
std::string calibName = elem->Value();
// Deserialize Matrix
elem->QueryDoubleAttribute("M00", &matrix[0][0]);
elem->QueryDoubleAttribute("M01", &matrix[0][1]);
elem->QueryDoubleAttribute("M02", &matrix[0][2]);
elem->QueryDoubleAttribute("M10", &matrix[1][0]);
elem->QueryDoubleAttribute("M11", &matrix[1][1]);
elem->QueryDoubleAttribute("M12", &matrix[1][2]);
elem->QueryDoubleAttribute("M20", &matrix[2][0]);
elem->QueryDoubleAttribute("M21", &matrix[2][1]);
elem->QueryDoubleAttribute("M22", &matrix[2][2]);
// Deserialize Offset
elem->QueryDoubleAttribute("T0", &translation[0]);
elem->QueryDoubleAttribute("T1", &translation[1]);
elem->QueryDoubleAttribute("T2", &translation[2]);
mitk::AffineTransform3D::Pointer calibration = mitk::AffineTransform3D::New();
calibration->SetMatrix(matrix);
calibration->SetTranslation(translation);
m_Calibrations[calibName] = calibration;
}
}
void mitk::AbstractUltrasoundTrackerDevice::SetNumberOfSmoothingValues(unsigned int numberOfSmoothingValues)
{
unsigned int oldNumber = m_NumberOfSmoothingValues;
m_NumberOfSmoothingValues = numberOfSmoothingValues;
// if filter should be activated or deactivated
if ((oldNumber == 0 && numberOfSmoothingValues != 0) || (oldNumber != 0 && numberOfSmoothingValues == 0))
{
this->RebuildFilterPipeline();
}
m_SmoothingFilter->SetNumerOfValues(numberOfSmoothingValues);
}
void mitk::AbstractUltrasoundTrackerDevice::SetDelayCount(unsigned int delayCount)
{
unsigned int oldCount = m_DelayCount;
m_DelayCount = delayCount;
// if filter should be activated or deactivated
if ((oldCount == 0 && delayCount != 0) || (oldCount != 0 && delayCount == 0))
{
this->RebuildFilterPipeline();
}
m_DelayFilter->SetDelay(delayCount);
}
void mitk::AbstractUltrasoundTrackerDevice::GenerateData() {}
std::string mitk::AbstractUltrasoundTrackerDevice::GetIdentifierForCurrentCalibration()
{
return this->GetIdentifierForCurrentProbe() + mitk::AbstractUltrasoundTrackerDevice::ProbeAndDepthSeperator +
this->GetCurrentDepthValue();
}
std::string mitk::AbstractUltrasoundTrackerDevice::GetIdentifierForCurrentProbe()
{
us::ServiceProperties usdeviceProperties = m_UltrasoundDevice->GetServiceProperties();
us::ServiceProperties::const_iterator probeIt =
usdeviceProperties.find(mitk::USDevice::GetPropertyKeys().US_PROPKEY_PROBES_SELECTED);
// get probe identifier from control interface for probes
std::string probeName = mitk::AbstractUltrasoundTrackerDevice::DefaultProbeIdentifier;
if (probeIt != usdeviceProperties.end())
{
probeName = (probeIt->second).ToString();
}
// make sure that there is no '/' which would cause problems for TinyXML
std::replace(probeName.begin(), probeName.end(), '/', '-');
return probeName;
}
std::string mitk::AbstractUltrasoundTrackerDevice::GetCurrentDepthValue()
{
us::ServiceProperties usdeviceProperties = m_UltrasoundDevice->GetServiceProperties();
// get string for depth value from the micro service properties
std::string depth;
us::ServiceProperties::iterator depthIterator =
usdeviceProperties.find(mitk::USDevice::GetPropertyKeys().US_PROPKEY_BMODE_DEPTH);
if (depthIterator != usdeviceProperties.end())
{
depth = depthIterator->second.ToString();
}
else
{
depth = "0";
}
return depth;
}
void mitk::AbstractUltrasoundTrackerDevice::RebuildFilterPipeline()
{
m_LastFilterOfIGTPipeline = m_TrackingDeviceDataSource;
if (m_NumberOfSmoothingValues > 0)
{
m_SmoothingFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer());
m_LastFilterOfIGTPipeline = m_SmoothingFilter;
}
if (m_DelayCount > 0)
{
m_DelayFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer());
m_LastFilterOfIGTPipeline = m_DelayFilter;
}
if (m_IsTrackedUltrasoundActive)
{
m_DisplacementFilter->ConnectTo(m_LastFilterOfIGTPipeline.GetPointer());
m_LastFilterOfIGTPipeline = m_DisplacementFilter;
}
}
void mitk::AbstractUltrasoundTrackerDevice::UnregisterOnService()
{
if (m_UltrasoundDevice->GetDeviceState() == USDevice::State_Activated)
{
m_UltrasoundDevice->Deactivate();
}
if (m_UltrasoundDevice->GetDeviceState() == USDevice::State_Connected)
{
m_UltrasoundDevice->Disconnect();
}
if (m_ServiceRegistration != nullptr)
m_ServiceRegistration.Unregister();
m_ServiceRegistration = 0;
}
void mitk::AbstractUltrasoundTrackerDevice::RegisterAsMicroservice()
{
// Get Context
us::ModuleContext *context = us::GetModuleContext();
// Define ServiceProps
// us::ServiceProperties props;
mitk::UIDGenerator uidGen = mitk::UIDGenerator("org.mitk.services.AbstractUltrasoundTrackerDevice");
m_ServiceProperties[US_PROPKEY_ID] = uidGen.GetUID();
m_ServiceProperties[US_PROPKEY_DEVICENAME] = m_UltrasoundDevice->GetName();
m_ServiceProperties[US_PROPKEY_CLASS] = mitk::AbstractUltrasoundTrackerDevice::DeviceClassIdentifier;
m_ServiceRegistration = context->RegisterService(this, m_ServiceProperties);
}
mitk::USAbstractControlInterface::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceCustom()
{
if (m_UltrasoundDevice.IsNull())
{
MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null.";
mitkThrow() << "UltrasoundDevice must not be null.";
}
return m_UltrasoundDevice->GetControlInterfaceCustom();
}
mitk::USControlInterfaceBMode::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceBMode()
{
if (m_UltrasoundDevice.IsNull())
{
MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null.";
mitkThrow() << "UltrasoundDevice must not be null.";
}
return m_UltrasoundDevice->GetControlInterfaceBMode();
}
mitk::USControlInterfaceProbes::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceProbes()
{
if (m_UltrasoundDevice.IsNull())
{
MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null.";
mitkThrow() << "UltrasoundDevice must not be null.";
}
return m_UltrasoundDevice->GetControlInterfaceProbes();
}
mitk::USControlInterfaceDoppler::Pointer mitk::AbstractUltrasoundTrackerDevice::GetControlInterfaceDoppler()
{
if (m_UltrasoundDevice.IsNull())
{
MITK_ERROR("USCombinedModality")("USDevice") << "UltrasoundDevice must not be null.";
mitkThrow() << "UltrasoundDevice must not be null.";
}
return m_UltrasoundDevice->GetControlInterfaceDoppler();
}
diff --git a/Modules/US/files.cmake b/Modules/US/files.cmake
index 42c099ed21..aa771c24a3 100644
--- a/Modules/US/files.cmake
+++ b/Modules/US/files.cmake
@@ -1,36 +1,36 @@
SET(CPP_FILES
## Module Activator
mitkUSActivator.cpp
## Model Classes
USModel/mitkUSImage.cpp
USModel/mitkUSImageMetadata.cpp
USModel/mitkUSDevice.cpp
USModel/mitkUSIGTLDevice.cpp
USModel/mitkUSVideoDevice.cpp
USModel/mitkUSVideoDeviceCustomControls.cpp
USModel/mitkUSProbe.cpp
USModel/mitkUSDevicePersistence.cpp
+USModel/mitkUSDeviceReaderWriterConstants.cpp
USModel/mitkUSDeviceReaderXML.cpp
USModel/mitkUSDeviceWriterXML.cpp
## Filters and Sources
USFilters/mitkUSImageLoggingFilter.cpp
USFilters/mitkUSImageSource.cpp
USFilters/mitkUSImageVideoSource.cpp
USFilters/mitkIGTLMessageToUSImageFilter.cpp
## Control Interfaces
USControlInterfaces/mitkUSAbstractControlInterface.cpp
USControlInterfaces/mitkUSControlInterfaceBMode.cpp
USControlInterfaces/mitkUSControlInterfaceProbes.cpp
USControlInterfaces/mitkUSControlInterfaceDoppler.cpp
-USControlInterfaces/mitkUSDiPhASDeviceCustomControls.cpp
)
set(RESOURCE_FILES
Interactions/USPointMarkInteractions.xml
Interactions/USZoneInteractions.xml
Interactions/USZoneInteractionsHold.xml
)
diff --git a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp b/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp
deleted file mode 100644
index 5a4864f72e..0000000000
--- a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp
+++ /dev/null
@@ -1,415 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "QmitkUSControlsCustomDiPhASDeviceWidget.h"
-#include "ui_QmitkUSControlsCustomDiPhASDeviceWidget.h"
-#include <QMessageBox>
-
-
-#include <mitkException.h>
-
-QmitkUSControlsCustomDiPhASDeviceWidget::QmitkUSControlsCustomDiPhASDeviceWidget()
- : ui(new Ui::QmitkUSControlsCustomDiPhASDeviceWidget)
-{
-}
-
-QmitkUSControlsCustomDiPhASDeviceWidget::QmitkUSControlsCustomDiPhASDeviceWidget(QWidget *parent)
- : QmitkUSAbstractCustomWidget(parent), ui(new Ui::QmitkUSControlsCustomDiPhASDeviceWidget)
-{
-}
-
-QmitkUSControlsCustomDiPhASDeviceWidget::~QmitkUSControlsCustomDiPhASDeviceWidget()
-{
- delete ui;
-}
-
-std::string QmitkUSControlsCustomDiPhASDeviceWidget::GetDeviceClass() const
-{
- return "org.mitk.modules.us.USDiPhASDevice";
-}
-
-QmitkUSAbstractCustomWidget* QmitkUSControlsCustomDiPhASDeviceWidget::Clone(QWidget* parent) const
-{
- QmitkUSAbstractCustomWidget* clonedWidget = new QmitkUSControlsCustomDiPhASDeviceWidget(parent);
- clonedWidget->SetDevice(this->GetDevice());
- return clonedWidget;
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnDeviceSet()
-{
- m_ControlInterface = dynamic_cast<mitk::USDiPhASDeviceCustomControls*>
- (this->GetDevice()->GetControlInterfaceCustom().GetPointer());
-
- if ( m_ControlInterface.IsNotNull() )
- {
- m_ControlInterface->passGUIOut([this](QString str)->void{
- if (this->ui) {
- this->ui->CurrentState->setText(str);
- } });
- }
- else
- {
- MITK_WARN("QmitkUSAbstractCustomWidget")("QmitkUSControlsCustomDiPhASDeviceWidget")
- << "Did not get a custom device control interface.";
- }
-
- //now pass the default values
-
- m_OldReconstructionLines = 0;
-
- m_ControlInterface->SetSilentUpdate(true); // don't update the scanmode everytime
-
- OnTransmitPhaseLengthChanged();
- OnExcitationFrequencyChanged();
- OnTransmitEventsChanged();
- OnVoltageChanged();
- OnScanDepthChanged(); // HERE
- OnAveragingCountChanged();
- OnTGCMinChanged();
- OnTGCMaxChanged();
- OnDataTypeChanged();
- OnPitchChanged();
- OnReconstructedSamplesChanged();
- OnReconstructedLinesChanged();
- OnSpeedOfSoundChanged();
- OnBandpassEnabledChanged();
- OnLowCutChanged();
- OnHighCutChanged();
- OnUseBModeFilterChanged(); // HERE
- OnVerticalSpacingChanged();
- OnScatteringCoefficientChanged();
- OnCompensateScatteringChanged();
- OnChangedSavingSettings();
- OnCompensateEnergyChanged();
-
- m_ControlInterface->SetSilentUpdate(false); // on the last update pass the scanmode and geometry!
-
- OnModeChanged(); // HERE
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::Initialize()
-{
- ui->setupUi(this);
-
- connect(ui->CompensateEnergy, SIGNAL(stateChanged(int)), this, SLOT(OnCompensateEnergyChanged()));
- connect(ui->UseBModeFilter, SIGNAL(stateChanged(int)), this, SLOT(OnUseBModeFilterChanged()));
- connect(ui->StartStopRecord, SIGNAL(clicked()), this, SLOT(OnRecordChanged()));
- connect(ui->ScatteringCoefficient, SIGNAL(valueChanged(int)), this, SLOT(OnScatteringCoefficientChanged()));
- connect(ui->CompensateScattering, SIGNAL(stateChanged(int)), this, SLOT(OnCompensateScatteringChanged()));
- connect(ui->VerticalSpacing, SIGNAL(valueChanged(double)), this, SLOT(OnVerticalSpacingChanged()));
- connect(ui->SaveBeamformed, SIGNAL(stateChanged(int)), this, SLOT(OnChangedSavingSettings()));
- connect(ui->SaveRaw, SIGNAL(stateChanged(int)), this, SLOT(OnChangedSavingSettings()));
- //transmit
- connect(ui->TransmitPhaseLength, SIGNAL(valueChanged(double)), this, SLOT(OnTransmitPhaseLengthChanged()));
- connect(ui->ExcitationFrequency, SIGNAL(valueChanged(double)), this, SLOT(OnExcitationFrequencyChanged()));
- connect(ui->TransmitEvents, SIGNAL(valueChanged(int)), this, SLOT(OnTransmitEventsChanged()));
- connect(ui->Voltage, SIGNAL(valueChanged(int)), this, SLOT(OnVoltageChanged()));
- connect(ui->Mode, SIGNAL(currentTextChanged(QString)), this, SLOT(OnModeChanged()));
-
- //Receive
- connect(ui->ScanDepth, SIGNAL(valueChanged(double)), this, SLOT(OnScanDepthChanged()));
- connect(ui->AveragingCount, SIGNAL(valueChanged(int)), this, SLOT(OnAveragingCountChanged()));
- connect(ui->TimeGainCompensationMinSlider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCMinChanged()));
- connect(ui->TimeGainCompensationMaxSlider, SIGNAL(valueChanged(int)), this, SLOT(OnTGCMaxChanged()));
- connect(ui->DataType, SIGNAL(currentTextChanged(QString)), this, SLOT(OnDataTypeChanged()));
-
- //Beamforming
- connect(ui->PitchOfTransducer, SIGNAL(valueChanged(double)), this, SLOT(OnPitchChanged()));
- connect(ui->ReconstructedSamplesPerLine, SIGNAL(valueChanged(int)), this, SLOT(OnReconstructedSamplesChanged()));
- connect(ui->ReconstructedLines, SIGNAL(valueChanged(int)), this, SLOT(OnReconstructedLinesChanged()));
- connect(ui->SpeedOfSound, SIGNAL(valueChanged(int)), this, SLOT(OnSpeedOfSoundChanged()));
-
- //Bandpass
- connect(ui->BandpassEnabled, SIGNAL(currentTextChanged(QString)), this, SLOT(OnBandpassEnabledChanged()));
- connect(ui->LowCut, SIGNAL(valueChanged(double)), this, SLOT(OnLowCutChanged()));
- connect(ui->HighCut, SIGNAL(valueChanged(double)), this, SLOT(OnHighCutChanged()));
-}
-
-//slots
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnCompensateEnergyChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- bool CompensateEnergy = ui->CompensateEnergy->isChecked();
- m_ControlInterface->SetCompensateEnergy(CompensateEnergy);
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnUseBModeFilterChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- bool UseBModeFilter = ui->UseBModeFilter->isChecked();
- m_ControlInterface->SetUseBModeFilter(UseBModeFilter);
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnRecordChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- if (ui->StartStopRecord->text() == "Start Recording")
- {
- ui->StartStopRecord->setText("Stop Recording");
-
- ui->UseBModeFilter->setEnabled(false);
- ui->ScatteringCoefficient->setEnabled(false);
- ui->CompensateScattering->setEnabled(false);
- ui->VerticalSpacing->setEnabled(false);
- ui->SaveBeamformed->setEnabled(false);
- ui->SaveRaw->setEnabled(false);
- ui->TransmitPhaseLength->setEnabled(false);
- ui->ExcitationFrequency->setEnabled(false);
- ui->TransmitEvents->setEnabled(false);
- ui->Voltage->setEnabled(false);
- ui->Mode->setEnabled(false);
- ui->ScanDepth->setEnabled(false);
- ui->AveragingCount->setEnabled(false);
- ui->TimeGainCompensationMinSlider->setEnabled(false);
- ui->TimeGainCompensationMaxSlider->setEnabled(false);
- ui->DataType->setEnabled(false);
- ui->PitchOfTransducer->setEnabled(false);
- ui->ReconstructedSamplesPerLine->setEnabled(false);
- ui->ReconstructedLines->setEnabled(false);
- ui->SpeedOfSound->setEnabled(false);
- ui->BandpassEnabled->setEnabled(false);
- ui->LowCut->setEnabled(false);
- ui->HighCut->setEnabled(false);
- ui->CompensateEnergy->setEnabled(false);
-
- m_ControlInterface->SetRecord(true);
- }
- else
- {
- ui->StartStopRecord->setText("Start Recording");
-
- ui->UseBModeFilter->setEnabled(true);
- ui->CompensateScattering->setEnabled(true);
- if(ui->CompensateScattering->isChecked())
- ui->ScatteringCoefficient->setEnabled(true);
- ui->VerticalSpacing->setEnabled(true);
- ui->SaveBeamformed->setEnabled(true);
- ui->SaveRaw->setEnabled(true);
- ui->TransmitPhaseLength->setEnabled(true);
- ui->ExcitationFrequency->setEnabled(true);
- ui->TransmitEvents->setEnabled(true);
- ui->Voltage->setEnabled(true);
- ui->Mode->setEnabled(true);
- ui->ScanDepth->setEnabled(true);
- ui->AveragingCount->setEnabled(true);
- ui->TimeGainCompensationMinSlider->setEnabled(true);
- ui->TimeGainCompensationMaxSlider->setEnabled(true);
- ui->DataType->setEnabled(true);
- ui->PitchOfTransducer->setEnabled(true);
- ui->ReconstructedSamplesPerLine->setEnabled(true);
- ui->ReconstructedLines->setEnabled(true);
- ui->SpeedOfSound->setEnabled(true);
- ui->BandpassEnabled->setEnabled(true);
- ui->LowCut->setEnabled(true);
- ui->HighCut->setEnabled(true);
- ui->CompensateEnergy->setEnabled(true);
-
- m_ControlInterface->SetRecord(false);
- }
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnVerticalSpacingChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetVerticalSpacing(ui->VerticalSpacing->value());
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnScatteringCoefficientChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetScatteringCoefficient(ui->ScatteringCoefficient->value());
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnCompensateScatteringChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- if (ui->CompensateScattering->isChecked())
- ui->ScatteringCoefficient->setEnabled(true);
- else
- ui->ScatteringCoefficient->setEnabled(false);
-
- m_ControlInterface->SetCompensateScattering(ui->CompensateScattering->isChecked());
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnChangedSavingSettings()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- mitk::USDiPhASDeviceCustomControls::SavingSettings settings;
-
- settings.saveBeamformed = ui->SaveBeamformed->isChecked();
- settings.saveRaw = ui->SaveRaw->isChecked();
-
- m_ControlInterface->SetSavingSettings(settings);
-}
-
-//Transmit
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnTransmitPhaseLengthChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetTransmitPhaseLength(ui->TransmitPhaseLength->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnExcitationFrequencyChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetExcitationFrequency(ui->ExcitationFrequency->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnTransmitEventsChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- m_ControlInterface->SetTransmitEvents(ui->TransmitEvents->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnVoltageChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetVoltage(ui->Voltage->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnModeChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- QString Mode = ui->Mode->currentText();
- bool silent = m_ControlInterface->GetSilentUpdate();
- m_ControlInterface->SetSilentUpdate(true);
-
- if (Mode == "Ultrasound only") {
- m_ControlInterface->SetMode(false);
- ui->TransmitEvents->setValue(1);
- }
- else if (Mode == "Interleaved") {
- m_ControlInterface->SetMode(true);
- ui->TransmitEvents->setValue(1);
- }
- if (!silent) { m_ControlInterface->SetSilentUpdate(false); }
- OnTransmitEventsChanged();
-}
-
-//Receive
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnScanDepthChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetScanDepth(ui->ScanDepth->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnAveragingCountChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetAveragingCount(ui->AveragingCount->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnTGCMinChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- int tgcMin = ui->TimeGainCompensationMinSlider->value();
- int tgcMax = ui->TimeGainCompensationMaxSlider->value();
- if (tgcMin > tgcMax) {
- ui->TimeGainCompensationMinSlider->setValue(tgcMax);
- MITK_INFO << "User tried to set tgcMin>tgcMax.";
- }
- QString text("TGC min = " + QString::fromStdString(std::to_string(ui->TimeGainCompensationMinSlider->value())));
- ui->TimeGainCompensationMinLabel->setText(text);
- m_ControlInterface->SetTGCMin(ui->TimeGainCompensationMinSlider->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnTGCMaxChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- int tgcMin = ui->TimeGainCompensationMinSlider->value();
- int tgcMax = ui->TimeGainCompensationMaxSlider->value();
- if (tgcMin > tgcMax) {
- ui->TimeGainCompensationMaxSlider->setValue(tgcMin);
- MITK_INFO << "User tried to set tgcMin>tgcMax.";
- }
- QString text("TGC max = "+QString::fromStdString(std::to_string(ui->TimeGainCompensationMaxSlider->value())));
- ui->TimeGainCompensationMaxLabel->setText(text);
- m_ControlInterface->SetTGCMax(ui->TimeGainCompensationMaxSlider->value());
-}
-
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnDataTypeChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- QString DataType = ui->DataType->currentText();
- if (DataType == "Image Data") {
- m_ControlInterface->SetDataType(mitk::USDiPhASDeviceCustomControls::DataType::Image_uChar);
- }
- else if (DataType == "Beamformed Data") {
- m_ControlInterface->SetDataType(mitk::USDiPhASDeviceCustomControls::DataType::Beamformed_Short);
- }
-}
-
-//Beamforming
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnPitchChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetPitch(ui->PitchOfTransducer->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnReconstructedSamplesChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- m_ControlInterface->SetReconstructedSamples(ui->ReconstructedSamplesPerLine->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnReconstructedLinesChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
- if (m_OldReconstructionLines == 0)
- m_OldReconstructionLines = ui->ReconstructedLines->value();
-
- m_ControlInterface->SetReconstructedLines(ui->ReconstructedLines->value());
-
- ui->PitchOfTransducer->setValue(ui->PitchOfTransducer->value()*((double)m_OldReconstructionLines / (double)ui->ReconstructedLines->value()));
- m_OldReconstructionLines = ui->ReconstructedLines->value();
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnSpeedOfSoundChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- m_ControlInterface->SetSpeedOfSound(ui->SpeedOfSound->value());
-}
-
-//Bandpass
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnBandpassEnabledChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- if (ui->BandpassEnabled->currentText() == "On") {
- m_ControlInterface->SetBandpassEnabled(true);
- }
- else {
- m_ControlInterface->SetBandpassEnabled(false);
- }
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnLowCutChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- unsigned int Low = ui->LowCut->value();
- unsigned int High = ui->HighCut->value();
- if (Low > High) {
- ui->LowCut->setValue(High);
- MITK_INFO << "User tried to set LowCut>HighCut.";
- }
-
- m_ControlInterface->SetLowCut(ui->LowCut->value());
-}
-void QmitkUSControlsCustomDiPhASDeviceWidget::OnHighCutChanged()
-{
- if (m_ControlInterface.IsNull()) { return; }
-
- unsigned int Low = ui->LowCut->value();
- unsigned int High = ui->HighCut->value();
- if (Low > High) {
- ui->HighCut->setValue(Low);
- MITK_INFO << "User tried to set LowCut>HighCut.";
- }
-
- m_ControlInterface->SetHighCut(ui->HighCut->value());
-}
diff --git a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.h b/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.h
deleted file mode 100644
index e8e1043630..0000000000
--- a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.h
+++ /dev/null
@@ -1,113 +0,0 @@
-
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef QmitkUSControlsCustomDiPhASDeviceWidget_H
-#define QmitkUSControlsCustomDiPhASDeviceWidget_H
-
-#include "QmitkUSAbstractCustomWidget.h"
-#include "mitkUSDiPhASDeviceCustomControls.h"
-
-#include "mitkUSDevice.h"
-
-#include <QSpinBox>
-
-namespace Ui {
-class QmitkUSControlsCustomDiPhASDeviceWidget;
-}
-
-/** \brief Widget for custom controls of mitk::USDiPhASDevice.
- * This class handles the itk::USDiPhASDeviceCustomControls of video device
- * objects.
- */
-class QmitkUSControlsCustomDiPhASDeviceWidget : public QmitkUSAbstractCustomWidget
-{
- Q_OBJECT
-
-private slots:
- virtual void OnCompensateEnergyChanged();
- virtual void OnUseBModeFilterChanged();
- virtual void OnVerticalSpacingChanged();
- virtual void OnRecordChanged();
- virtual void OnScatteringCoefficientChanged();
- virtual void OnCompensateScatteringChanged();
- virtual void OnChangedSavingSettings();
-
- //Transmit
- virtual void OnTransmitPhaseLengthChanged();
- virtual void OnExcitationFrequencyChanged();
- virtual void OnTransmitEventsChanged();
- virtual void OnVoltageChanged();
- virtual void OnModeChanged();
-
- //Receive
- virtual void OnScanDepthChanged();
- virtual void OnAveragingCountChanged();
- virtual void OnTGCMinChanged();
- virtual void OnTGCMaxChanged();
- virtual void OnDataTypeChanged();
-
- //Beamforming
- virtual void OnPitchChanged();
- virtual void OnReconstructedSamplesChanged();
- virtual void OnReconstructedLinesChanged();
- virtual void OnSpeedOfSoundChanged();
-
- //Bandpass
- virtual void OnBandpassEnabledChanged();
- virtual void OnLowCutChanged();
- virtual void OnHighCutChanged();
-
-public:
- /**
- * Constructs widget object. All gui control elements will be disabled until
- * QmitkUSAbstractCustomWidget::SetDevice() was called.
- */
- QmitkUSControlsCustomDiPhASDeviceWidget();
- ~QmitkUSControlsCustomDiPhASDeviceWidget() override;
-
- /**
- * Getter for the device class of mitk:USDiPhASDevice.
- */
- std::string GetDeviceClass() const override;
-
- /**
- * Creates new QmitkUSAbstractCustomWidget with the same mitk::USDiPhASDevice
- * and the same mitk::USDiPhASDeviceCustomControls which were set on the
- * original object.
- *
- * This method is just for being calles by the factory. Use
- * QmitkUSAbstractCustomWidget::CloneForQt() instead, if you want a clone of
- * an object.
- */
- QmitkUSAbstractCustomWidget* Clone(QWidget* parent = nullptr) const override;
-
- /**
- * Gets control interface from the device which was currently set. Control
- * elements are according to current crop area of the device. If custom
- * control interface is null, the control elements stay disabled.
- */
- void OnDeviceSet() override;
-
- void Initialize() override;
-
-protected:
- void BlockSignalAndSetValue(QSpinBox* target, int value);
-
-private:
- QmitkUSControlsCustomDiPhASDeviceWidget(QWidget *parent);
- Ui::QmitkUSControlsCustomDiPhASDeviceWidget* ui;
- mitk::USDiPhASDeviceCustomControls::Pointer m_ControlInterface;
- int m_OldReconstructionLines;
-};
-
-#endif // QmitkUSControlsCustomDiPhASDeviceWidget_H
diff --git a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui b/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui
deleted file mode 100644
index f45bef1372..0000000000
--- a/Modules/USUI/Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui
+++ /dev/null
@@ -1,663 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkUSControlsCustomDiPhASDeviceWidget</class>
- <widget class="QWidget" name="QmitkUSControlsCustomDiPhASDeviceWidget">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>351</width>
- <height>903</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Form</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QLabel" name="CurrentState">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="frameShape">
- <enum>QFrame::WinPanel</enum>
- </property>
- <property name="frameShadow">
- <enum>QFrame::Raised</enum>
- </property>
- <property name="text">
- <string>Started</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignCenter</set>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="RecordingLabel">
- <property name="text">
- <string><html><head/><body><p><span style=" font-weight:600;">Record Images</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="General">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <widget class="QCheckBox" name="SaveBeamformed">
- <property name="text">
- <string>Save Beamformed</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="SaveRaw">
- <property name="text">
- <string>Save Raw</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QPushButton" name="StartStopRecord">
- <property name="minimumSize">
- <size>
- <width>100</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Start Recording</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="ReceiveLabel">
- <property name="text">
- <string><html><head/><body><p><span style=" font-weight:600;">Receive Parameters</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QGridLayout" name="Receive">
- <item row="2" column="0">
- <widget class="QSlider" name="TimeGainCompensationMinSlider">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="maximum">
- <number>42</number>
- </property>
- <property name="value">
- <number>10</number>
- </property>
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QSlider" name="TimeGainCompensationMaxSlider">
- <property name="maximum">
- <number>42</number>
- </property>
- <property name="value">
- <number>20</number>
- </property>
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="tickInterval">
- <number>0</number>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLabel" name="ScanDepthLabel">
- <property name="text">
- <string>Scan Depth [mm]</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QSpinBox" name="AveragingCount">
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>100</number>
- </property>
- <property name="value">
- <number>1</number>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLabel" name="AveragingCountLabel">
- <property name="text">
- <string>Averaging Count</string>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QComboBox" name="DataType">
- <property name="editable">
- <bool>false</bool>
- </property>
- <item>
- <property name="text">
- <string>Beamformed Data</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Image Data</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QDoubleSpinBox" name="ScanDepth">
- <property name="minimum">
- <double>3.000000000000000</double>
- </property>
- <property name="maximum">
- <double>200.000000000000000</double>
- </property>
- <property name="value">
- <double>50.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="4" column="1">
- <widget class="QLabel" name="DataTypeLabel">
- <property name="text">
- <string>DataType</string>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QLabel" name="TimeGainCompensationMinLabel">
- <property name="text">
- <string>TGC Min</string>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QLabel" name="TimeGainCompensationMaxLabel">
- <property name="text">
- <string>TGC Max</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <widget class="QCheckBox" name="CompensateScattering">
- <property name="text">
- <string>Compensate Fluence For Scattering</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QSpinBox" name="ScatteringCoefficient">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="minimum">
- <number>5</number>
- </property>
- <property name="maximum">
- <number>25</number>
- </property>
- <property name="value">
- <number>15</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="labelScattering">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Avg. μs' [1/cm]</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="BeamformingLabel">
- <property name="text">
- <string><html><head/><body><p><span style=" font-weight:600;">Beamforming Parameters</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QGridLayout" name="Beamforming">
- <item row="2" column="0">
- <widget class="QSpinBox" name="ReconstructedSamplesPerLine">
- <property name="minimum">
- <number>256</number>
- </property>
- <property name="maximum">
- <number>4096</number>
- </property>
- <property name="singleStep">
- <number>256</number>
- </property>
- <property name="value">
- <number>2048</number>
- </property>
- </widget>
- </item>
- <item row="6" column="0">
- <widget class="QDoubleSpinBox" name="PitchOfTransducer">
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.050000000000000</double>
- </property>
- <property name="value">
- <double>0.300000000000000</double>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QSpinBox" name="ReconstructedLines">
- <property name="contextMenuPolicy">
- <enum>Qt::PreventContextMenu</enum>
- </property>
- <property name="minimum">
- <number>128</number>
- </property>
- <property name="maximum">
- <number>1024</number>
- </property>
- <property name="singleStep">
- <number>128</number>
- </property>
- <property name="value">
- <number>128</number>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QLabel" name="ReconstructedSamplesPerLineLabel">
- <property name="text">
- <string>Samples per Line</string>
- </property>
- </widget>
- </item>
- <item row="4" column="1">
- <widget class="QLabel" name="ReconstructedLinesLabel">
- <property name="text">
- <string>Reconstructed Lines</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QSpinBox" name="SpeedOfSound">
- <property name="minimum">
- <number>1000</number>
- </property>
- <property name="maximum">
- <number>1000000</number>
- </property>
- <property name="singleStep">
- <number>5</number>
- </property>
- <property name="value">
- <number>1480</number>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLabel" name="SpeedOfSoundLabel">
- <property name="text">
- <string>Speed of Sound [m/s]</string>
- </property>
- </widget>
- </item>
- <item row="6" column="1">
- <widget class="QLabel" name="PitchOfTransducerLabel">
- <property name="text">
- <string>Pitch of Transducer [mm]</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="DisplayLabel">
- <property name="text">
- <string><html><head/><body><p><span style=" font-weight:600;">Display Parameters</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QVBoxLayout" name="DisplayParameters">
- <item>
- <widget class="QCheckBox" name="UseBModeFilter">
- <property name="text">
- <string>Envelope Filter</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="CompensateEnergy">
- <property name="text">
- <string>Compensate Energy Values</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="VerticalSpacingSubGroup">
- <item>
- <widget class="QDoubleSpinBox" name="VerticalSpacing">
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1.200000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.050000000000000</double>
- </property>
- <property name="value">
- <double>0.300000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="VerticalSpacingLabel">
- <property name="text">
- <string>Vertical Spacing</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="TransmitLabel">
- <property name="text">
- <string><html><head/><body><p><span style=" font-weight:600;">Transmit Parameters</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QGridLayout" name="Transmit">
- <item row="1" column="0">
- <widget class="QDoubleSpinBox" name="ExcitationFrequency">
- <property name="minimum">
- <double>1.000000000000000</double>
- </property>
- <property name="maximum">
- <double>15.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>7.500000000000000</double>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QSpinBox" name="TransmitEvents">
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>11</number>
- </property>
- <property name="singleStep">
- <number>2</number>
- </property>
- <property name="value">
- <number>1</number>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QLabel" name="TransmitEventsLabel">
- <property name="text">
- <string>Transmit Events</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QDoubleSpinBox" name="TransmitPhaseLength">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="readOnly">
- <bool>false</bool>
- </property>
- <property name="decimals">
- <number>1</number>
- </property>
- <property name="minimum">
- <double>1.000000000000000</double>
- </property>
- <property name="maximum">
- <double>10000.000000000000000</double>
- </property>
- <property name="value">
- <double>4.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLabel" name="TransmitPhaseLengthLabel">
- <property name="text">
- <string>Transmit Phase Length [us]</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLabel" name="ExcitationFrequencyLabel">
- <property name="text">
- <string>Excitation Frequency [MHz]</string>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QComboBox" name="Mode">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <item>
- <property name="text">
- <string>Interleaved</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Ultrasound only</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QSpinBox" name="Voltage">
- <property name="readOnly">
- <bool>false</bool>
- </property>
- <property name="minimum">
- <number>6</number>
- </property>
- <property name="maximum">
- <number>75</number>
- </property>
- <property name="value">
- <number>70</number>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QLabel" name="VoltageLabel">
- <property name="text">
- <string>Voltage [V]</string>
- </property>
- </widget>
- </item>
- <item row="4" column="1">
- <widget class="QLabel" name="ModeLabel">
- <property name="text">
- <string> Mode</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="BandpassLabel">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string><html><head/><body><p><span style=" font-weight:600;">Bandpass Parameters</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QGridLayout" name="BandpassParameters">
- <item row="2" column="1">
- <widget class="QLabel" name="HighCutLabel">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>High Cut [MHz]</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QLabel" name="LowCutLabel">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Low Cut [MHz]</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QLabel" name="BandpassEnabledLabel">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Bandpass Enabled</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QDoubleSpinBox" name="LowCut">
- <property name="enabled">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QDoubleSpinBox" name="HighCut">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="value">
- <double>5.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QComboBox" name="BandpassEnabled">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <item>
- <property name="text">
- <string>Off</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>On</string>
- </property>
- </item>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Modules/USUI/files.cmake b/Modules/USUI/files.cmake
index 828924aadc..70fadd9c46 100644
--- a/Modules/USUI/files.cmake
+++ b/Modules/USUI/files.cmake
@@ -1,37 +1,34 @@
set(CPP_FILES
mitkUSUIActivator.cpp
Qmitk/QmitkUSDeviceManagerWidget.cpp
Qmitk/QmitkUSNewVideoDeviceWidget.cpp
Qmitk/QmitkUSControlsBModeWidget.cpp
Qmitk/QmitkUSControlsDopplerWidget.cpp
Qmitk/QmitkUSControlsProbesWidget.cpp
Qmitk/QmitkUSControlsCustomVideoDeviceWidget.cpp
- Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.cpp
Qmitk/QmitkUSAbstractCustomWidget.cpp
Qmitk/QmitkComboBoxStepThrough.cpp
)
set(UI_FILES
Qmitk/QmitkUSDeviceManagerWidgetControls.ui
Qmitk/QmitkUSNewVideoDeviceWidgetControls.ui
Qmitk/QmitkUSControlsBModeWidget.ui
Qmitk/QmitkUSControlsDopplerWidget.ui
Qmitk/QmitkUSControlsProbesWidget.ui
Qmitk/QmitkUSControlsCustomVideoDeviceWidget.ui
- Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.ui
)
set(MOC_H_FILES
Qmitk/QmitkUSDeviceManagerWidget.h
Qmitk/QmitkUSNewVideoDeviceWidget.h
Qmitk/QmitkUSControlsBModeWidget.h
Qmitk/QmitkUSControlsDopplerWidget.h
Qmitk/QmitkUSControlsProbesWidget.h
Qmitk/QmitkUSControlsCustomVideoDeviceWidget.h
- Qmitk/QmitkUSControlsCustomDiPhASDeviceWidget.h
Qmitk/QmitkUSAbstractCustomWidget.h
Qmitk/QmitkComboBoxStepThrough.h
)
set(QRC_FILES
resources/USUI.qrc
)
diff --git a/Modules/USUI/mitkUSUIActivator.cpp b/Modules/USUI/mitkUSUIActivator.cpp
index 5e2a510c6c..08e217f7ae 100644
--- a/Modules/USUI/mitkUSUIActivator.cpp
+++ b/Modules/USUI/mitkUSUIActivator.cpp
@@ -1,42 +1,40 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkUSUIActivator.h"
#include "QmitkUSControlsCustomVideoDeviceWidget.h"
-#include "QmitkUSControlsCustomDiPhASDeviceWidget.h"
mitk::USUIActivator::USUIActivator()
{
}
mitk::USUIActivator::~USUIActivator()
{
}
void mitk::USUIActivator::Load(us::ModuleContext* context)
{
m_USCustomWidgets.push_back(new QmitkUSControlsCustomVideoDeviceWidget());
- m_USCustomWidgets.push_back(new QmitkUSControlsCustomDiPhASDeviceWidget());
for (auto &widget : m_USCustomWidgets)
{
context->RegisterService(widget, widget->GetServiceProperties());
}
}
void mitk::USUIActivator::Unload(us::ModuleContext* /*context*/)
{
for (auto &widget : m_USCustomWidgets)
{
delete widget;
}
}
diff --git a/Plugins/PluginList.cmake b/Plugins/PluginList.cmake
index 0d16bd73bc..ac518360a0 100644
--- a/Plugins/PluginList.cmake
+++ b/Plugins/PluginList.cmake
@@ -1,97 +1,90 @@
# Plug-ins must be ordered according to their dependencies
set(MITK_PLUGINS
org.blueberry.core.runtime:ON
org.blueberry.core.expressions:OFF
org.blueberry.core.commands:OFF
org.blueberry.core.jobs:OFF
org.blueberry.ui.qt:OFF
org.blueberry.ui.qt.help:ON
org.blueberry.ui.qt.log:ON
org.blueberry.ui.qt.objectinspector:OFF
org.mitk.core.services:ON
org.mitk.gui.common:ON
org.mitk.planarfigure:ON
org.mitk.core.ext:OFF
org.mitk.core.jobs:OFF
org.mitk.gui.qt.application:ON
org.mitk.gui.qt.ext:OFF
org.mitk.gui.qt.extapplication:OFF
org.mitk.gui.qt.mitkworkbench.intro:OFF
org.mitk.gui.qt.common:ON
org.mitk.gui.qt.stdmultiwidgeteditor:ON
org.mitk.gui.qt.mxnmultiwidgeteditor:OFF
org.mitk.gui.qt.common.legacy:OFF
org.mitk.gui.qt.cmdlinemodules:OFF
org.mitk.gui.qt.chartExample:OFF
org.mitk.gui.qt.datamanager:ON
org.mitk.gui.qt.datamanagerlight:OFF
org.mitk.gui.qt.datastorageviewertest:OFF
org.mitk.gui.qt.properties:ON
org.mitk.gui.qt.basicimageprocessing:OFF
org.mitk.gui.qt.dicombrowser:OFF
org.mitk.gui.qt.dicominspector:OFF
org.mitk.gui.qt.dosevisualization:OFF
org.mitk.gui.qt.geometrytools:OFF
org.mitk.gui.qt.igtexamples:OFF
org.mitk.gui.qt.igttracking:OFF
- org.mitk.gui.qt.lasercontrol:OFF
org.mitk.gui.qt.openigtlink:OFF
org.mitk.gui.qt.imagecropper:OFF
org.mitk.gui.qt.imagenavigator:ON
org.mitk.gui.qt.viewnavigator:OFF
org.mitk.gui.qt.materialeditor:OFF
org.mitk.gui.qt.measurementtoolbox:OFF
org.mitk.gui.qt.moviemaker:OFF
org.mitk.gui.qt.pointsetinteraction:OFF
org.mitk.gui.qt.pointsetinteractionmultispectrum:OFF
org.mitk.gui.qt.python:OFF
org.mitk.gui.qt.remeshing:OFF
org.mitk.gui.qt.segmentation:OFF
org.mitk.gui.qt.deformableclippingplane:OFF
org.mitk.gui.qt.aicpregistration:OFF
org.mitk.gui.qt.renderwindowmanager:OFF
org.mitk.gui.qt.semanticrelations:OFF
org.mitk.gui.qt.toftutorial:OFF
org.mitk.gui.qt.tofutil:OFF
org.mitk.gui.qt.tubegraph:OFF
org.mitk.gui.qt.ugvisualization:OFF
- org.mitk.gui.qt.photoacoustics.pausviewer:OFF
- org.mitk.gui.qt.photoacoustics.pausmotioncompensation:OFF
- org.mitk.gui.qt.photoacoustics.imageprocessing:OFF
- org.mitk.gui.qt.photoacoustics.simulation:OFF
- org.mitk.gui.qt.photoacoustics.spectralunmixing:OFF
org.mitk.gui.qt.ultrasound:OFF
org.mitk.gui.qt.volumevisualization:OFF
org.mitk.gui.qt.eventrecorder:OFF
org.mitk.gui.qt.xnat:OFF
org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation:OFF
- org.mitk.gui.qt.spectrocamrecorder:OFF
org.mitk.gui.qt.classificationsegmentation:OFF
org.mitk.gui.qt.overlaymanager:OFF
org.mitk.gui.qt.igt.app.hummelprotocolmeasurements:OFF
org.mitk.gui.qt.multilabelsegmentation:OFF
org.mitk.matchpoint.core.helper:OFF
org.mitk.gui.qt.matchpoint.algorithm.browser:OFF
org.mitk.gui.qt.matchpoint.algorithm.control:OFF
org.mitk.gui.qt.matchpoint.mapper:OFF
org.mitk.gui.qt.matchpoint.framereg:OFF
org.mitk.gui.qt.matchpoint.visualizer:OFF
org.mitk.gui.qt.matchpoint.evaluator:OFF
org.mitk.gui.qt.matchpoint.manipulator:OFF
org.mitk.gui.qt.preprocessing.resampling:OFF
org.mitk.gui.qt.radiomics:OFF
org.mitk.gui.qt.cest:OFF
org.mitk.gui.qt.fit.demo:OFF
org.mitk.gui.qt.fit.inspector:OFF
org.mitk.gui.qt.fit.genericfitting:OFF
org.mitk.gui.qt.pharmacokinetics.mri:OFF
org.mitk.gui.qt.pharmacokinetics.pet:OFF
org.mitk.gui.qt.pharmacokinetics.simulation:OFF
org.mitk.gui.qt.pharmacokinetics.curvedescriptor:OFF
org.mitk.gui.qt.pharmacokinetics.concentration.mri:OFF
org.mitk.gui.qt.flowapplication:OFF
org.mitk.gui.qt.flow.segmentation:OFF
)
diff --git a/Plugins/org.blueberry.core.runtime/CMakeLists.txt b/Plugins/org.blueberry.core.runtime/CMakeLists.txt
index 89f0868d11..fe06634e4c 100644
--- a/Plugins/org.blueberry.core.runtime/CMakeLists.txt
+++ b/Plugins/org.blueberry.core.runtime/CMakeLists.txt
@@ -1,21 +1,18 @@
project(org_blueberry_core_runtime)
mitk_create_plugin(
EXPORT_DIRECTIVE org_blueberry_core_runtime_EXPORT
EXPORTED_INCLUDE_SUFFIXES
src
src/application
src/dynamichelpers
src/registry
MODULE_DEPENDS PUBLIC mbilog
+ PACKAGE_DEPENDS
+ PUBLIC Poco|Foundation+Util+XML
+ PRIVATE Qt5|Gui+Xml
)
-target_link_libraries(${PLUGIN_TARGET} PUBLIC Poco::Foundation Poco::Util Poco::XML)
-
-if(MITK_USE_Qt5)
- target_link_libraries(${PLUGIN_TARGET} PRIVATE Qt5::Gui Qt5::Xml)
-endif()
-
target_compile_definitions(${PLUGIN_TARGET} PUBLIC "$<$<PLATFORM_ID:Windows>:POCO_NO_UNWINDOWS;WIN32_LEAN_AND_MEAN>")
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/src/berryConfig.h.in" "${CMAKE_CURRENT_BINARY_DIR}/berryConfig.h" @ONLY)
diff --git a/Plugins/org.blueberry.ui.qt.log/CMakeLists.txt b/Plugins/org.blueberry.ui.qt.log/CMakeLists.txt
index fa9f780cf1..f4dca98e14 100644
--- a/Plugins/org.blueberry.ui.qt.log/CMakeLists.txt
+++ b/Plugins/org.blueberry.ui.qt.log/CMakeLists.txt
@@ -1,8 +1,7 @@
project(org_blueberry_ui_qt_log)
mitk_create_plugin(
EXPORT_DIRECTIVE org_blueberry_ui_qt_log_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
+ PACKAGE_DEPENDS PUBLIC Qt5|Widgets
)
-
-target_link_libraries(${PLUGIN_TARGET} PUBLIC Qt5::Widgets)
diff --git a/Plugins/org.blueberry.ui.qt/CMakeLists.txt b/Plugins/org.blueberry.ui.qt/CMakeLists.txt
index a03b353eda..78f964fda1 100644
--- a/Plugins/org.blueberry.ui.qt/CMakeLists.txt
+++ b/Plugins/org.blueberry.ui.qt/CMakeLists.txt
@@ -1,24 +1,29 @@
project(org_blueberry_ui_qt)
set(PLUGIN_exported_include_suffixes
src
src/actions
src/application
src/commands
src/guitk
src/handlers
src/intro
src/model
src/presentations
src/services
src/testing
src/tweaklets
src/util
)
-mitk_create_plugin(EXPORT_DIRECTIVE BERRY_UI_QT
- EXPORTED_INCLUDE_SUFFIXES ${PLUGIN_exported_include_suffixes})
-
if(MITK_USE_Qt5)
- target_link_libraries(${PLUGIN_TARGET} PUBLIC Qt5::Widgets Qt5::PrintSupport Qt5::Svg)
+ set(PLUGIN_package_depends
+ PUBLIC Qt5|Widgets+PrintSupport+Svg
+ )
endif()
+
+mitk_create_plugin(
+ EXPORT_DIRECTIVE BERRY_UI_QT
+ EXPORTED_INCLUDE_SUFFIXES ${PLUGIN_exported_include_suffixes}
+ PACKAGE_DEPENDS ${PLUGIN_package_depends}
+)
diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.basicimageprocessing/CMakeLists.txt
index b40272d0df..a6f5a3fb89 100644
--- a/Plugins/org.mitk.gui.qt.basicimageprocessing/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.basicimageprocessing/CMakeLists.txt
@@ -1,9 +1,7 @@
-
project(org_mitk_gui_qt_basicimageprocessing)
mitk_create_plugin(
EXPORT_DIRECTIVE BASICIMAGEPROCESSING_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgetsExt MitkMapperExt MitkImageDenoising
- PACKAGE_DEPENDS ITK|ITKMathematicalMorphology
)
diff --git a/Plugins/org.mitk.gui.qt.fit.genericfitting/CMakeLists.txt b/Plugins/org.mitk.gui.qt.fit.genericfitting/CMakeLists.txt
index 5727a1f439..1b91d44be3 100644
--- a/Plugins/org.mitk.gui.qt.fit.genericfitting/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.fit.genericfitting/CMakeLists.txt
@@ -1,9 +1,7 @@
project(org_mitk_gui_qt_fit_genericfitting)
mitk_create_plugin(
EXPORT_DIRECTIVE MRPERFUSION_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgetsExt MitkModelFit MitkModelFitUI
- PACKAGE_DEPENDS
- PRIVATE Boost
)
diff --git a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h
index d1f9457d9e..003b7c3787 100644
--- a/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h
+++ b/Plugins/org.mitk.gui.qt.igt.app.hummelprotocolmeasurements/src/internal/mitkNavigationDataCSVSequentialPlayer.h
@@ -1,150 +1,148 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_
#define MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_
#include <mitkNavigationDataPlayerBase.h>
-#include "tinyxml.h"
-
namespace mitk
{
/**Documentation
* \brief This class is a NavigationDataPlayer which can play CSV formatted
* files in sequential order, which means it doesn't care about timestamps and just
* outputs the navigationdatas in their sequential order.
*
* It is thought to interpret custom csv files. To do so please adapt the column
* numbers of position and orientation in the internal method GetNavigationDataOutOfOneLine().
*
* So far only one (the first) tool is read in as required for the hummel protocol measurements.
*
* This class can also interpret MITK style csv files (set filetype to NavigationDataCSV), but
* you can also use the MITK navigation data player class inside the MITK-IGT module which
* is newer and better maintained.
*
* \ingroup IGT
*/
class NavigationDataCSVSequentialPlayer
: public NavigationDataPlayerBase
{
public:
mitkClassMacro(NavigationDataCSVSequentialPlayer, NavigationDataPlayerBase);
itkNewMacro(Self);
/**
* \brief sets the file name and path (if XMLString is set, this is neglected)
*/
void SetFileName(const std::string& _FileName);
/**
* @brief SetOptions sets the options for reading out the data out of the correct postions of the file. They need to be set before using the player
* @param rightHanded true if the used coordinate System is right handed, false if it is left handed
* @param seperatorSign symbol that is used to separate the values in the .csv file
* @param sampleCount every n-th sample in the file that should be used
* @param headerRow true if the .csv file has a header row otherwise false
* @param xPos number of the colum in the .csv file for the x-coordinates of the position
* @param yPos number of the colum in the .csv file for the y-coordinates of the position
* @param zPos number of the colum in the .csv file for the z-coordinates of the position
* @param useQuats true if Quaternions are used to construct the orientation, false if Euler Angles are used
* @param qx number of the column in the .csv file for the x component of the quaternion
* @param qy number of the column in the .csv file for the y component of the quaternion
* @param qz number of the column in the .csv file for the z component of the quaternion
* @param qr number of the column in the .csv file for the r component of the quaternion
* @param azimuth number of the colum in the .csv file for Azimuth (Euler Angles). Set < 0 if angle is not defined
* @param elevatino number of the colum in the .csv file for Elevation (Euler Angles) Set < 0 if angle is not defined
* @param roll number of the colum in the .csv file for Roll (Euler Angles) Set < 0 if angle is not defined
* @param eulerInRadiants true if the Euler Angles in the .csv file are in radiants, false if they are in degrees
* @param minNumberOfColumns
*/
void SetOptions(bool rightHanded, char seperatorSign, int sampleCount, bool headerRow, int xPos, int yPos, int zPos, bool useQuats,
int qx, int qy, int qz, int qr, int azimuth, int elevatino, int roll, bool eulerInRadiants, int minNumberOfColums);
/**
* \brief returns the file name and path
*/
itkGetStringMacro(FileName);
enum Filetype
{
NavigationDataCSV, //for csv files from the MITK navigation data player
ManualLoggingCSV //for custum csv files
};
/**
* \brief Sets the file type. ManualLoggingCSV is default and is thought for your
* custom csv files. You can also set it to NavigationDataCSV, then this
* player interprets MITK style csv files.
*/
itkSetMacro(Filetype, Filetype);
/**
* \return Returns true if the player reached the end of the file.
*/
bool IsAtEnd();
/**
* \brief Used for pipeline update just to tell the pipeline
* that we always have to update
*/
void UpdateOutputInformation() override;
int GetNumberOfSnapshots();
protected:
NavigationDataCSVSequentialPlayer();
~NavigationDataCSVSequentialPlayer() override;
///
/// do the work here
///
void GenerateData() override;
std::string m_FileName;
int m_CurrentPos;
Filetype m_Filetype;
//member for the navigation datas which were read (only one output is supported at the moment)
std::vector<mitk::NavigationData::Pointer> m_NavigationDatas;
std::vector<mitk::NavigationData::Pointer> GetNavigationDatasFromFile(std::string filename);
std::vector<std::string> GetFileContentLineByLine(std::string filename);
mitk::NavigationData::Pointer GetNavigationDataOutOfOneLine(std::string line);
void FillOutputEmpty(int number);
mitk::NavigationData::Pointer GetEmptyNavigationData();
bool m_RightHanded; //true if the used coordinate System is right handed, false if it is left handed
char m_SeparatorSign; //symbol that is used to separate the values in the .csv file
int m_SampleCount; //every n-th sample in the file that should be used
bool m_HeaderRow; //true if the .csv file has a header row otherwise false
int m_XPos; //number of the colum in the .csv file for the x-coordinates of the position
int m_YPos; //number of the colum in the .csv file for the y-coordinates of the position
int m_ZPos; //number of the colum in the .csv file for the z-coordinates of the position
bool m_UseQuats; //true if Quaternions are used to construct the orientation, false if Euler Angles are used
int m_Qx; //number of the column in the .csv file for the x component of the quaternion
int m_Qy; //number of the column in the .csv file for the y component of the quaternion
int m_Qz; //number of the column in the .csv file for the z component of the quaternion
int m_Qr; //number of the column in the .csv file for the r component of the quaternion
int m_Azimuth; //number of the colum in the .csv file for Azimuth (Euler Angles)
int m_Elevation; //number of the colum in the .csv file for Elevation (Euler Angles)
int m_Roll; //number of the colum in the .csv file for Roll (Euler Angles)
bool m_EulersInRadiants; // true if the Euler Angles in the .csv file are in radiants, false if they are in degrees
int m_MinNumberOfColumns; //minimal number of columns the file has to have (e.g. if you read data from column 8 the file has to have at least 8 columns)
};
} // namespace mitk
#endif /* MITKNavigationDataCSVSequentialPlayer_H_HEADER_INCLUDED_ */
diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/CMakeLists.txt b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/CMakeLists.txt
index 6581e2a790..b5c7ec2ed4 100644
--- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/CMakeLists.txt
@@ -1,16 +1,16 @@
project(org_mitk_gui_qt_igt_app_ultrasoundtrackingnavigation)
mitk_create_plugin(
EXPORT_DIRECTIVE IGTAPPUSTRACKINGNAVIGATION_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
- PACKAGE_DEPENDS CTK Poco
- MODULE_DEPENDS MitkUSUI MitkUSNavigation MitkIGTUI MitkSceneSerialization MitkContourModel ITKLabelMap
+ PACKAGE_DEPENDS PRIVATE CTK ITK|LabelMap Poco
+ MODULE_DEPENDS MitkUSUI MitkUSNavigation MitkIGTUI MitkSceneSerialization MitkContourModel
)
#usFunctionAddResources(TARGET ${PLUGIN_TARGET}
# MODULE_NAME liborg_mitk_gui_qt_usnavigation
# WORKING_DIRECTORY resources
# FILES Interactions/USPointMarkInteractions.xml
# Interactions/USZoneInteractions.xml
# Interactions/USZoneInteractionsHold.xml
#)
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/CMakeLists.txt b/Plugins/org.mitk.gui.qt.lasercontrol/CMakeLists.txt
deleted file mode 100644
index d22b896c7e..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/CMakeLists.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-project(org_mitk_gui_qt_lasercontrol)
-
-if(WIN32)
- foreach(config_type ${CMAKE_CONFIGURATION_TYPES})
- execute_process(COMMAND "${CMAKE_COMMAND}" -E make_directory "${MITK_BINARY_DIR}/bin/${config_type}")
- endforeach()
- if(MITK_USE_GALIL_HARDWARE)
- configure_file( ${MITK_GALIL_API_PATH}/dll/x64/gclib.dll ${MITK_BINARY_DIR}/bin/Debug/ COPYONLY )
- configure_file( ${MITK_GALIL_API_PATH}/dll/x64/gclibo.dll ${MITK_BINARY_DIR}/bin/Debug/ COPYONLY )
- configure_file( ${MITK_GALIL_API_PATH}/dll/x64/gclib.dll ${MITK_BINARY_DIR}/bin/Release/ COPYONLY )
- configure_file( ${MITK_GALIL_API_PATH}/dll/x64/gclibo.dll ${MITK_BINARY_DIR}/bin/Release/ COPYONLY )
- endif()
- if(MITK_USE_OPHIR_PYRO_HARDWARE)
- configure_file( ${MITK_OPHIR_API_PATH}/Debug/OphirPyroWrapper.dll ${MITK_BINARY_DIR}/bin/Debug/ COPYONLY )
- configure_file( ${MITK_OPHIR_API_PATH}/Release/OphirPyroWrapper.dll ${MITK_BINARY_DIR}/bin/Release/ COPYONLY )
- configure_file( ${MITK_OPHIR_API_PATH}/Debug/OphirLMMeasurement.dll ${MITK_BINARY_DIR}/bin/Debug/ COPYONLY )
- configure_file( ${MITK_OPHIR_API_PATH}/Release/OphirLMMeasurement.dll ${MITK_BINARY_DIR}/bin/Release/ COPYONLY )
- configure_file( ${MITK_OPHIR_API_PATH}/Debug/Interop.OphirLMMeasurementLib.dll ${MITK_BINARY_DIR}/bin/Debug/ COPYONLY )
- configure_file( ${MITK_OPHIR_API_PATH}/Release/Interop.OphirLMMeasurementLib.dll ${MITK_BINARY_DIR}/bin/Release/ COPYONLY )
- endif()
-endif()
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE LASERCONTROL_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt MitkPhotoacousticsHardware
-)
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/files.cmake b/Plugins/org.mitk.gui.qt.lasercontrol/files.cmake
deleted file mode 100644
index ebb9b41a94..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/files.cmake
+++ /dev/null
@@ -1,37 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- mitkLaserControlPluginActivator.cpp
- QmitkLaserControl.cpp
-
-)
-
-set(UI_FILES
- src/internal/QmitkLaserControlControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/mitkLaserControlPluginActivator.h
- src/internal/QmitkLaserControl.h
-)
-
-set(CACHED_RESOURCE_FILES
- resources/iconLaserControl.svg
- plugin.xml
-)
-
-set(QRC_FILES
-
-)
-
-set(CPP_FILES)
-
-foreach(file ${SRC_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/${file})
-endforeach(file ${SRC_CPP_FILES})
-
-foreach(file ${INTERNAL_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/internal/${file})
-endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.lasercontrol/manifest_headers.cmake
deleted file mode 100644
index 11faba1fd4..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "MITK OPO Laser Control")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
-set(Plugin-ContactAddress "http://www.mitk.org")
-set(Require-Plugin org.mitk.gui.qt.common.legacy)
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/plugin.xml b/Plugins/org.mitk.gui.qt.lasercontrol/plugin.xml
deleted file mode 100644
index e2c8781409..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/plugin.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.lasercontrol"
- name="OPO Laser Control"
- category="Photoacoustics"
- class="OPOLaserControl"
- icon="resources/iconLaserControl.svg" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/resources/iconLaser.xpm b/Plugins/org.mitk.gui.qt.lasercontrol/resources/iconLaser.xpm
deleted file mode 100644
index e2c5d7c620..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/resources/iconLaser.xpm
+++ /dev/null
@@ -1,133 +0,0 @@
-/* XPM */
-static char * iconLaser_xpm[] = {
-"128 128 2 1",
-" c None",
-". c #000000",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .......... ",
-" .. .......... ",
-" .... .......... ",
-" ....... .......... ",
-" ........ .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" .......... .......... ",
-" ......... .......... ",
-" .......... .......... ",
-" ......... .......... ",
-" .......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .......... ",
-" ......... .............. ",
-" ......... .................. ",
-" ...... .................... ",
-" .... ...................... ",
-" .. ........................ ",
-" ........................ ",
-" .......................... ",
-" ............................ ",
-" ............................ ",
-" ............................ ",
-" .............................. .................. ",
-" .............................. ........................................ ",
-" .............................. ........................................ ",
-" .............................. ........................................ ",
-" .............................. ......................................... ",
-" .............................. ................................. ",
-" .............................. ..... ",
-" ............................ ",
-" ............................ ",
-" ............................ ",
-" .......................... ",
-" . ........................ ",
-" ... ........................ ",
-" ...... ...................... ",
-" ........ .................... ",
-" ........... .................. .. ",
-" ........... .............. .... ",
-" .......... .......... ....... ",
-" ......... ........ ",
-" ........ . ........ ",
-" ..... ... ........ ",
-" ... ...... ........ ",
-" ... ..... ....... ",
-" ..... ...... ....... ",
-" ..... ..... ....... ",
-" ..... ...... ....... ",
-" ...... ..... ....... ",
-" ..... ...... ....... ",
-" ..... ..... ....... ",
-" ..... ...... ....... ",
-" ...... ..... ....... ",
-" ..... ...... ........ ",
-" ..... ..... ........ ",
-" ..... ...... ........ ",
-" ...... ..... ........ ",
-" ..... ...... ....... ",
-" ..... ..... ....... ",
-" ..... ...... ....... ",
-" ...... ..... ....... ",
-" ..... ...... ....... ",
-" ..... ..... ....... ",
-" ..... ...... ....... ",
-" ...... ..... ....... ",
-" ..... ...... ....... ",
-" ..... ..... ....... ",
-" ..... ...... ........ ",
-" ...... ..... ........ ",
-" ..... ...... ........ ",
-" ..... ...... ........ ",
-" ..... ...... ........ ",
-" ...... ...... ..... ",
-" ..... ...... ... ",
-" ..... ...... . ",
-" ..... ...... ",
-" ...... ..... ",
-" ..... ... ",
-" . ",
-" ",
-" ",
-" ",
-" ",
-" "};
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/resources/iconLaserControl.svg b/Plugins/org.mitk.gui.qt.lasercontrol/resources/iconLaserControl.svg
deleted file mode 100644
index 639a54b9c3..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/resources/iconLaserControl.svg
+++ /dev/null
@@ -1,88 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<svg
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://creativecommons.org/ns#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:svg="http://www.w3.org/2000/svg"
- xmlns="http://www.w3.org/2000/svg"
- xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
- xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- xml:space="preserve"
- enable-background="new 0 0 1792 1792"
- viewBox="0 0 1792 1792"
- height="128"
- width="128"
- y="0px"
- x="0px"
- id="Layer_1"
- version="1.1"
- inkscape:version="0.91 r13725"
- sodipodi:docname="lasercontrol.svg"><sodipodi:namedview
- pagecolor="#ffffff"
- bordercolor="#666666"
- borderopacity="1"
- objecttolerance="10"
- gridtolerance="10"
- guidetolerance="10"
- inkscape:pageopacity="0"
- inkscape:pageshadow="2"
- inkscape:window-width="1549"
- inkscape:window-height="1176"
- id="namedview7"
- showgrid="false"
- inkscape:zoom="0.13169643"
- inkscape:cx="-261.4391"
- inkscape:cy="1848.2955"
- inkscape:window-x="51"
- inkscape:window-y="24"
- inkscape:window-maximized="1"
- inkscape:current-layer="Layer_1"
- showguides="false" /><metadata
- id="metadata11"><rdf:RDF><cc:Work
- rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
- rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title></dc:title></cc:Work></rdf:RDF></metadata><defs
- id="defs9" /><path
- style="fill:#00ff00;fill-opacity:1"
- d="m 1546.475,971.52948 c -2.5396,17.0678 -11.6742,28.4607 -20.2992,25.3173 -8.625,-3.1434 -110.6423,-28.9171 -226.7051,-57.2748 -75.7963,-20.9626 -216.6504,-49.80976 -206.3877,-82.50378 11.7207,-32.52789 54.1509,-25.24622 225.1105,16.68961 113.1343,27.75147 211.8189,54.12067 219.2989,58.59817 7.48,4.4775 11.5223,22.1055 8.9826,39.1735 z M 1311.2534,589.61494 c -228.186,113.36811 -232.9991,115.05479 -246.1737,86.26771 -12.7024,-27.75541 -0.6477,-35.86131 220.4119,-148.21061 189.7548,-96.4393 236.1344,-115.2543 245.9685,-99.7835 6.6656,10.4863 12.2117,25.1481 12.3245,32.5818 0.1072,7.4337 -104.5262,65.5488 -232.5312,129.1446 z m -29.8664,-221.2506 c -122.7177,131.2618 -228.1348,244.1059 -234.2601,250.7646 -11.6961,12.7145 -52.46764,-13.1762 -52.46764,-33.3179 0,-9.1074 137.50324,-159.4617 441.53964,-482.8061 21.4778,-22.841802 23.3294,-22.782902 45.3515,1.4437 22.0667,24.2753 14.2816,34.5401 -200.1634,263.9157 z m -214.2461,824.18936 c -31.1499,11.9004 -42.0531,1.1165 -85.49364,-84.5576 -18.058,-45.0662 -41.3136,-71.738 -9.7489,-90.443 26.5485,-11.8182 33.72344,-5.7277 72.59894,61.6266 49.1763,85.2012 52.5232,101.9589 22.6436,113.374 z M 1004.708,893.81718 c -43.10534,62.8701 -110.93438,96.319 -180.79161,89.1546 -62.4626,-6.4061 -133.55682,-63.996 -157.5127,-102.49139 -19.63107,-31.54571 -20.2332,-26.6869 -382.75741,-26.6869 l -290.249663,0 0,-66.69492 0,-66.69491 290.249663,0 c 372.01574,0 372.6179,1.06221 382.75741,-26.68691 15.56116,-42.58671 95.0501,-96.08531 157.5127,-102.49141 112.85747,-11.5744 210.93781,79.50131 210.93781,195.87323 0,43.15328 -9.4145,76.48097 -30.1462,106.71861 z M 838.34579,533.65784 c -56.04137,-3.7966 -50.24585,-188.9999 -50.24585,-268.7299 -1.13119,-101.1803 -15.5521,-256.072992 36.06495,-267.520292 53.23243,-2.721504 42.08403,128.847192 43.71773,259.003892 0.2628,228.0256 20.6447,253.6837 -29.53683,277.2463 z M 552.4167,1310.6537 c -95.54787,144.8947 -179.09448,263.4449 -185.65914,263.4449 -6.56468,0 -26.64121,-19.9216 -35.33391,-30.3493 -12.7512,-15.2962 25.79193,-59.2139 167.7782,-274.8611 161.38614,-245.1114 178.12674,-265.9629 201.74064,-251.281 14.1629,8.8057 25.6263,19.0684 25.4742,22.806 -0.1522,3.7376 -78.4521,125.3458 -173.99999,270.2405 z"
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diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControl.cpp b/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControl.cpp
deleted file mode 100644
index 35d1bde864..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControl.cpp
+++ /dev/null
@@ -1,375 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// Qmitk
-#include "QmitkLaserControl.h"
-
-// Qt
-#include <QMessageBox>
-#include <QtConcurrentRun>
-
-const std::string OPOLaserControl::VIEW_ID = "org.mitk.views.lasercontrol";
-
-void OPOLaserControl::SetFocus()
-{
-}
-
-void OPOLaserControl::CreateQtPartControl(QWidget *parent)
-{
- // create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi(parent);
- connect(m_Controls.buttonInitLaser, SIGNAL(clicked()), this, SLOT(InitResetLaser()));
- connect(m_Controls.buttonTune, SIGNAL(clicked()), this, SLOT(TuneWavelength()));
- connect(m_Controls.buttonFastTuning, SIGNAL(clicked()), this, SLOT(StartFastTuning()));
- connect(m_Controls.buttonFlashlamp, SIGNAL(clicked()), this, SLOT(ToggleFlashlamp()));
- connect(m_Controls.buttonQSwitch, SIGNAL(clicked()), this, SLOT(ToggleQSwitch()));
- connect(m_Controls.sliderWavelength, SIGNAL(valueChanged(int)), this, SLOT(SyncWavelengthSetBySlider()));
- connect(m_Controls.spinBoxWavelength, SIGNAL(valueChanged(double)), this, SLOT(SyncWavelengthSetBySpinBox()));
- connect(&m_ShutterWatcher, SIGNAL(finished()), this, SLOT(EnableLaser()));
-
- m_SyncFromSpinBox = true;
- m_SyncFromSlider = true;
-
- m_PumpLaserConnected = false;
- m_OPOConnected = false;
- m_PyroConnected = false;
-}
-
-void OPOLaserControl::EnableLaser()
-{
- m_Controls.buttonQSwitch->setEnabled(true);
- m_Controls.buttonQSwitch->setText("Start Laser");
- this->GetState();
-}
-
-void OPOLaserControl::SyncWavelengthSetBySlider()
-{
- if (m_SyncFromSlider)
- {
- m_SyncFromSpinBox = false;
- m_Controls.spinBoxWavelength->setValue(m_Controls.sliderWavelength->value() / 10);
- }
- else
- m_SyncFromSlider = true;
-}
-
-void OPOLaserControl::SyncWavelengthSetBySpinBox()
-{
- if (m_SyncFromSpinBox)
- {
- m_SyncFromSlider = false;
- m_Controls.sliderWavelength->setValue(m_Controls.spinBoxWavelength->value() * 10);
- }
- else
- m_SyncFromSpinBox = true;
-}
-
-void OPOLaserControl::InitResetLaser()
-{
- m_Controls.buttonInitLaser->setEnabled(false);
- m_Controls.buttonInitLaser->setText("working ...");
-
- if (!m_PumpLaserConnected && !m_OPOConnected)
- {
- m_PumpLaserController = mitk::QuantelLaser::New();
- m_OPOMotor = mitk::GalilMotor::New();
- InitThread *initThread = new InitThread(m_PumpLaserController, m_OPOMotor);
- connect(initThread, SIGNAL(result(bool, bool)), this, SLOT(InitLaser(bool, bool)));
- connect(initThread, SIGNAL(finished()), initThread, SLOT(deleteLater()));
- initThread->start();
- }
- else
- {
- // destroy and free
- m_Controls.buttonFlashlamp->setEnabled(false);
- m_Controls.buttonQSwitch->setEnabled(false);
- m_Controls.buttonTune->setEnabled(false);
- m_Controls.buttonFastTuning->setEnabled(false);
-
- ResetThread *resetThread = new ResetThread(m_PumpLaserController, m_OPOMotor);
- connect(resetThread, SIGNAL(result(bool, bool)), this, SLOT(ResetLaser(bool, bool)));
- connect(resetThread, SIGNAL(finished()), resetThread, SLOT(deleteLater()));
- resetThread->start();
- }
- /*
- try
- {
- if (!m_PyroConnected)
- {
- m_Pyro = mitk::OphirPyro::New();
- MITK_INFO << "[Pyro Debug] OpenConnection: " << m_Pyro->OpenConnection();
- MITK_INFO << "[Pyro Debug] StartDataAcquisition: " << m_Pyro->StartDataAcquisition();
- m_CurrentPulseEnergy = 0;
- m_PyroConnected = true;
- //QFuture<void> future = QtConcurrent::run(this, &OPOLaserControl::ShowEnergy);
- //m_EnergyWatcher.setFuture(future);
- }
- else
- {
- m_PyroConnected = false;
- }
- } catch (...) {
- MITK_INFO << " While trying to connect to the Pyro an exception was caught (this almost always happens on the first try after reboot - try again!)";
- m_PyroConnected = false;
- }*/
-}
-
-void OPOLaserControl::InitLaser(bool successLaser, bool successMotor)
-{
- if (successLaser && successMotor)
- {
- m_Controls.buttonFlashlamp->setEnabled(true);
- m_Controls.buttonQSwitch->setEnabled(false);
- m_Controls.buttonInitLaser->setText("Reset and Release Laser");
-
- std::string answer("");
- std::string triggerCommand("TRIG ");
- if (m_Controls.checkBoxTriggerExternally->isChecked())
- {
- triggerCommand.append("EE"); // set both Triggers external
- m_PumpLaserController->SendAndReceiveLine(&triggerCommand, &answer);
- MITK_INFO << answer;
- }
- else
- {
- triggerCommand.append("II"); // set both Triggers internal
- m_PumpLaserController->SendAndReceiveLine(&triggerCommand, &answer);
- MITK_INFO << answer;
- std::string energyCommand("QDLY 30");
- m_PumpLaserController->SendAndReceiveLine(&energyCommand, &answer);
- MITK_INFO << answer;
- }
-
- m_PumpLaserConnected = true;
-
- m_Controls.buttonTune->setEnabled(true);
- m_Controls.buttonFastTuning->setEnabled(true);
- m_Controls.sliderWavelength->setMinimum(m_OPOMotor->GetMinWavelength() * 10);
- m_Controls.sliderWavelength->setMaximum(m_OPOMotor->GetMaxWavelength() * 10);
- m_Controls.spinBoxWavelength->setMinimum(m_OPOMotor->GetMinWavelength());
- m_Controls.spinBoxWavelength->setMaximum(m_OPOMotor->GetMaxWavelength());
- m_Controls.sliderWavelength->setValue(m_OPOMotor->GetCurrentWavelength() * 10);
- m_Controls.spinBoxWavelength->setValue(m_OPOMotor->GetCurrentWavelength());
-
- m_OPOConnected = true; // not always right FIXME
-
- this->GetState();
- }
- else
- {
- if(!successLaser)
- QMessageBox::warning(NULL, "Laser Control", "Opotek Pump Laser Initialization Failed.");
- if(!successMotor)
- QMessageBox::warning(NULL, "Laser Control", "OPO Initialization Failed.");
-
- m_Controls.buttonInitLaser->setText("Init Laser");
- return;
- }
-
- m_Controls.buttonInitLaser->setEnabled(true);
- this->GetState();
-}
-
-void OPOLaserControl::ResetLaser(bool successLaser, bool successMotor)
-{
- if (successLaser && successMotor)
- {
- m_Controls.buttonFlashlamp->setEnabled(false);
- m_Controls.buttonQSwitch->setEnabled(false);
- m_Controls.buttonInitLaser->setText("Init Laser");
- m_PumpLaserConnected = false;
-
- m_Controls.buttonTune->setEnabled(false);
- m_Controls.buttonFastTuning->setEnabled(false);
- m_Controls.buttonInitLaser->setText("Init Laser");
- m_OPOConnected = false;
- }
- else
- {
- if(!successMotor)
- QMessageBox::warning(NULL, "Laser Control", "OPO Release Failed.");
- if(!successLaser)
- QMessageBox::warning(NULL, "Laser Control", "Opotek Pump Laser Release Failed.");
-
- m_Controls.buttonInitLaser->setText("Reset and Release Laser");
- }
-
- m_Controls.buttonInitLaser->setEnabled(true);
- this->GetState();
-}
-
-void OPOLaserControl::TuneWavelength()
-{
- if (m_Controls.checkBoxCalibration->isChecked())
- {
- m_OPOMotor->TuneToWavelength(m_Controls.spinBoxPosition->value(), true);
- }
- else
- {
- m_OPOMotor->TuneToWavelength(m_Controls.spinBoxWavelength->value(), false);
- }
- QString wavelengthText = QString::number(m_OPOMotor->GetCurrentWavelength());
- wavelengthText.append("nm");
- m_Controls.labelWavelength->setText(wavelengthText);
-}
-
-void OPOLaserControl::StartFastTuning()
-{
- std::vector<double> listOfWavelengths;
- double tmpWavelength = 0;
- int currentRow = 0;
- bool success = false;
-
- do
- {
- if (currentRow != 0) listOfWavelengths.push_back(tmpWavelength);
- if (m_Controls.tableFastTuningWavelengths->item(0, currentRow))
- {
- QString test = m_Controls.tableFastTuningWavelengths->item(0, currentRow)->text();
- tmpWavelength = test.toDouble(&success);
- currentRow++;
- }
- else
- tmpWavelength = 0;
-
- if (success == 0)
- tmpWavelength = 0;
- } while (tmpWavelength<950.1 && tmpWavelength>689.9);
-
- m_OPOMotor->FastTuneWavelengths(listOfWavelengths);
-}
-
-void OPOLaserControl::ShutterCountDown()
-{
- m_Controls.buttonFlashlamp->setText("Stop Lamp");
- m_Controls.buttonQSwitch->setEnabled(false);
- m_Controls.buttonQSwitch->setText("10s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("9s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("8s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("7s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("6s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("5s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("4s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("3s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("2s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- m_Controls.buttonQSwitch->setText("1s ...");
- std::this_thread::sleep_for(std::chrono::seconds(1));
- return;
-}
-
-void OPOLaserControl::ShowEnergy()
-{
- /*forever
- {
- std::this_thread::sleep_for(std::chrono::milliseconds(500));
- MITK_INFO << "[Pyro Debug] ShowEnergy()";
- if (!m_PyroConnected)
- {
- MITK_INFO << "[Pyro Debug] StopDataAcquisition: " << m_Pyro->StopDataAcquisition();
- MITK_INFO << "[Pyro Debug] CloseConnection: " << m_Pyro->CloseConnection();
- m_CurrentPulseEnergy = 0;
- return;
- }
- // m_Pyro->GetDataFromSensor();
- m_CurrentPulseEnergy = 60000 * m_Pyro->LookupCurrentPulseEnergy();
- m_Controls.labelEnergy->setText(std::to_string(m_CurrentPulseEnergy).append(" mJ").c_str());
- }*/
-}
-
-void OPOLaserControl::ToggleFlashlamp()
-{
- m_Controls.buttonFlashlamp->setText("...");
- if (!m_PumpLaserController->IsFlashing())
- {
- if (m_PumpLaserController->StartFlashing())
- {
- QFuture<void> future = QtConcurrent::run(this, &OPOLaserControl::ShutterCountDown);
- m_ShutterWatcher.setFuture(future);
- }
- else
- m_Controls.buttonFlashlamp->setText("Start Lamp");
- }
- else
- {
- if (m_PumpLaserController->StopFlashing())
- {
- m_Controls.buttonFlashlamp->setText("Start Lamp");
- m_Controls.buttonQSwitch->setText("Start Laser");
- m_Controls.buttonQSwitch->setEnabled(false);
- }
- else
- m_Controls.buttonFlashlamp->setText("Stop Lamp");
- }
- this->GetState();
-}
-
-void OPOLaserControl::ToggleQSwitch()
-{
- m_Controls.buttonQSwitch->setText("...");
- if (!m_PumpLaserController->IsEmitting())
- {
- if (m_PumpLaserController->StartQswitching())
- m_Controls.buttonQSwitch->setText("Stop Laser");
- else
- m_Controls.buttonQSwitch->setText("Start Laser");
- }
- else
- {
- if (m_PumpLaserController->StopQswitching())
- m_Controls.buttonQSwitch->setText("Start Laser");
- else
- m_Controls.buttonQSwitch->setText("Stop Laser");
- }
- this->GetState();
-}
-
-void OPOLaserControl::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer>& nodes)
-{
-}
-
-void OPOLaserControl::GetState()
-{
- mitk::QuantelLaser::LaserState pumpLaserState = m_PumpLaserController->GetState();
-
- if (pumpLaserState == mitk::QuantelLaser::STATE0)
- m_Controls.labelStatus->setText("PL0: Boot Fault.");
- else if (pumpLaserState == mitk::QuantelLaser::STATE1)
- m_Controls.labelStatus->setText("PL1: Warm Up.");
- else if (pumpLaserState == mitk::QuantelLaser::STATE2)
- m_Controls.labelStatus->setText("PL2: Laser Ready.");
- else if (pumpLaserState == mitk::QuantelLaser::STATE3)
- m_Controls.labelStatus->setText("PL3: Flashing. Pulse Disabled.");
- else if (pumpLaserState == mitk::QuantelLaser::STATE4)
- m_Controls.labelStatus->setText("PL4: Flashing. Shutter Closed.");
- else if (pumpLaserState == mitk::QuantelLaser::STATE5)
- m_Controls.labelStatus->setText("PL5: Flashing. Shutter Open.");
- else if (pumpLaserState == mitk::QuantelLaser::STATE6)
- m_Controls.labelStatus->setText("PL6: Flashing. Pulse Enabled.");
- else if (pumpLaserState == mitk::QuantelLaser::STATE7)
- m_Controls.labelStatus->setText("PL7: Undefined State.");
- else if (pumpLaserState == mitk::QuantelLaser::UNCONNECTED)
- m_Controls.labelStatus->setText("PL Not Connected.");
-}
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControl.h b/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControl.h
deleted file mode 100644
index fe93a60379..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControl.h
+++ /dev/null
@@ -1,138 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef OPOLaserControl_h
-#define OPOLaserControl_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-
-#include "ui_QmitkLaserControlControls.h"
-
-#include <QFuture>
-#include <QFutureWatcher>
-#include <qthread.h>
-
-// Photoacoustics Hardware
-#include <mitkQuantelLaser.h>
-#include <mitkGalilMotor.h>
-//#include <mitkOphirPyro.h>
-
-#include <vector>
-
-/**
- \brief OPOLaserControl
-
- \warning This class is not yet documented. Use "git blame" and ask the author why he is a lazy fuck.
-
- \sa QmitkAbstractView
- \ingroup ${plugin_target}_internal
-*/
-class OPOLaserControl : public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- protected slots:
-
- /// \brief Called when the user clicks the GUI button
- void GetState();
-
- void InitLaser(bool successLaser, bool successMotor);
- void ResetLaser(bool successLaser, bool successMotor);
- void InitResetLaser();
- void TuneWavelength();
- void StartFastTuning();
-
- void ShutterCountDown();
- void EnableLaser();
- void ShowEnergy();
-
- void ToggleFlashlamp();
- void ToggleQSwitch();
- void SyncWavelengthSetBySlider();
- void SyncWavelengthSetBySpinBox();
-
- protected:
-
- virtual void CreateQtPartControl(QWidget *parent) override;
-
- virtual void SetFocus() override;
-
- /// \brief called by QmitkFunctionality when DataManager's selection has changed
- virtual void OnSelectionChanged( berry::IWorkbenchPart::Pointer source,
- const QList<mitk::DataNode::Pointer>& nodes ) override;
-
- Ui::OPOLaserControlControls m_Controls;
- bool m_PumpLaserConnected;
- bool m_OPOConnected;
- bool m_PyroConnected;
- bool m_SyncFromSpinBox;
- bool m_SyncFromSlider;
- double m_CurrentPulseEnergy;
-
- QFutureWatcher<void> m_ShutterWatcher;
- QFutureWatcher<void> m_EnergyWatcher;
-
- mitk::QuantelLaser::Pointer m_PumpLaserController;
- mitk::GalilMotor::Pointer m_OPOMotor;
- //mitk::OphirPyro::Pointer m_Pyro;
-
-};
-
-class InitThread : public QThread
-{
- Q_OBJECT
- void run() Q_DECL_OVERRIDE
- {
- emit result(m_PumpLaserController->OpenConnection("OpotekPhocusMobile"), m_OPOMotor->OpenConnection("OpotekPhocusMobile"));
- }
- signals:
- void result(bool, bool);
- public:
- InitThread(mitk::QuantelLaser::Pointer ql, mitk::GalilMotor::Pointer gm)
- {
- m_PumpLaserController = ql;
- m_OPOMotor = gm;
- }
- mitk::QuantelLaser::Pointer m_PumpLaserController;
- mitk::GalilMotor::Pointer m_OPOMotor;
-};
-
-class ResetThread : public QThread
-{
- Q_OBJECT
- void run() Q_DECL_OVERRIDE
- {
- emit result(m_PumpLaserController->CloseConnection(), m_OPOMotor->CloseConnection());
- }
-signals:
- void result(bool, bool);
-public:
- ResetThread(mitk::QuantelLaser::Pointer ql, mitk::GalilMotor::Pointer gm)
- {
- m_PumpLaserController = ql;
- m_OPOMotor = gm;
- }
- mitk::QuantelLaser::Pointer m_PumpLaserController;
- mitk::GalilMotor::Pointer m_OPOMotor;
-};
-
-#endif // OPOLaserControl_h
-
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControlControls.ui b/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControlControls.ui
deleted file mode 100644
index 8eb85c86e6..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/QmitkLaserControlControls.ui
+++ /dev/null
@@ -1,775 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>OPOLaserControlControls</class>
- <widget class="QWidget" name="OPOLaserControlControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>343</width>
- <height>528</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>9</pointsize>
- </font>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QGroupBox" name="groupBox_3">
- <property name="font">
- <font>
- <pointsize>9</pointsize>
- </font>
- </property>
- <property name="title">
- <string>OPOTEK Phocus Control</string>
- </property>
- <widget class="QWidget" name="verticalLayoutWidget_3">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>20</y>
- <width>301</width>
- <height>431</height>
- </rect>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_5">
- <item>
- <widget class="QCheckBox" name="checkBoxTriggerExternally">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Trigger Externally</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonInitLaser">
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Init Laser</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QPushButton" name="buttonFlashlamp">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Start Lamp</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonQSwitch">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="text">
- <string>Start Laser</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="labelStatus">
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Laser Status</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Current Wavelength</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="labelWavelength">
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- <stylestrategy>PreferDefault</stylestrategy>
- <kerning>true</kerning>
- </font>
- </property>
- <property name="text">
- <string>750.0 nm</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>Pulse Energy</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="labelEnergy">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- <stylestrategy>PreferDefault</stylestrategy>
- <kerning>true</kerning>
- </font>
- </property>
- <property name="text">
- <string>0 mJ</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QSlider" name="sliderWavelength">
- <property name="minimum">
- <number>6900</number>
- </property>
- <property name="maximum">
- <number>9500</number>
- </property>
- <property name="singleStep">
- <number>5</number>
- </property>
- <property name="pageStep">
- <number>100</number>
- </property>
- <property name="sliderPosition">
- <number>7500</number>
- </property>
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="tickPosition">
- <enum>QSlider::NoTicks</enum>
- </property>
- <property name="tickInterval">
- <number>10000</number>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QDoubleSpinBox" name="spinBoxWavelength">
- <property name="decimals">
- <number>1</number>
- </property>
- <property name="minimum">
- <double>690.000000000000000</double>
- </property>
- <property name="maximum">
- <double>950.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.500000000000000</double>
- </property>
- <property name="value">
- <double>750.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>nm</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonTune">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Tune</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_2">
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>Fast Tuning Wavelengths</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QTableWidget" name="tableFastTuningWavelengths">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>75</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>75</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="showGrid">
- <bool>true</bool>
- </property>
- <property name="gridStyle">
- <enum>Qt::SolidLine</enum>
- </property>
- <attribute name="horizontalHeaderDefaultSectionSize">
- <number>42</number>
- </attribute>
- <attribute name="horizontalHeaderMinimumSectionSize">
- <number>50</number>
- </attribute>
- <attribute name="verticalHeaderDefaultSectionSize">
- <number>30</number>
- </attribute>
- <attribute name="verticalHeaderMinimumSectionSize">
- <number>30</number>
- </attribute>
- <row>
- <property name="text">
- <string>λ/nm</string>
- </property>
- </row>
- <column>
- <property name="text">
- <string>1</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>2</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>3</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>4</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>5</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>6</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>7</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>8</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>9</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>10</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>11</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>12</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>13</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>14</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>15</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>16</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>17</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>18</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>19</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>20</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>21</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>22</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>23</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>24</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>25</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>26</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>27</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>28</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>29</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>30</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>31</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>32</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>33</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>34</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>35</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>36</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>37</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>38</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>39</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>40</string>
- </property>
- </column>
- <item row="0" column="0">
- <property name="text">
- <string>700</string>
- </property>
- </item>
- <item row="0" column="1">
- <property name="text">
- <string>710</string>
- </property>
- </item>
- <item row="0" column="2">
- <property name="text">
- <string>720</string>
- </property>
- </item>
- <item row="0" column="3">
- <property name="text">
- <string>730</string>
- </property>
- </item>
- <item row="0" column="4">
- <property name="text">
- <string>740</string>
- </property>
- </item>
- <item row="0" column="5">
- <property name="text">
- <string>750</string>
- </property>
- </item>
- <item row="0" column="6">
- <property name="text">
- <string>760</string>
- </property>
- </item>
- <item row="0" column="7">
- <property name="text">
- <string>770</string>
- </property>
- </item>
- <item row="0" column="8">
- <property name="text">
- <string>780</string>
- </property>
- </item>
- <item row="0" column="9">
- <property name="text">
- <string>790</string>
- </property>
- </item>
- <item row="0" column="10">
- <property name="text">
- <string>800</string>
- </property>
- </item>
- <item row="0" column="11">
- <property name="text">
- <string>810</string>
- </property>
- </item>
- <item row="0" column="12">
- <property name="text">
- <string>820</string>
- </property>
- </item>
- <item row="0" column="13">
- <property name="text">
- <string>830</string>
- </property>
- </item>
- <item row="0" column="14">
- <property name="text">
- <string>840</string>
- </property>
- </item>
- <item row="0" column="15">
- <property name="text">
- <string>850</string>
- </property>
- </item>
- <item row="0" column="16">
- <property name="text">
- <string>860</string>
- </property>
- </item>
- <item row="0" column="17">
- <property name="text">
- <string>870</string>
- </property>
- </item>
- <item row="0" column="18">
- <property name="text">
- <string>880</string>
- </property>
- </item>
- <item row="0" column="19">
- <property name="text">
- <string>890</string>
- </property>
- </item>
- <item row="0" column="20">
- <property name="text">
- <string>900</string>
- </property>
- </item>
- <item row="0" column="21">
- <property name="text">
- <string>910</string>
- </property>
- </item>
- <item row="0" column="22">
- <property name="text">
- <string>920</string>
- </property>
- </item>
- <item row="0" column="23">
- <property name="text">
- <string>930</string>
- </property>
- </item>
- <item row="0" column="24">
- <property name="text">
- <string>940</string>
- </property>
- </item>
- <item row="0" column="25">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="26">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="27">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="28">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="29">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="30">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="31">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="32">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="33">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="34">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="35">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="36">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="37">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="38">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="39">
- <property name="text">
- <string/>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonFastTuning">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="text">
- <string>Start Fast Tuning</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QCheckBox" name="checkBoxCalibration">
- <property name="text">
- <string>calibrate OPO</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinBoxPosition">
- <property name="maximum">
- <number>50000</number>
- </property>
- <property name="singleStep">
- <number>400</number>
- </property>
- <property name="value">
- <number>24400</number>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/mitkLaserControlPluginActivator.cpp b/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/mitkLaserControlPluginActivator.cpp
deleted file mode 100644
index 5bc8a2de7c..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/mitkLaserControlPluginActivator.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#include "mitkLaserControlPluginActivator.h"
-#include "QmitkLaserControl.h"
-
-namespace mitk {
-
-void org_mitk_gui_qt_lasercontrol_Activator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(OPOLaserControl, context)
-}
-
-void org_mitk_gui_qt_lasercontrol_Activator::stop(ctkPluginContext* context)
-{
- Q_UNUSED(context)
-}
-
-}
diff --git a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/mitkLaserControlPluginActivator.h b/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/mitkLaserControlPluginActivator.h
deleted file mode 100644
index dca635ac4f..0000000000
--- a/Plugins/org.mitk.gui.qt.lasercontrol/src/internal/mitkLaserControlPluginActivator.h
+++ /dev/null
@@ -1,37 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef org_mitk_gui_qt_lasercontrol_Activator_h
-#define org_mitk_gui_qt_lasercontrol_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
-class org_mitk_gui_qt_lasercontrol_Activator :
- public QObject, public ctkPluginActivator
-{
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_lasercontrol")
- Q_INTERFACES(ctkPluginActivator)
-
-public:
-
- void start(ctkPluginContext* context);
- void stop(ctkPluginContext* context);
-
-}; // org_mitk_gui_qt_lasercontrol_Activator
-
-}
-
-#endif // org_mitk_gui_qt_lasercontrol_Activator_h
diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp
index b1d6ae2ba9..7af75c5031 100644
--- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp
+++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp
@@ -1,1104 +1,1102 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "QmitkMultiLabelSegmentationView.h"
// blueberry
#include <berryConstants.h>
#include <berryIWorkbenchPage.h>
// mitk
#include "mitkApplicationCursor.h"
#include "mitkLabelSetImage.h"
#include "mitkStatusBar.h"
#include "mitkToolManagerProvider.h"
#include "mitkInteractionEventObserver.h"
#include "mitkPlanePositionManager.h"
#include "mitkPluginActivator.h"
#include "mitkSegTool2D.h"
#include "mitkImageTimeSelector.h"
#include "mitkNodePredicateSubGeometry.h"
// Qmitk
#include <QmitkStyleManager.h>
#include "QmitkNewSegmentationDialog.h"
#include "QmitkRenderWindow.h"
#include "QmitkSegmentationOrganNamesHandling.cpp"
#include "QmitkCreateMultiLabelPresetAction.h"
#include "QmitkLoadMultiLabelPresetAction.h"
// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
#include <usModuleResourceStream.h>
// Qt
#include <QDateTime>
#include <QFileDialog>
#include <QInputDialog>
#include <QMessageBox>
#include <QShortcut>
-#include "tinyxml.h"
-
#include <itksys/SystemTools.hxx>
#include <regex>
const std::string QmitkMultiLabelSegmentationView::VIEW_ID = "org.mitk.views.multilabelsegmentation";
QmitkMultiLabelSegmentationView::QmitkMultiLabelSegmentationView()
: m_Parent(nullptr),
m_IRenderWindowPart(nullptr),
m_ToolManager(nullptr),
m_ReferenceNode(nullptr),
m_WorkingNode(nullptr),
m_AutoSelectionEnabled(false),
m_MouseCursorSet(false)
{
m_SegmentationPredicate = mitk::NodePredicateAnd::New();
m_SegmentationPredicate->AddPredicate(mitk::TNodePredicateDataType<mitk::LabelSetImage>::New());
m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")));
mitk::TNodePredicateDataType<mitk::Image>::Pointer isImage = mitk::TNodePredicateDataType<mitk::Image>::New();
mitk::NodePredicateProperty::Pointer isBinary =
mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
mitk::NodePredicateAnd::Pointer isMask = mitk::NodePredicateAnd::New(isBinary, isImage);
mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage");
mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage");
mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage");
auto isSegment = mitk::NodePredicateDataType::New("Segment");
mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New();
validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment)));
validImages->AddPredicate(isDwi);
validImages->AddPredicate(isDti);
validImages->AddPredicate(isOdf);
m_ReferencePredicate = mitk::NodePredicateAnd::New();
m_ReferencePredicate->AddPredicate(validImages);
m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(m_SegmentationPredicate));
m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(isMask));
m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")));
}
QmitkMultiLabelSegmentationView::~QmitkMultiLabelSegmentationView()
{
// Loose LabelSetConnections
OnLooseLabelSetConnection();
}
void QmitkMultiLabelSegmentationView::CreateQtPartControl(QWidget *parent)
{
// setup the basic GUI of this view
m_Parent = parent;
m_Controls.setupUi(parent);
m_Controls.m_tbSavePreset->setIcon(QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/document-save.svg")));
m_Controls.m_tbLoadPreset->setIcon(QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/document-open.svg")));
// *------------------------
// * Shortcuts
// *------------------------
QShortcut* visibilityShortcut = new QShortcut(QKeySequence("CTRL+H"), parent);
connect(visibilityShortcut, &QShortcut::activated, this, &QmitkMultiLabelSegmentationView::OnVisibilityShortcutActivated);
QShortcut* labelToggleShortcut = new QShortcut(QKeySequence("CTRL+L"), parent);
connect(labelToggleShortcut, &QShortcut::activated, this, &QmitkMultiLabelSegmentationView::OnLabelToggleShortcutActivated);
// *------------------------
// * DATA SELECTION WIDGETS
// *------------------------
m_Controls.m_ReferenceNodeSelector->SetNodePredicate(m_ReferencePredicate);
m_Controls.m_ReferenceNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.m_ReferenceNodeSelector->SetInvalidInfo("Select an image");
m_Controls.m_ReferenceNodeSelector->SetPopUpTitel("Select an image");
m_Controls.m_ReferenceNodeSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation.");
m_Controls.m_WorkingNodeSelector->SetNodePredicate(m_SegmentationPredicate);
m_Controls.m_WorkingNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.m_WorkingNodeSelector->SetInvalidInfo("Select a segmentation");
m_Controls.m_WorkingNodeSelector->SetPopUpTitel("Select a segmentation");
m_Controls.m_WorkingNodeSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected.");
connect(m_Controls.m_ReferenceNodeSelector,
&QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this,&QmitkMultiLabelSegmentationView::OnReferenceSelectionChanged);
connect(m_Controls.m_WorkingNodeSelector,
&QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this,&QmitkMultiLabelSegmentationView::OnSegmentationSelectionChanged);
// *------------------------
// * ToolManager
// *------------------------
m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION);
m_ToolManager->SetDataStorage(*(this->GetDataStorage()));
m_ToolManager->InitializeTools();
m_Controls.m_ManualToolSelectionBox2D->SetToolManager(*m_ToolManager);
m_Controls.m_ManualToolSelectionBox3D->SetToolManager(*m_ToolManager);
// *------------------------
// * LabelSetWidget
// *------------------------
m_Controls.m_LabelSetWidget->SetDataStorage(this->GetDataStorage());
m_Controls.m_LabelSetWidget->SetOrganColors(mitk::OrganNamesHandling::GetDefaultOrganColorString());
m_Controls.m_LabelSetWidget->hide();
// *------------------------
// * Interpolation
// *------------------------
m_Controls.m_SurfaceBasedInterpolatorWidget->SetDataStorage(*(this->GetDataStorage()));
m_Controls.m_SliceBasedInterpolatorWidget->SetDataStorage(*(this->GetDataStorage()));
connect(m_Controls.m_cbInterpolation, SIGNAL(activated(int)), this, SLOT(OnInterpolationSelectionChanged(int)));
m_Controls.m_cbInterpolation->setCurrentIndex(0);
m_Controls.m_swInterpolation->hide();
m_Controls.m_gbInterpolation->hide(); // See T27436
QString segTools2D = tr("Add Subtract Fill Erase Paint Wipe 'Region Growing' FastMarching2D Correction 'Live Wire'");
QString segTools3D = tr("Threshold 'Two Thresholds' 'Auto Threshold' 'Multiple Otsu'");
std::regex extSegTool2DRegEx("SegTool2D$");
std::regex extSegTool3DRegEx("SegTool3D$");
auto tools = m_ToolManager->GetTools();
for (const auto &tool : tools)
{
if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx))
{
segTools2D.append(QString(" '%1'").arg(tool->GetName()));
}
else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx))
{
segTools3D.append(QString(" '%1'").arg(tool->GetName()));
}
}
// *------------------------
// * ToolSelection 2D
// *------------------------
m_Controls.m_ManualToolSelectionBox2D->SetGenerateAccelerators(true);
m_Controls.m_ManualToolSelectionBox2D->SetToolGUIArea(m_Controls.m_ManualToolGUIContainer2D);
m_Controls.m_ManualToolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString()); // todo: "Correction
// 'Live Wire'"
m_Controls.m_ManualToolSelectionBox2D->SetEnabledMode(
QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible);
connect(m_Controls.m_ManualToolSelectionBox2D, SIGNAL(ToolSelected(int)), this, SLOT(OnManualTool2DSelected(int)));
// *------------------------
// * ToolSelection 3D
// *------------------------
m_Controls.m_ManualToolSelectionBox3D->SetGenerateAccelerators(true);
m_Controls.m_ManualToolSelectionBox3D->SetToolGUIArea(m_Controls.m_ManualToolGUIContainer3D);
m_Controls.m_ManualToolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString()); // todo add : FastMarching3D RegionGrowing Watershed
m_Controls.m_ManualToolSelectionBox3D->SetLayoutColumns(2);
m_Controls.m_ManualToolSelectionBox3D->SetEnabledMode(
QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible);
// *------------------------*
// * Connect PushButtons (pb)
// *------------------------*
connect(m_Controls.m_pbNewLabel, SIGNAL(clicked()), this, SLOT(OnNewLabel()));
connect(m_Controls.m_tbSavePreset, SIGNAL(clicked()), this, SLOT(OnSavePreset()));
connect(m_Controls.m_tbLoadPreset, SIGNAL(clicked()), this, SLOT(OnLoadPreset()));
connect(m_Controls.m_pbNewSegmentationSession, SIGNAL(clicked()), this, SLOT(OnNewSegmentationSession()));
connect(m_Controls.m_pbShowLabelTable, SIGNAL(toggled(bool)), this, SLOT(OnShowLabelTable(bool)));
// *------------------------*
// * Connect LabelSetWidget
// *------------------------*
connect(m_Controls.m_LabelSetWidget,
SIGNAL(goToLabel(const mitk::Point3D &)),
this,
SLOT(OnGoToLabel(const mitk::Point3D &)));
connect(m_Controls.m_LabelSetWidget, SIGNAL(resetView()), this, SLOT(OnResetView()));
// *------------------------*
// * DATA SLECTION WIDGET
// *------------------------*
m_IRenderWindowPart = this->GetRenderWindowPart();
if (m_IRenderWindowPart)
{
QList<mitk::SliceNavigationController *> controllers;
controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController());
controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController());
controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController());
m_Controls.m_SliceBasedInterpolatorWidget->SetSliceNavigationControllers(controllers);
}
// this->InitializeListeners();
connect(m_Controls.m_btAddLayer, SIGNAL(clicked()), this, SLOT(OnAddLayer()));
connect(m_Controls.m_btDeleteLayer, SIGNAL(clicked()), this, SLOT(OnDeleteLayer()));
connect(m_Controls.m_btPreviousLayer, SIGNAL(clicked()), this, SLOT(OnPreviousLayer()));
connect(m_Controls.m_btNextLayer, SIGNAL(clicked()), this, SLOT(OnNextLayer()));
connect(m_Controls.m_btLockExterior, SIGNAL(toggled(bool)), this, SLOT(OnLockExteriorToggled(bool)));
connect(m_Controls.m_cbActiveLayer, SIGNAL(currentIndexChanged(int)), this, SLOT(OnChangeLayer(int)));
m_Controls.m_btAddLayer->setEnabled(false);
m_Controls.m_btDeleteLayer->setEnabled(false);
m_Controls.m_btNextLayer->setEnabled(false);
m_Controls.m_btPreviousLayer->setEnabled(false);
m_Controls.m_cbActiveLayer->setEnabled(false);
m_Controls.m_pbNewLabel->setEnabled(false);
m_Controls.m_btLockExterior->setEnabled(false);
m_Controls.m_tbSavePreset->setEnabled(false);
m_Controls.m_tbLoadPreset->setEnabled(false);
m_Controls.m_pbShowLabelTable->setEnabled(false);
// Make sure the GUI notices if appropriate data is already present on creation
m_Controls.m_ReferenceNodeSelector->SetAutoSelectNewNodes(true);
m_Controls.m_WorkingNodeSelector->SetAutoSelectNewNodes(true);
}
void QmitkMultiLabelSegmentationView::Activated()
{
m_ToolManager->SetReferenceData(m_Controls.m_ReferenceNodeSelector->GetSelectedNode());
m_ToolManager->SetWorkingData(m_Controls.m_WorkingNodeSelector->GetSelectedNode());
}
void QmitkMultiLabelSegmentationView::Deactivated()
{
// Not yet implemented
}
void QmitkMultiLabelSegmentationView::Visible()
{
// Not yet implemented
}
void QmitkMultiLabelSegmentationView::Hidden()
{
// Not yet implemented
}
int QmitkMultiLabelSegmentationView::GetSizeFlags(bool width)
{
if (!width)
{
return berry::Constants::MIN | berry::Constants::MAX | berry::Constants::FILL;
}
else
{
return 0;
}
}
int QmitkMultiLabelSegmentationView::ComputePreferredSize(bool width,
int /*availableParallel*/,
int /*availablePerpendicular*/,
int preferredResult)
{
if (width == false)
{
return 100;
}
else
{
return preferredResult;
}
}
/************************************************************************/
/* protected slots */
/************************************************************************/
void QmitkMultiLabelSegmentationView::OnVisibilityShortcutActivated()
{
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
bool isVisible = false;
workingNode->GetBoolProperty("visible", isVisible);
workingNode->SetVisibility(!isVisible);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkMultiLabelSegmentationView::OnLabelToggleShortcutActivated()
{
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
mitk::LabelSetImage* workingImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
assert(workingImage);
WaitCursorOn();
workingImage->GetActiveLabelSet()->SetNextActiveLabel();
workingImage->Modified();
WaitCursorOff();
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void QmitkMultiLabelSegmentationView::OnManualTool2DSelected(int id)
{
this->ResetMouseCursor();
mitk::StatusBar::GetInstance()->DisplayText("");
if (id >= 0)
{
std::string text = "Active Tool: \"";
text += m_ToolManager->GetToolById(id)->GetName();
text += "\"";
mitk::StatusBar::GetInstance()->DisplayText(text.c_str());
us::ModuleResource resource = m_ToolManager->GetToolById(id)->GetCursorIconResource();
this->SetMouseCursor(resource, 0, 0);
}
}
void QmitkMultiLabelSegmentationView::OnNewLabel()
{
m_ToolManager->ActivateTool(-1);
if (m_ReferenceNode.IsNull())
{
QMessageBox::information(
m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action.");
return;
}
if (nullptr == m_ReferenceNode->GetData())
{
QMessageBox::information(
m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action.");
return;
}
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
if (!workingNode)
{
QMessageBox::information(
m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action.");
return;
}
mitk::LabelSetImage* workingImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
if (!workingImage)
{
QMessageBox::information(
m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action.");
return;
}
QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog(m_Parent);
dialog->SetSuggestionList(mitk::OrganNamesHandling::GetDefaultOrganColorString());
dialog->setWindowTitle("New Label");
int dialogReturnValue = dialog->exec();
if (dialogReturnValue == QDialog::Rejected)
{
return;
}
QString segName = dialog->GetSegmentationName();
if (segName.isEmpty())
{
segName = "Unnamed";
}
workingImage->GetActiveLabelSet()->AddLabel(segName.toStdString(), dialog->GetColor());
UpdateControls();
m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems();
this->ReinitializeViews();
}
void QmitkMultiLabelSegmentationView::OnSavePreset()
{
QmitkAbstractNodeSelectionWidget::NodeList nodes;
nodes.append(m_WorkingNode);
QmitkCreateMultiLabelPresetAction action;
action.Run(nodes);
}
void QmitkMultiLabelSegmentationView::OnLoadPreset()
{
QmitkAbstractNodeSelectionWidget::NodeList nodes;
nodes.append(m_WorkingNode);
QmitkLoadMultiLabelPresetAction action;
action.Run(nodes);
}
void QmitkMultiLabelSegmentationView::OnShowLabelTable(bool value)
{
if (value)
m_Controls.m_LabelSetWidget->show();
else
m_Controls.m_LabelSetWidget->hide();
}
void QmitkMultiLabelSegmentationView::OnNewSegmentationSession()
{
mitk::DataNode *referenceNode = m_Controls.m_ReferenceNodeSelector->GetSelectedNode();
if (!referenceNode)
{
QMessageBox::information(
m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action.");
return;
}
m_ToolManager->ActivateTool(-1);
mitk::Image::ConstPointer referenceImage = dynamic_cast<mitk::Image*>(referenceNode->GetData());
assert(referenceImage);
const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
unsigned int imageTimeStep = 0;
if (referenceImage->GetTimeGeometry()->IsValidTimePoint(currentTimePoint))
{
imageTimeStep = referenceImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint);
}
auto segTemplateImage = referenceImage;
if (referenceImage->GetDimension() > 3)
{
auto result = QMessageBox::question(m_Parent, tr("Generate a static mask?"), tr("The selected image has multiple time steps. You can either generate a simple/static masks resembling the geometry of the first timestep of the image. Or you can generate a dynamic mask that equals the selected image in geometry and number of timesteps; thus a dynamic mask can change over time (e.g. according to the image)."), tr("Yes, generate a static mask"), tr("No, generate a dynamic mask"), QString(), 0, 0);
if (result == 0)
{
auto selector = mitk::ImageTimeSelector::New();
selector->SetInput(referenceImage);
selector->SetTimeNr(0);
selector->Update();
const auto refTimeGeometry = referenceImage->GetTimeGeometry();
auto newTimeGeometry = mitk::ProportionalTimeGeometry::New();
newTimeGeometry->SetFirstTimePoint(refTimeGeometry->GetMinimumTimePoint());
newTimeGeometry->SetStepDuration(refTimeGeometry->GetMaximumTimePoint() - refTimeGeometry->GetMinimumTimePoint());
mitk::Image::Pointer newImage = selector->GetOutput();
newTimeGeometry->SetTimeStepGeometry(referenceImage->GetGeometry(imageTimeStep), 0);
newImage->SetTimeGeometry(newTimeGeometry);
segTemplateImage = newImage;
}
}
QString newName = QString::fromStdString(referenceNode->GetName());
newName.append("-labels");
bool ok = false;
newName = QInputDialog::getText(m_Parent, "New Segmentation Session", "New name:", QLineEdit::Normal, newName, &ok);
if (!ok)
{
return;
}
this->WaitCursorOn();
mitk::LabelSetImage::Pointer workingImage = mitk::LabelSetImage::New();
try
{
workingImage->Initialize(segTemplateImage);
}
catch (mitk::Exception& e)
{
this->WaitCursorOff();
MITK_ERROR << "Exception caught: " << e.GetDescription();
QMessageBox::information(m_Parent, "New Segmentation Session", "Could not create a new segmentation session.\n");
return;
}
this->WaitCursorOff();
mitk::DataNode::Pointer workingNode = mitk::DataNode::New();
workingNode->SetData(workingImage);
workingNode->SetName(newName.toStdString());
workingImage->GetExteriorLabel()->SetProperty("name.parent", mitk::StringProperty::New(referenceNode->GetName().c_str()));
workingImage->GetExteriorLabel()->SetProperty("name.image", mitk::StringProperty::New(newName.toStdString().c_str()));
if (!GetDataStorage()->Exists(workingNode))
{
GetDataStorage()->Add(workingNode, referenceNode);
}
m_Controls.m_WorkingNodeSelector->SetCurrentSelectedNode(workingNode);
OnNewLabel();
}
void QmitkMultiLabelSegmentationView::OnGoToLabel(const mitk::Point3D& pos)
{
if (m_IRenderWindowPart)
m_IRenderWindowPart->SetSelectedPosition(pos);
}
void QmitkMultiLabelSegmentationView::OnResetView()
{
if (m_IRenderWindowPart)
m_IRenderWindowPart->ForceImmediateUpdate();
}
void QmitkMultiLabelSegmentationView::OnAddLayer()
{
m_ToolManager->ActivateTool(-1);
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
mitk::LabelSetImage* workingImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
assert(workingImage);
QString question = "Do you really want to add a layer to the current segmentation session?";
QMessageBox::StandardButton answerButton = QMessageBox::question(
m_Controls.m_LabelSetWidget, "Add layer", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes);
if (answerButton != QMessageBox::Yes) return;
try
{
WaitCursorOn();
workingImage->AddLayer();
WaitCursorOff();
}
catch ( mitk::Exception& e )
{
WaitCursorOff();
MITK_ERROR << "Exception caught: " << e.GetDescription();
QMessageBox::information(
m_Controls.m_LabelSetWidget, "Add Layer", "Could not add a new layer. See error log for details.\n");
return;
}
OnNewLabel();
}
void QmitkMultiLabelSegmentationView::OnDeleteLayer()
{
m_ToolManager->ActivateTool(-1);
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
mitk::LabelSetImage* workingImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
assert(workingImage);
if (workingImage->GetNumberOfLayers() < 2)
return;
QString question = "Do you really want to delete the current layer?";
QMessageBox::StandardButton answerButton = QMessageBox::question(
m_Controls.m_LabelSetWidget, "Delete layer", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes);
if (answerButton != QMessageBox::Yes)
{
return;
}
try
{
this->WaitCursorOn();
workingImage->RemoveLayer();
this->WaitCursorOff();
}
catch (mitk::Exception& e)
{
this->WaitCursorOff();
MITK_ERROR << "Exception caught: " << e.GetDescription();
QMessageBox::information(m_Controls.m_LabelSetWidget, "Delete Layer",
"Could not delete the currently active layer. See error log for details.\n");
return;
}
UpdateControls();
m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems();
}
void QmitkMultiLabelSegmentationView::OnPreviousLayer()
{
m_ToolManager->ActivateTool(-1);
mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
mitk::LabelSetImage *workingImage = dynamic_cast<mitk::LabelSetImage *>(workingNode->GetData());
assert(workingImage);
OnChangeLayer(workingImage->GetActiveLayer() - 1);
}
void QmitkMultiLabelSegmentationView::OnNextLayer()
{
m_ToolManager->ActivateTool(-1);
mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
mitk::LabelSetImage *workingImage = dynamic_cast<mitk::LabelSetImage *>(workingNode->GetData());
assert(workingImage);
OnChangeLayer(workingImage->GetActiveLayer() + 1);
}
void QmitkMultiLabelSegmentationView::OnChangeLayer(int layer)
{
m_ToolManager->ActivateTool(-1);
mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
mitk::LabelSetImage *workingImage = dynamic_cast<mitk::LabelSetImage *>(workingNode->GetData());
assert(workingImage);
this->WaitCursorOn();
workingImage->SetActiveLayer(layer);
this->WaitCursorOff();
UpdateControls();
m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems();
}
void QmitkMultiLabelSegmentationView::OnDeactivateActiveTool()
{
m_ToolManager->ActivateTool(-1);
}
void QmitkMultiLabelSegmentationView::OnLockExteriorToggled(bool checked)
{
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
assert(workingNode);
mitk::LabelSetImage* workingImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
assert(workingImage);
workingImage->GetLabel(0)->SetLocked(checked);
}
void QmitkMultiLabelSegmentationView::OnReferenceSelectionChanged(QList<mitk::DataNode::Pointer> /*nodes*/)
{
m_ToolManager->ActivateTool(-1);
auto refNode = m_Controls.m_ReferenceNodeSelector->GetSelectedNode();
m_ReferenceNode = refNode;
m_ToolManager->SetReferenceData(m_ReferenceNode);
if (m_ReferenceNode.IsNotNull())
{
auto segPredicate = mitk::NodePredicateAnd::New(m_SegmentationPredicate.GetPointer(), mitk::NodePredicateSubGeometry::New(refNode->GetData()->GetGeometry()));
m_Controls.m_WorkingNodeSelector->SetNodePredicate(segPredicate);
if (m_AutoSelectionEnabled)
{
// hide all image nodes to later show only the automatically selected ones
mitk::DataStorage::SetOfObjects::ConstPointer patientNodes = GetDataStorage()->GetSubset(m_ReferencePredicate);
for (mitk::DataStorage::SetOfObjects::const_iterator iter = patientNodes->begin(); iter != patientNodes->end(); ++iter)
{
(*iter)->SetVisibility(false);
}
}
m_ReferenceNode->SetVisibility(true);
}
UpdateControls();
}
void QmitkMultiLabelSegmentationView::OnSegmentationSelectionChanged(QList<mitk::DataNode::Pointer> /*nodes*/)
{
m_ToolManager->ActivateTool(-1);
if (m_WorkingNode.IsNotNull())
OnLooseLabelSetConnection();
m_WorkingNode = m_Controls.m_WorkingNodeSelector->GetSelectedNode();
m_ToolManager->SetWorkingData(m_WorkingNode);
if (m_WorkingNode.IsNotNull())
{
OnEstablishLabelSetConnection();
if (m_AutoSelectionEnabled)
{
// hide all segmentation nodes to later show only the automatically selected ones
mitk::DataStorage::SetOfObjects::ConstPointer segmentationNodes = GetDataStorage()->GetSubset(m_SegmentationPredicate);
for (mitk::DataStorage::SetOfObjects::const_iterator iter = segmentationNodes->begin(); iter != segmentationNodes->end(); ++iter)
{
(*iter)->SetVisibility(false);
}
}
m_WorkingNode->SetVisibility(true);
}
UpdateControls();
if (m_WorkingNode.IsNotNull())
{
m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems();
this->ReinitializeViews();
}
}
void QmitkMultiLabelSegmentationView::OnInterpolationSelectionChanged(int index)
{
if (index == 1)
{
m_Controls.m_SurfaceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false);//OnToggleWidgetActivation(false);
m_Controls.m_swInterpolation->setCurrentIndex(0);
m_Controls.m_swInterpolation->show();
}
else if (index == 2)
{
m_Controls.m_SliceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false);
m_Controls.m_swInterpolation->setCurrentIndex(1);
m_Controls.m_swInterpolation->show();
}
else
{
m_Controls.m_SurfaceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false);
m_Controls.m_SliceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false);
m_Controls.m_swInterpolation->setCurrentIndex(2);
m_Controls.m_swInterpolation->hide();
}
}
/************************************************************************/
/* protected */
/************************************************************************/
void QmitkMultiLabelSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs)
{
if (m_Parent && m_WorkingNode.IsNotNull())
{
m_AutoSelectionEnabled = prefs->GetBool("auto selection", false);
mitk::BoolProperty::Pointer drawOutline = mitk::BoolProperty::New(prefs->GetBool("draw outline", true));
mitk::BoolProperty::Pointer volumeRendering = mitk::BoolProperty::New(prefs->GetBool("volume rendering", false));
mitk::LabelSetImage* labelSetImage;
mitk::DataNode* segmentation;
// iterate all segmentations (binary (single label) and LabelSetImages)
mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
mitk::NodePredicateOr::Pointer allSegmentationsPredicate = mitk::NodePredicateOr::New(isBinaryPredicate, m_SegmentationPredicate);
mitk::DataStorage::SetOfObjects::ConstPointer allSegmentations = GetDataStorage()->GetSubset(allSegmentationsPredicate);
for (mitk::DataStorage::SetOfObjects::const_iterator it = allSegmentations->begin(); it != allSegmentations->end(); ++it)
{
segmentation = *it;
labelSetImage = dynamic_cast<mitk::LabelSetImage*>(segmentation->GetData());
if (nullptr != labelSetImage)
{
// segmentation node is a multi label segmentation
segmentation->SetProperty("labelset.contour.active", drawOutline);
//segmentation->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f));
segmentation->SetProperty("volumerendering", volumeRendering);
// force render window update to show outline
segmentation->GetData()->Modified();
}
else if (nullptr != segmentation->GetData())
{
// node is actually a 'single label' segmentation,
// but its outline property can be set in the 'multi label' segmentation preference page as well
bool isBinary = false;
segmentation->GetBoolProperty("binary", isBinary);
if (isBinary)
{
segmentation->SetProperty("outline binary", drawOutline);
segmentation->SetProperty("outline width", mitk::FloatProperty::New(2.0));
//segmentation->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f));
segmentation->SetProperty("volumerendering", volumeRendering);
// force render window update to show outline
segmentation->GetData()->Modified();
}
}
else
{
// "interpolation feedback" data nodes have binary flag but don't have a data set. So skip them for now.
MITK_INFO << "DataNode " << segmentation->GetName() << " doesn't contain a base data.";
}
}
}
}
void QmitkMultiLabelSegmentationView::NodeRemoved(const mitk::DataNode *node)
{
bool isHelperObject(false);
node->GetBoolProperty("helper object", isHelperObject);
if (isHelperObject)
{
return;
}
if (m_ReferenceNode.IsNotNull() && dynamic_cast<mitk::LabelSetImage *>(node->GetData()))
{
// remove all possible contour markers of the segmentation
mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations(
node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true)));
ctkPluginContext *context = mitk::PluginActivator::getContext();
ctkServiceReference ppmRef = context->getServiceReference<mitk::PlanePositionManagerService>();
mitk::PlanePositionManagerService *service = context->getService<mitk::PlanePositionManagerService>(ppmRef);
for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it)
{
std::string nodeName = node->GetName();
unsigned int t = nodeName.find_last_of(" ");
unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1;
service->RemovePlanePosition(id);
this->GetDataStorage()->Remove(it->Value());
}
context->ungetService(ppmRef);
service = nullptr;
}
}
void QmitkMultiLabelSegmentationView::OnEstablishLabelSetConnection()
{
if (m_WorkingNode.IsNull())
{
return;
}
mitk::LabelSetImage *workingImage = dynamic_cast<mitk::LabelSetImage *>(m_WorkingNode->GetData());
assert(workingImage);
workingImage->GetActiveLabelSet()->AddLabelEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->RemoveLabelEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ModifyLabelEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent += mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ActiveLabelEvent +=
mitk::MessageDelegate1<QmitkLabelSetWidget, mitk::Label::PixelType>(m_Controls.m_LabelSetWidget,
&QmitkLabelSetWidget::SelectLabelByPixelValue);
// Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something?
// workingImage->BeforeChangeLayerEvent += mitk::MessageDelegate<QmitkMultiLabelSegmentationView>(
// this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection);
workingImage->AfterChangeLayerEvent += mitk::MessageDelegate<QmitkMultiLabelSegmentationView>(
this, &QmitkMultiLabelSegmentationView::UpdateControls);
}
void QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection()
{
if (m_WorkingNode.IsNull())
return;
auto* workingImage = dynamic_cast<mitk::LabelSetImage *>(m_WorkingNode->GetData());
if (nullptr == workingImage)
return; // data (type) was changed in-place, e.g. LabelSetImage -> Image
// Reset LabelSetWidget Events
workingImage->GetActiveLabelSet()->AddLabelEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ModifyLabelEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent -= mitk::MessageDelegate<QmitkLabelSetWidget>(
m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems);
workingImage->GetActiveLabelSet()->ActiveLabelEvent -=
mitk::MessageDelegate1<QmitkLabelSetWidget, mitk::Label::PixelType>(m_Controls.m_LabelSetWidget,
&QmitkLabelSetWidget::SelectLabelByPixelValue);
// Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something?
// workingImage->BeforeChangeLayerEvent -= mitk::MessageDelegate<QmitkMultiLabelSegmentationView>(
// this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection);
workingImage->AfterChangeLayerEvent -= mitk::MessageDelegate<QmitkMultiLabelSegmentationView>(
this, &QmitkMultiLabelSegmentationView::UpdateControls);
}
void QmitkMultiLabelSegmentationView::SetFocus()
{
}
void QmitkMultiLabelSegmentationView::UpdateControls()
{
mitk::DataNode* referenceNode = m_ToolManager->GetReferenceData(0);
bool hasReferenceNode = referenceNode != nullptr;
mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0);
bool hasValidWorkingNode = workingNode != nullptr;
m_Controls.m_pbNewLabel->setEnabled(false);
m_Controls.m_gbInterpolation->setEnabled(false);
m_Controls.m_SliceBasedInterpolatorWidget->setEnabled(false);
m_Controls.m_SurfaceBasedInterpolatorWidget->setEnabled(false);
m_Controls.m_LabelSetWidget->setEnabled(false);
m_Controls.m_btAddLayer->setEnabled(false);
m_Controls.m_btDeleteLayer->setEnabled(false);
m_Controls.m_cbActiveLayer->setEnabled(false);
m_Controls.m_btPreviousLayer->setEnabled(false);
m_Controls.m_btNextLayer->setEnabled(false);
m_Controls.m_btLockExterior->setChecked(false);
m_Controls.m_btLockExterior->setEnabled(false);
m_Controls.m_tbSavePreset->setEnabled(false);
m_Controls.m_tbLoadPreset->setEnabled(false);
m_Controls.m_pbShowLabelTable->setChecked(false);
m_Controls.m_pbShowLabelTable->setEnabled(false);
m_Controls.m_ManualToolSelectionBox3D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible);
m_Controls.m_ManualToolSelectionBox2D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible);
if (hasValidWorkingNode)
{
// TODO adapt tool manager so that this check is done there, e.g. convenience function
mitk::LabelSetImage* workingImage = dynamic_cast<mitk::LabelSetImage*>(workingNode->GetData());
hasValidWorkingNode = workingImage != nullptr;
if (hasValidWorkingNode)
{
m_Controls.m_pbNewLabel->setEnabled(true);
m_Controls.m_btLockExterior->setEnabled(true);
m_Controls.m_tbSavePreset->setEnabled(true);
m_Controls.m_tbLoadPreset->setEnabled(true);
m_Controls.m_pbShowLabelTable->setEnabled(true);
m_Controls.m_gbInterpolation->setEnabled(true);
m_Controls.m_SliceBasedInterpolatorWidget->setEnabled(true);
m_Controls.m_SurfaceBasedInterpolatorWidget->setEnabled(true);
m_Controls.m_LabelSetWidget->setEnabled(true);
m_Controls.m_btAddLayer->setEnabled(true);
int activeLayer = workingImage->GetActiveLayer();
int numberOfLayers = workingImage->GetNumberOfLayers();
m_Controls.m_cbActiveLayer->blockSignals(true);
m_Controls.m_cbActiveLayer->clear();
for (unsigned int lidx = 0; lidx < workingImage->GetNumberOfLayers(); ++lidx)
{
m_Controls.m_cbActiveLayer->addItem(QString::number(lidx));
}
m_Controls.m_cbActiveLayer->setCurrentIndex(activeLayer);
m_Controls.m_cbActiveLayer->blockSignals(false);
m_Controls.m_cbActiveLayer->setEnabled(numberOfLayers > 1);
m_Controls.m_btDeleteLayer->setEnabled(numberOfLayers > 1);
m_Controls.m_btPreviousLayer->setEnabled(activeLayer > 0);
m_Controls.m_btNextLayer->setEnabled(activeLayer != numberOfLayers - 1);
m_Controls.m_btLockExterior->setChecked(workingImage->GetLabel(0, activeLayer)->GetLocked());
m_Controls.m_pbShowLabelTable->setChecked(workingImage->GetNumberOfLabels() > 1 /*1st is exterior*/);
//MLI TODO
//m_Controls.m_ManualToolSelectionBox2D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithWorkingDataVisible);
}
}
if (hasValidWorkingNode && hasReferenceNode)
{
int layer = -1;
referenceNode->GetIntProperty("layer", layer);
workingNode->SetIntProperty("layer", layer + 1);
}
this->RequestRenderWindowUpdate(mitk::RenderingManager::REQUEST_UPDATE_ALL);
}
void QmitkMultiLabelSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart)
{
if (m_IRenderWindowPart != renderWindowPart)
{
m_IRenderWindowPart = renderWindowPart;
m_Parent->setEnabled(true);
QList<mitk::SliceNavigationController*> controllers;
controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController());
controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController());
controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController());
m_Controls.m_SliceBasedInterpolatorWidget->SetSliceNavigationControllers(controllers);
}
}
void QmitkMultiLabelSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/)
{
m_ToolManager->ActivateTool(-1);
m_IRenderWindowPart = nullptr;
m_Parent->setEnabled(false);
}
void QmitkMultiLabelSegmentationView::ResetMouseCursor()
{
if (m_MouseCursorSet)
{
mitk::ApplicationCursor::GetInstance()->PopCursor();
m_MouseCursorSet = false;
}
}
void QmitkMultiLabelSegmentationView::SetMouseCursor(const us::ModuleResource resource, int hotspotX, int hotspotY)
{
// Remove previously set mouse cursor
if (m_MouseCursorSet)
this->ResetMouseCursor();
if (resource)
{
us::ModuleResourceStream cursor(resource, std::ios::binary);
mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY);
m_MouseCursorSet = true;
}
}
void QmitkMultiLabelSegmentationView::InitializeListeners()
{
if (m_Interactor.IsNull())
{
us::Module* module = us::GetModuleContext()->GetModule();
std::vector<us::ModuleResource> resources = module->FindResources("/", "*", true);
for (std::vector<us::ModuleResource>::iterator iter = resources.begin(); iter != resources.end(); ++iter)
{
MITK_INFO << iter->GetResourcePath();
}
m_Interactor = mitk::SegmentationInteractor::New();
if (!m_Interactor->LoadStateMachine("SegmentationInteraction.xml", module))
{
MITK_WARN << "Error loading state machine";
}
if (!m_Interactor->SetEventConfig("ConfigSegmentation.xml", module))
{
MITK_WARN << "Error loading state machine configuration";
}
// Register as listener via micro services
us::ServiceProperties props;
props["name"] = std::string("SegmentationInteraction");
m_ServiceRegistration =
us::GetModuleContext()->RegisterService<mitk::InteractionEventObserver>(m_Interactor.GetPointer(), props);
}
}
void QmitkMultiLabelSegmentationView::ReinitializeViews() const
{
if (m_ReferenceNode.IsNotNull() && nullptr != m_ReferenceNode->GetData())
{
const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
unsigned int imageTimeStep = 0;
if (m_ReferenceNode->GetData()->GetTimeGeometry()->IsValidTimePoint(currentTimePoint))
{
imageTimeStep = m_ReferenceNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint);
}
mitk::RenderingManager::GetInstance()->InitializeViews(m_ReferenceNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true);
mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->SetPos(imageTimeStep);
}
}
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/CMakeLists.txt b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/CMakeLists.txt
index 840fc6a0da..a66107ab60 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.concentration.mri/CMakeLists.txt
@@ -1,9 +1,7 @@
project(org_mitk_gui_qt_pharmacokinetics_concentration_mri)
mitk_create_plugin(
- EXPORT_DIRECTIVE CONCENTRATIONCURVECONVERTER_EXPORT
+ EXPORT_DIRECTIVE CONCENTRATIONCURVECONVERTER_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt MitkPharmacokinetics
- PACKAGE_DEPENDS ITK|ITKOptimizers
-
+ MODULE_DEPENDS MitkQtWidgetsExt MitkPharmacokinetics
)
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/CMakeLists.txt b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/CMakeLists.txt
index b0d7d47b86..7b5a25be6e 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/CMakeLists.txt
@@ -1,9 +1,7 @@
project(org_mitk_gui_qt_pharmacokinetics_mri)
mitk_create_plugin(
EXPORT_DIRECTIVE MRPERFUSION_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgetsExt MitkPharmacokinetics MitkModelFitUI
- PACKAGE_DEPENDS
- PRIVATE Boost
)
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/CMakeLists.txt b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/CMakeLists.txt
index 945352fc13..36631e1ce9 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/CMakeLists.txt
@@ -1,9 +1,7 @@
project(org_mitk_gui_qt_pharmacokinetics_simulation)
mitk_create_plugin(
EXPORT_DIRECTIVE PERFUSIONDATASIMULATION_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgetsExt MitkPharmacokinetics
- PACKAGE_DEPENDS
- PRIVATE Boost
)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/CMakeLists.txt
deleted file mode 100644
index 0b44d554e6..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-project(org_mitk_gui_qt_photoacoustics_imageprocessing)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE IMAGEPROCESSING_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt MitkPhotoacousticsAlgorithms
-)
-
-IF(MITK_USE_OpenCL)
- add_definitions(-DPHOTOACOUSTICS_USE_GPU)
-ENDIF(MITK_USE_OpenCL)
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox
deleted file mode 100644
index 4add60b8c5..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/Manual.dox
+++ /dev/null
@@ -1,66 +0,0 @@
-/**
-\page org_mitk_views_photoacoustics_imageprocessing The Photoacoustics Imageprocessing Plugin
-
-\imageMacro{pai-dox.png,"Icon of Imageprocessing",2.00}
-
-\tableofcontents
-
-\section org_mitk_gui_qt_photoacoustics_imageprocessingOverview Overview
-This plugin offers an interface to perform image processing on photoacoustic, as well as ultrasound images, i.e. to use beamforming and post-processing filters.
-For convenience, image processing can be done automatically for a whole batch of files containing PA or US data.
-
-\section org_mitk_gui_qt_photoacoustics_imageprocessingPrerequisites Prerequisites
-To use the much more performant openCL filters which run on the graphics card, MITK has to be able to use openCL, for which it is necessary to install the openCL implementation provided by your graphics card vendor.
-
-\section org_mitk_gui_qt_photoacoustics_imageprocessingFiltering Using the filters
-To perform image processing, simply load an image into MITK and select it in the Data manager. Only the selected image will be processed by the filters.
-\imageMacro{QmikPhotoacousticsImageProcessing_DataManager.png,"Select the image to be processed",7.62}
-Before performing reconstruction or using other filters those can be configured using the plugin's settings panel.
-\imageMacro{QmikPhotoacousticsImageProcessing_Settings.png,"The plugin's GUI",7.62}
-
-\subsection org_mitk_gui_qt_photoacoustics_imageprocessingImageDetails Image Details
-To create the .nrrd images necessary for the plugin from raw data, one can use e.g. <a href="https://github.com/mhe/pynrrd">pynrrd</a>, a python package for very straightforward creation of .nrrd images.
-The Beamforming Filter is also able to read certain paramters, as the scan depth and the transducer pitch from the selected image. To this end, the image must have a time-axis spacing in µs and a horizontal spacing in mm.
-
-\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBeamforming The Beamforming Settings
-For beamforming, three beamforming algorithms are available:
-<ul>
-<li>DAS (Delay And Sum)
-<li>DMAS (Delay Multiply And Sum)
-<li>sDMAS (signed Delay Multiply And Sum)
-</ul>
-Each of those can be coupled with either spherical delay calculation or a quadratic approximation for the delays. To supress noise, one of the following apodizations can be chosen to be used when beamforming:
-<ul>
-<li>Box (No apodization)
-<li>Hamming
-<li>Von Hann
-</ul>
-Other Standard beamforming parameters are available, which have to be chosen depending on the source image to attain a correctly reconstructed image.
-As mentioned above, Plugin is able to calculate the used scan depth as well as the transducer pitch from the selected image if the time-axis spacing is in microseconds, and the horizontal spacing in mm. If such a spacing is given,
-check the box "Auto Get Depth" to make the plugin read those values by itself.
-If the US source or the laser used for imaging is not located at the top of the image, an option is given to cut off pixels at the top of the image until the source. This value should be calibrated by the user
-to match the used hardware.
-If one wishes to beamform only certain slices of a given image, those can be selected by checking "select slices" and setting the "min" and "max" values accordingly, which are to be understood as closed interval boundaries.
-
-\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBandpass The Bandpass Settings
-The bandpass uses an itk implementation of an 1D Fast Fourier Transform (FFT) to transform the image vertically, then filters the image using a Tukey window in the frequency domain and performs an inverse 1D FFT to get the filtered image.
-The "smoothness" of the tukey window can be chosen by using the "Tukey window alpha" parameter. The Tukey window interpolates between a Box window (alpha = 0) and a Von Hann window (alpha = 1).
-The filtered frequencies can be set by defining the High and Low pass frequencies.
-
-\subsection org_mitk_gui_qt_photoacoustics_imageprocessingCrop The Crop Filter Settings
-The crop filter cuts off parts of the image at the top and the bottom. The amount of pixels cut off can be configured using the "Cut Top" and "Cut Bottom" parameters.
-
-\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBMode The BMode Filter Settings
-The B-mode filters available are:
-<ul>
-<li>An absolute filter
-<li>An envelope detection filter
-</ul>
-If desired, the filter can also resample the image to a given spacing; to do this, check the "Do Resampling" box and set the desired spacing in mm.
-Afterwards a logarithmic filter can be applied, if "Add Logfilter" is checked.
-
-\subsection org_mitk_gui_qt_photoacoustics_imageprocessingBatch Batch Processing
-When processing large amounts of data, an option is available to automatically process multiple images by applying all filters in order to those images and saving the resulting images.
-In the first row of the Batch Processing Panel one can select which filters should be applied to the image; in the second row one can select whether the resulting image from the filter should be saved.
-After pressing the "Start Batch Processing" button, one can choose first the images to be processed, and then the folder where they will be saved.
-*/
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_DataManager.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_DataManager.png
deleted file mode 100644
index 29b7b0e002..0000000000
Binary files a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_DataManager.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_Settings.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_Settings.png
deleted file mode 100644
index f8210298cf..0000000000
Binary files a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/QmikPhotoacousticsImageProcessing_Settings.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai-dox.png b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai-dox.png
deleted file mode 100644
index 1b8dc34c11..0000000000
Binary files a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/UserManual/pai-dox.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/doxygen/modules.dox
deleted file mode 100644
index 5bd6326234..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/documentation/doxygen/modules.dox
+++ /dev/null
@@ -1,16 +0,0 @@
-/**
- \defgroup org_mitk_gui_qt_photoacoustics_imageprocessing org.mitk.gui.qt.photoacoustics.imageprocessing
- \ingroup MITKPlugins
-
- \brief Describe your plugin here.
-
-*/
-
-/**
- \defgroup org_mitk_gui_qt_photoacoustics_imageprocessing_internal Internal
- \ingroup org_mitk_gui_qt_photoacoustics_imageprocessing
-
- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.photoacoustics.imageprocessing plugin. Other
- plugins must not rely on these classes. They contain implementation details and their interface
- may change at any time. We mean it.
-*/
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/files.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/files.cmake
deleted file mode 100644
index 4b9c855389..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/files.cmake
+++ /dev/null
@@ -1,36 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.cpp
- PAImageProcessing.cpp
-)
-
-set(UI_FILES
- src/internal/PAImageProcessingControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.h
- src/internal/PAImageProcessing.h
-)
-
-set(CACHED_RESOURCE_FILES
- resources/pai.svg
- plugin.xml
-)
-
-set(QRC_FILES
-
-)
-
-set(CPP_FILES )
-
-foreach(file ${SRC_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/${file})
-endforeach(file ${SRC_CPP_FILES})
-
-foreach(file ${INTERNAL_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/internal/${file})
-endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/manifest_headers.cmake
deleted file mode 100644
index 948e85963d..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Imageprocessing")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "DKFZ")
-set(Plugin-ContactAddress "")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/plugin.xml b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/plugin.xml
deleted file mode 100644
index 1ef31f0130..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/plugin.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.paimageprocessing"
- name="PA Image Processing"
- category="Photoacoustics"
- class="PAImageProcessing"
- icon="resources/pai.svg" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.svg b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.svg
deleted file mode 100644
index 8002f7c6ec..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/resources/pai.svg
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<svg
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://creativecommons.org/ns#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:svg="http://www.w3.org/2000/svg"
- xmlns="http://www.w3.org/2000/svg"
- xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
- xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- xml:space="preserve"
- enable-background="new 0 0 1792 1792"
- viewBox="0 0 1792 1792"
- height="128"
- width="128"
- y="0px"
- x="0px"
- id="Layer_1"
- version="1.1"
- inkscape:version="0.91 r13725"
- sodipodi:docname="pai.svg"><sodipodi:namedview
- pagecolor="#ffffff"
- bordercolor="#666666"
- borderopacity="1"
- objecttolerance="10"
- gridtolerance="10"
- guidetolerance="10"
- inkscape:pageopacity="0"
- inkscape:pageshadow="2"
- inkscape:window-width="686"
- inkscape:window-height="480"
- id="namedview7"
- showgrid="false"
- inkscape:zoom="0.13169643"
- inkscape:cx="896"
- inkscape:cy="896"
- inkscape:window-x="0"
- inkscape:window-y="0"
- inkscape:window-maximized="0"
- inkscape:current-layer="Layer_1" /><metadata
- id="metadata11"><rdf:RDF><cc:Work
- rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
- rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title /></cc:Work></rdf:RDF></metadata><defs
- id="defs9" /><path
- id="path3"
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diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp
deleted file mode 100644
index 7285a94907..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.cpp
+++ /dev/null
@@ -1,1142 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// Qmitk
-#include "PAImageProcessing.h"
-
-// Qt
-#include <QMessageBox>
-#include <QApplication>
-#include <QMetaType>
-#include <QFileDialog>
-
-//mitk image
-#include <mitkImage.h>
-#include "mitkPhotoacousticFilterService.h"
-#include "mitkCastToFloatImageFilter.h"
-#include "mitkBeamformingFilter.h"
-
-//other
-#include <thread>
-#include <functional>
-#include <mitkIOUtil.h>
-
-#define GPU_BATCH_SIZE 32
-
-const std::string PAImageProcessing::VIEW_ID = "org.mitk.views.paimageprocessing";
-
-PAImageProcessing::PAImageProcessing() : m_ResampleSpacing(0), m_UseLogfilter(false), m_FilterBank(mitk::PhotoacousticFilterService::New())
-{
- qRegisterMetaType<mitk::Image::Pointer>();
- qRegisterMetaType<std::string>();
-}
-
-void PAImageProcessing::SetFocus()
-{
- m_Controls.buttonApplyBModeFilter->setFocus();
-}
-
-void PAImageProcessing::CreateQtPartControl(QWidget *parent)
-{
- // create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi(parent);
- connect(m_Controls.buttonApplyBModeFilter, SIGNAL(clicked()), this, SLOT(StartBmodeThread()));
- connect(m_Controls.Geometry, SIGNAL(currentIndexChanged(int)), this, SLOT(ChangedProbe()));
- connect(m_Controls.DoResampling, SIGNAL(clicked()), this, SLOT(UseResampling()));
- connect(m_Controls.Logfilter, SIGNAL(clicked()), this, SLOT(UseLogfilter()));
- connect(m_Controls.ResamplingValue, SIGNAL(valueChanged(double)), this, SLOT(SetResampling()));
- connect(m_Controls.buttonApplyBeamforming, SIGNAL(clicked()), this, SLOT(StartBeamformingThread()));
- connect(m_Controls.buttonApplyCropFilter, SIGNAL(clicked()), this, SLOT(StartCropThread()));
- connect(m_Controls.buttonApplyBandpass, SIGNAL(clicked()), this, SLOT(StartBandpassThread()));
- connect(m_Controls.UseImageSpacing, SIGNAL(clicked()), this, SLOT(UseImageSpacing()));
- connect(m_Controls.ScanDepth, SIGNAL(valueChanged(double)), this, SLOT(UpdateImageInfo()));
- connect(m_Controls.SpeedOfSound, SIGNAL(valueChanged(double)), this, SLOT(UpdateImageInfo()));
- connect(m_Controls.SpeedOfSound, SIGNAL(valueChanged(double)), this, SLOT(ChangedSOSBeamforming()));
- connect(m_Controls.BPSpeedOfSound, SIGNAL(valueChanged(double)), this, SLOT(ChangedSOSBandpass()));
- connect(m_Controls.Samples, SIGNAL(valueChanged(int)), this, SLOT(UpdateImageInfo()));
- connect(m_Controls.UseImageSpacing, SIGNAL(clicked()), this, SLOT(UpdateImageInfo()));
- connect(m_Controls.boundLow, SIGNAL(valueChanged(int)), this, SLOT(LowerSliceBoundChanged()));
- connect(m_Controls.boundHigh, SIGNAL(valueChanged(int)), this, SLOT(UpperSliceBoundChanged()));
- connect(m_Controls.Partial, SIGNAL(clicked()), this, SLOT(SliceBoundsEnabled()));
- connect(m_Controls.BatchProcessing, SIGNAL(clicked()), this, SLOT(BatchProcessing()));
- connect(m_Controls.StepBeamforming, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes()));
- connect(m_Controls.StepCropping, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes()));
- connect(m_Controls.StepBandpass, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes()));
- connect(m_Controls.StepBMode, SIGNAL(clicked()), this, SLOT(UpdateSaveBoxes()));
- connect(m_Controls.UseSignalDelay, SIGNAL(clicked()), this, SLOT(UseSignalDelay()));
- connect(m_Controls.IsBFImage, SIGNAL(clicked()), this, SLOT(UpdateImageInfo()));
- UpdateSaveBoxes();
- UseSignalDelay();
- m_Controls.ResamplingValue->setEnabled(false);
- m_Controls.progressBar->setMinimum(0);
- m_Controls.progressBar->setMaximum(100);
- m_Controls.progressBar->setVisible(false);
- m_Controls.UseImageSpacing->setToolTip("Image spacing of y-Axis must be in us, x-Axis in mm.");
- m_Controls.UseImageSpacing->setToolTipDuration(5000);
- m_Controls.ProgressInfo->setVisible(false);
- m_Controls.UseGPUBmode->hide();
-
-#ifndef PHOTOACOUSTICS_USE_GPU
- m_Controls.UseGPUBf->setEnabled(false);
- m_Controls.UseGPUBf->setChecked(false);
- m_Controls.UseGPUBmode->setEnabled(false);
- m_Controls.UseGPUBmode->setChecked(false);
-#endif
-
- UseImageSpacing();
- ChangedProbe();
-}
-
-void PAImageProcessing::ChangedProbe()
-{
- if (m_Controls.Geometry->currentText() == "Concave")
- {
- m_Controls.ProbeRadius->setEnabled(true);
- }
- else
- {
- m_Controls.ProbeRadius->setEnabled(false);
- }
-}
-
-void PAImageProcessing::UseSignalDelay()
-{
- if (m_Controls.UseSignalDelay->isChecked())
- {
- m_Controls.SignalDelay->setEnabled(true);
- }
- else
- {
- m_Controls.SignalDelay->setEnabled(false);
- }
-}
-
-void PAImageProcessing::ChangedSOSBandpass()
-{
- m_Controls.SpeedOfSound->setValue(m_Controls.BPSpeedOfSound->value());
-}
-
-void PAImageProcessing::ChangedSOSBeamforming()
-{
- m_Controls.BPSpeedOfSound->setValue(m_Controls.SpeedOfSound->value());
-}
-
-std::vector<std::string> splitpath(
- const std::string& str
- , const std::set<char> delimiters)
-{
- std::vector<std::string> result;
-
- char const* pch = str.c_str();
- char const* start = pch;
- for (; *pch; ++pch)
- {
- if (delimiters.find(*pch) != delimiters.end())
- {
- if (start != pch)
- {
- std::string str(start, pch);
- result.push_back(str);
- }
- else
- {
- result.push_back("");
- }
- start = pch + 1;
- }
- }
- result.push_back(start);
-
- return result;
-}
-
-void PAImageProcessing::UpdateSaveBoxes()
-{
- if (m_Controls.StepBeamforming->isChecked())
- m_Controls.SaveBeamforming->setEnabled(true);
- else
- m_Controls.SaveBeamforming->setEnabled(false);
-
- if (m_Controls.StepCropping->isChecked())
- m_Controls.SaveCropping->setEnabled(true);
- else
- m_Controls.SaveCropping->setEnabled(false);
-
- if (m_Controls.StepBandpass->isChecked())
- m_Controls.SaveBandpass->setEnabled(true);
- else
- m_Controls.SaveBandpass->setEnabled(false);
-
- if (m_Controls.StepBMode->isChecked())
- m_Controls.SaveBMode->setEnabled(true);
- else
- m_Controls.SaveBMode->setEnabled(false);
-}
-
-void PAImageProcessing::BatchProcessing()
-{
- QFileDialog LoadDialog(nullptr, "Select Files to be processed");
- LoadDialog.setFileMode(QFileDialog::FileMode::ExistingFiles);
- LoadDialog.setNameFilter(tr("Images (*.nrrd)"));
- LoadDialog.setViewMode(QFileDialog::Detail);
-
- QStringList fileNames;
- if (LoadDialog.exec())
- fileNames = LoadDialog.selectedFiles();
-
- QString saveDir = QFileDialog::getExistingDirectory(nullptr, tr("Select Directory To Save To"),
- "",
- QFileDialog::ShowDirsOnly
- | QFileDialog::DontResolveSymlinks);
-
- DisableControls();
-
- std::set<char> delims{ '/' };
-
- bool doSteps[] = { m_Controls.StepBeamforming->isChecked(), m_Controls.StepCropping->isChecked() , m_Controls.StepBandpass->isChecked(), m_Controls.StepBMode->isChecked() };
- bool saveSteps[] = { m_Controls.SaveBeamforming->isChecked(), m_Controls.SaveCropping->isChecked() , m_Controls.SaveBandpass->isChecked(), m_Controls.SaveBMode->isChecked() };
-
- for (int fileNumber = 0; fileNumber < fileNames.size(); ++fileNumber)
- {
- m_Controls.progressBar->setValue(0);
- m_Controls.progressBar->setVisible(true);
- m_Controls.ProgressInfo->setVisible(true);
- m_Controls.ProgressInfo->setText("loading file");
-
- QString filename = fileNames.at(fileNumber);
- auto split = splitpath(filename.toStdString(), delims);
- std::string imageName = split.at(split.size() - 1);
-
- // remove ".nrrd"
- imageName = imageName.substr(0, imageName.size() - 5);
-
- mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(filename.toStdString().c_str());
- auto BFconfig = CreateBeamformingSettings(image);
-
- // Beamforming
- if (doSteps[0])
- {
- if (m_Controls.UseSignalDelay->isChecked())
- {
- float signalDelay = m_Controls.SignalDelay->value();
- if (signalDelay != 0)
- {
- int cropPixels = std::round(signalDelay / BFconfig->GetTimeSpacing() / 1000000);
- MITK_INFO << cropPixels;
- int errCode = 0;
- image = m_FilterBank->ApplyCropping(image, cropPixels, 0, 0, 0, 0, 0, &errCode);
-
- if (errCode == -1)
- {
- QMessageBox Msgbox;
- Msgbox.setText("It has been attempted to cut off more pixels than the image contains. Aborting batch processing.");
- Msgbox.exec();
- m_Controls.progressBar->setVisible(false);
- EnableControls();
- return;
- }
-
- BFconfig = mitk::BeamformingSettings::New(BFconfig->GetPitchInMeters(), BFconfig->GetSpeedOfSound(),
- BFconfig->GetTimeSpacing(), BFconfig->GetAngle(), BFconfig->GetIsPhotoacousticImage(), BFconfig->GetSamplesPerLine(),
- BFconfig->GetReconstructionLines(), image->GetDimensions(), BFconfig->GetReconstructionDepth(),
- BFconfig->GetUseGPU(), BFconfig->GetGPUBatchSize(), BFconfig->GetApod(),
- BFconfig->GetApodizationArraySize(), BFconfig->GetAlgorithm(), BFconfig->GetGeometry(), BFconfig->GetProbeRadius());
- }
- }
-
- std::function<void(int, std::string)> progressHandle = [this](int progress, std::string progressInfo) {
- this->UpdateProgress(progress, progressInfo);
- };
- m_Controls.progressBar->setValue(100);
-
- image = m_FilterBank->ApplyBeamforming(image, BFconfig, progressHandle);
-
- if (saveSteps[0])
- {
- std::string saveFileName = saveDir.toStdString() + "/" + imageName + " beamformed" + ".nrrd";
- mitk::IOUtil::Save(image, saveFileName);
- }
- }
-
- // Cropping
- if (doSteps[1])
- {
- m_Controls.ProgressInfo->setText("cropping image");
-
- int errCode = 0;
- image = m_FilterBank->ApplyCropping(image, m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), m_Controls.CutoffRight->value(), m_Controls.CutoffLeft->value(), 0, 0, &errCode);
-
- if (errCode == -1)
- {
- QMessageBox Msgbox;
- Msgbox.setText("It has been attempted to cut off more pixels than the image contains. Aborting batch processing.");
- Msgbox.exec();
- m_Controls.progressBar->setVisible(false);
- EnableControls();
- return;
- }
-
- if (saveSteps[1])
- {
- std::string saveFileName = saveDir.toStdString() + "/" + imageName + " cropped" + ".nrrd";
- mitk::IOUtil::Save(image, saveFileName);
- }
- }
-
- // Bandpass
- if (doSteps[2])
- {
- m_Controls.ProgressInfo->setText("applying bandpass");
- float recordTime = image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] / 1000 / m_Controls.BPSpeedOfSound->value();
- // add a safeguard so the program does not chrash when applying a Bandpass that reaches out of the bounds of the image
- float maxFrequency = 1 / (recordTime / image->GetDimension(1)) * image->GetDimension(1) / 2 / 2 / 1000;
- float BPHighPass = 1000000 * m_Controls.BPhigh->value(); // [Hz]
- float BPLowPass = maxFrequency - 1000000 * m_Controls.BPlow->value(); // [Hz]
-
- if (BPLowPass > maxFrequency)
- {
- QMessageBox Msgbox;
- Msgbox.setText("LowPass too low, disabled it.");
- Msgbox.exec();
-
- BPLowPass = 0;
- }
- if (BPLowPass < 0)
- {
- QMessageBox Msgbox;
- Msgbox.setText("LowPass too high, disabled it.");
- Msgbox.exec();
-
- BPLowPass = 0;
- }
- if (BPHighPass > maxFrequency)
- {
- QMessageBox Msgbox;
- Msgbox.setText("HighPass too high, disabled it.");
- Msgbox.exec();
-
- BPHighPass = 0;
- }
- if (BPHighPass > maxFrequency - BPLowPass)
- {
- QMessageBox Msgbox;
- Msgbox.setText("HighPass higher than LowPass, disabled both.");
- Msgbox.exec();
-
- BPHighPass = 0;
- BPLowPass = 0;
- }
-
- image = m_FilterBank->ApplyBandpassFilter(image, BPHighPass, BPLowPass,
- m_Controls.BPFalloffHigh->value(),
- m_Controls.BPFalloffLow->value(),
- BFconfig->GetTimeSpacing(),
- BFconfig->GetSpeedOfSound(),
- m_Controls.IsBFImage->isChecked());
-
- if (saveSteps[2])
- {
- std::string saveFileName = saveDir.toStdString() + "/" + imageName + " bandpassed" + ".nrrd";
- mitk::IOUtil::Save(image, saveFileName);
- }
- }
- // Bmode
- if (doSteps[3])
- {
- m_Controls.ProgressInfo->setText("applying bmode filter");
-
- if (m_Controls.BModeMethod->currentText() == "Absolute Filter")
- image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticFilterService::BModeMethod::Abs, m_UseLogfilter);
- else if (m_Controls.BModeMethod->currentText() == "Envelope Detection")
- image = m_FilterBank->ApplyBmodeFilter(image, mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection, m_UseLogfilter);
-
- if (m_ResampleSpacing != 0)
- {
- double desiredSpacing[2]{ image->GetGeometry()->GetSpacing()[0], m_ResampleSpacing };
-
- image = m_FilterBank->ApplyResampling(image, desiredSpacing);
- }
-
- if (saveSteps[3])
- {
- std::string saveFileName = saveDir.toStdString() + "/" + imageName + " bmode" + ".nrrd";
- mitk::IOUtil::Save(image, saveFileName);
- }
- }
- m_Controls.progressBar->setVisible(false);
- }
-
- EnableControls();
-}
-
-void PAImageProcessing::StartBeamformingThread()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- if (nodes.empty()) return;
-
- mitk::DataStorage::Pointer storage = this->GetDataStorage();
-
- mitk::DataNode::Pointer node = nodes.front();
-
- if (!node)
- {
- // Nothing selected. Inform the user and return
- QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image processing.");
- return;
- }
-
- mitk::BaseData* data = node->GetData();
- if (data)
- {
- // test if this data item is an image or not (could also be a surface or something totally different)
- mitk::Image* image = dynamic_cast<mitk::Image*>(data);
- if (image)
- {
- auto BFconfig = CreateBeamformingSettings(image);
- std::stringstream message;
- std::string name;
- message << "Performing beamforming for image ";
- if (node->GetName(name))
- {
- // a property called "name" was found for this DataNode
- message << "'" << name << "'";
- m_OldNodeName = name;
- }
- else
- m_OldNodeName = " ";
-
- message << ".";
- MITK_INFO << message.str();
-
- m_Controls.progressBar->setValue(0);
- m_Controls.progressBar->setVisible(true);
- m_Controls.ProgressInfo->setVisible(true);
- m_Controls.ProgressInfo->setText("started");
- DisableControls();
-
- BeamformingThread *thread = new BeamformingThread();
- connect(thread, &BeamformingThread::result, this, &PAImageProcessing::HandleResults);
- connect(thread, &BeamformingThread::updateProgress, this, &PAImageProcessing::UpdateProgress);
- connect(thread, &BeamformingThread::finished, thread, &QObject::deleteLater);
-
- thread->setConfig(BFconfig);
-
- if (m_Controls.UseSignalDelay->isChecked())
- thread->setSignalDelay(m_Controls.SignalDelay->value());
-
- thread->setInputImage(image);
- thread->setFilterBank(m_FilterBank);
-
- MITK_INFO << "Started new thread for Beamforming";
- thread->start();
- }
- }
-}
-
-void PAImageProcessing::HandleResults(mitk::Image::Pointer image, std::string nameExtension)
-{
- if (image == nullptr)
- {
- QMessageBox Msgbox;
- Msgbox.setText("An error has occurred during processing; please see the console output.");
- Msgbox.exec();
-
- // disable progress bar
- m_Controls.progressBar->setVisible(false);
- m_Controls.ProgressInfo->setVisible(false);
- EnableControls();
-
- return;
- }
- MITK_INFO << "Handling results...";
- auto newNode = mitk::DataNode::New();
- newNode->SetData(image);
-
- newNode->SetName(m_OldNodeName + nameExtension);
-
- // update level window for the current dynamic range
- mitk::LevelWindow levelWindow;
- newNode->GetLevelWindow(levelWindow);
- levelWindow.SetAuto(image, true, true);
- newNode->SetLevelWindow(levelWindow);
-
- // add new node to data storage
- this->GetDataStorage()->Add(newNode);
-
- // disable progress bar
- m_Controls.progressBar->setVisible(false);
- m_Controls.ProgressInfo->setVisible(false);
- EnableControls();
-
- // update rendering
- mitk::RenderingManager::GetInstance()->InitializeViews(image->GetGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true);
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
- MITK_INFO << "Handling results...[Done]";
-}
-
-void PAImageProcessing::StartBmodeThread()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- if (nodes.empty()) return;
-
- mitk::DataStorage::Pointer storage = this->GetDataStorage();
-
- mitk::DataNode::Pointer node = nodes.front();
-
- if (!node)
- {
- // Nothing selected. Inform the user and return
- QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image processing.");
- return;
- }
-
- mitk::BaseData* data = node->GetData();
- if (data)
- {
- // test if this data item is an image or not (could also be a surface or something totally different)
- mitk::Image* image = dynamic_cast<mitk::Image*>(data);
- if (image)
- {
- std::stringstream message;
- std::string name;
- message << "Performing image processing for image ";
- if (node->GetName(name))
- {
- // a property called "name" was found for this DataNode
- message << "'" << name << "'";
- m_OldNodeName = name;
- }
- else
- m_OldNodeName = " ";
-
- message << ".";
- MITK_INFO << message.str();
-
- DisableControls();
-
- BmodeThread *thread = new BmodeThread();
- connect(thread, &BmodeThread::result, this, &PAImageProcessing::HandleResults);
- connect(thread, &BmodeThread::finished, thread, &QObject::deleteLater);
-
- bool useGPU = m_Controls.UseGPUBmode->isChecked();
-
- if (m_Controls.BModeMethod->currentText() == "Absolute Filter")
- thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticFilterService::BModeMethod::Abs, useGPU);
- else if (m_Controls.BModeMethod->currentText() == "Envelope Detection")
- thread->setConfig(m_UseLogfilter, m_ResampleSpacing, mitk::PhotoacousticFilterService::BModeMethod::EnvelopeDetection, useGPU);
- thread->setInputImage(image);
- thread->setFilterBank(m_FilterBank);
-
- MITK_INFO << "Started new thread for Image Processing";
- thread->start();
- }
- }
-}
-
-void PAImageProcessing::StartCropThread()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- if (nodes.empty()) return;
-
- mitk::DataStorage::Pointer storage = this->GetDataStorage();
-
- mitk::DataNode::Pointer node = nodes.front();
-
- if (!node)
- {
- // Nothing selected. Inform the user and return
- QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image cropping.");
- return;
- }
-
- mitk::BaseData* data = node->GetData();
- if (data)
- {
- // test if this data item is an image or not (could also be a surface or something totally different)
- mitk::Image* image = dynamic_cast<mitk::Image*>(data);
- if (image)
- {
- std::stringstream message;
- std::string name;
- message << "Performing image cropping for image ";
- if (node->GetName(name))
- {
- // a property called "name" was found for this DataNode
- message << "'" << name << "'";
- m_OldNodeName = name;
- }
- else
- m_OldNodeName = " ";
-
- message << ".";
- MITK_INFO << message.str();
-
- DisableControls();
-
- CropThread *thread = new CropThread();
- connect(thread, &CropThread::result, this, &PAImageProcessing::HandleResults);
- connect(thread, &CropThread::finished, thread, &QObject::deleteLater);
-
- if(m_Controls.Partial->isChecked())
- thread->setConfig(m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), m_Controls.CutoffRight->value(), m_Controls.CutoffLeft->value(), m_Controls.boundLow->value(), m_Controls.boundHigh->value());
- else
- thread->setConfig(m_Controls.CutoffAbove->value(), m_Controls.CutoffBelow->value(), m_Controls.CutoffRight->value(), m_Controls.CutoffLeft->value(), 0, image->GetDimension(2) - 1);
-
- thread->setInputImage(image);
- thread->setFilterBank(m_FilterBank);
-
- MITK_INFO << "Started new thread for Image Cropping";
- thread->start();
- }
- }
-}
-
-void PAImageProcessing::StartBandpassThread()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- if (nodes.empty()) return;
-
- mitk::DataStorage::Pointer storage = this->GetDataStorage();
-
- mitk::DataNode::Pointer node = nodes.front();
-
- if (!node)
- {
- // Nothing selected. Inform the user and return
- QMessageBox::information(nullptr, "Template", "Please load and select an image before applying a bandpass filter.");
- return;
- }
-
- mitk::BaseData* data = node->GetData();
- if (data)
- {
- // test if this data item is an image or not (could also be a surface or something totally different)
- mitk::Image* image = dynamic_cast<mitk::Image*>(data);
- if (image)
- {
- auto config = CreateBeamformingSettings(image);
- std::stringstream message;
- std::string name;
- message << "Performing Bandpass filter on image ";
- if (node->GetName(name))
- {
- // a property called "name" was found for this DataNode
- message << "'" << name << "'";
- m_OldNodeName = name;
- }
- else
- m_OldNodeName = " ";
-
- message << ".";
- MITK_INFO << message.str();
-
- DisableControls();
-
- BandpassThread *thread = new BandpassThread();
- connect(thread, &BandpassThread::result, this, &PAImageProcessing::HandleResults);
- connect(thread, &BandpassThread::finished, thread, &QObject::deleteLater);
-
- float BPHighPass = 1000000.0f * m_Controls.BPhigh->value(); // [Now in Hz]
- float BPLowPass = 1000000.0f * m_Controls.BPlow->value(); // [Now in Hz]
-
- thread->setConfig(BPHighPass, BPLowPass, m_Controls.BPFalloffLow->value(), m_Controls.BPFalloffHigh->value(),
- config->GetTimeSpacing(), config->GetSpeedOfSound(), m_Controls.IsBFImage->isChecked());
- thread->setInputImage(image);
- thread->setFilterBank(m_FilterBank);
-
- MITK_INFO << "Started new thread for Bandpass filter";
- thread->start();
- }
- }
-}
-
-void PAImageProcessing::SliceBoundsEnabled()
-{
- if (!m_Controls.Partial->isChecked())
- {
- m_Controls.boundLow->setEnabled(false);
- m_Controls.boundHigh->setEnabled(false);
- return;
- }
- else
- {
- m_Controls.boundLow->setEnabled(true);
- m_Controls.boundHigh->setEnabled(true);
- }
-}
-
-void PAImageProcessing::UpperSliceBoundChanged()
-{
- if (m_Controls.boundLow->value() > m_Controls.boundHigh->value())
- {
- m_Controls.boundLow->setValue(m_Controls.boundHigh->value());
- }
-}
-
-void PAImageProcessing::LowerSliceBoundChanged()
-{
- if (m_Controls.boundLow->value() > m_Controls.boundHigh->value())
- {
- m_Controls.boundHigh->setValue(m_Controls.boundLow->value());
- }
-}
-
-void PAImageProcessing::UpdateProgress(int progress, std::string progressInfo)
-{
- if (progress < 100)
- m_Controls.progressBar->setValue(progress);
- else
- m_Controls.progressBar->setValue(100);
- m_Controls.ProgressInfo->setText(progressInfo.c_str());
- qApp->processEvents();
-}
-
-void PAImageProcessing::PAMessageBox(std::string message)
-{
- if (0 != message.compare("noMessage"))
- {
- QMessageBox msgBox;
- msgBox.setText(message.c_str());
- msgBox.exec();
- }
-}
-
-void PAImageProcessing::UpdateImageInfo()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- if (nodes.empty()) return;
-
- mitk::DataNode::Pointer node = nodes.front();
-
- if (!node)
- {
- // Nothing selected
- return;
- }
-
- mitk::BaseData* data = node->GetData();
- if (data)
- {
- // test if this data item is an image or not (could also be a surface or something totally different)
- mitk::Image* image = dynamic_cast<mitk::Image*>(data);
-
- if (image)
- {
- // beamforming configs
- if (m_Controls.UseImageSpacing->isChecked())
- {
- m_Controls.ElementCount->setValue(image->GetDimension(0));
- m_Controls.Pitch->setValue(image->GetGeometry()->GetSpacing()[0]);
- }
-
- m_Controls.boundLow->setMaximum(image->GetDimension(2) - 1);
- m_Controls.boundHigh->setMaximum(image->GetDimension(2) - 1);
-
- float speedOfSound = m_Controls.SpeedOfSound->value(); // [m/s]
- std::stringstream frequency;
- float timeSpacing;
- if (m_Controls.UseImageSpacing->isChecked())
- {
- timeSpacing = image->GetGeometry()->GetSpacing()[1] / 1000000.0f;
- MITK_INFO << "Calculated Scan Depth of " << (image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] /
- 1000000) * speedOfSound * 100 / 2 << "cm";
- }
- else
- {
- timeSpacing = (2 * m_Controls.ScanDepth->value() / 1000 / speedOfSound) / image->GetDimension(1);
- }
- float maxFrequency = (1 / timeSpacing) / 2;
- if(m_Controls.IsBFImage->isChecked())
- maxFrequency = ( 1 / (image->GetGeometry()->GetSpacing()[1] / 1e3 / speedOfSound)) / 2;
- frequency << maxFrequency / 1e6; //[MHz]
- frequency << "MHz";
-
- m_Controls.BPhigh->setMaximum(maxFrequency / 1e6);
- m_Controls.BPlow->setMaximum(maxFrequency / 1e6);
-
- frequency << " is the maximal allowed frequency for the selected image.";
- m_Controls.BPhigh->setToolTip(frequency.str().c_str());
- m_Controls.BPlow->setToolTip(frequency.str().c_str());
- m_Controls.BPhigh->setToolTipDuration(5000);
- m_Controls.BPlow->setToolTipDuration(5000);
- }
- }
-}
-
-void PAImageProcessing::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer>& nodes)
-{
- // iterate all selected objects, adjust warning visibility
- foreach(mitk::DataNode::Pointer node, nodes)
- {
- if (node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()))
- {
- m_Controls.labelWarning->setVisible(false);
- m_Controls.buttonApplyBModeFilter->setEnabled(true);
- m_Controls.labelWarning2->setVisible(false);
- m_Controls.buttonApplyCropFilter->setEnabled(true);
- m_Controls.labelWarning3->setVisible(false);
- m_Controls.buttonApplyBandpass->setEnabled(true);
- m_Controls.labelWarning4->setVisible(false);
- m_Controls.buttonApplyBeamforming->setEnabled(true);
- UpdateImageInfo();
- return;
- }
- }
- m_Controls.labelWarning->setVisible(true);
- m_Controls.buttonApplyBModeFilter->setEnabled(false);
- m_Controls.labelWarning2->setVisible(true);
- m_Controls.buttonApplyCropFilter->setEnabled(false);
- m_Controls.labelWarning3->setVisible(true);
- m_Controls.buttonApplyBandpass->setEnabled(false);
- m_Controls.labelWarning4->setVisible(true);
- m_Controls.buttonApplyBeamforming->setEnabled(false);
-}
-
-void PAImageProcessing::UseResampling()
-{
- if (m_Controls.DoResampling->isChecked())
- {
- m_Controls.ResamplingValue->setEnabled(true);
- m_ResampleSpacing = m_Controls.ResamplingValue->value();
- }
- else
- {
- m_Controls.ResamplingValue->setEnabled(false);
- m_ResampleSpacing = 0;
- }
-}
-
-void PAImageProcessing::UseLogfilter()
-{
- m_UseLogfilter = m_Controls.Logfilter->isChecked();
-}
-
-void PAImageProcessing::SetResampling()
-{
- m_ResampleSpacing = m_Controls.ResamplingValue->value();
-}
-
-mitk::BeamformingSettings::Pointer PAImageProcessing::CreateBeamformingSettings(mitk::Image::Pointer image)
-{
- mitk::BeamformingSettings::BeamformingAlgorithm algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS;
- if ("DAS" == m_Controls.BFAlgorithm->currentText())
- algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DAS;
- else if ("DMAS" == m_Controls.BFAlgorithm->currentText())
- algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::DMAS;
- else if ("sDMAS" == m_Controls.BFAlgorithm->currentText())
- algorithm = mitk::BeamformingSettings::BeamformingAlgorithm::sDMAS;
-
- mitk::BeamformingSettings::Apodization apod = mitk::BeamformingSettings::Apodization::Box;
- if ("Von Hann" == m_Controls.Apodization->currentText())
- {
- apod = mitk::BeamformingSettings::Apodization::Hann;
- }
- else if ("Hamming" == m_Controls.Apodization->currentText())
- {
- apod = mitk::BeamformingSettings::Apodization::Hamm;
- }
- else if ("Box" == m_Controls.Apodization->currentText())
- {
- apod = mitk::BeamformingSettings::Apodization::Box;
- }
-
- float pitchInMeters = m_Controls.Pitch->value() / 1000; // [m]
- float speedOfSound = m_Controls.SpeedOfSound->value(); // [m/s]
- unsigned int samplesPerLine = m_Controls.Samples->value();
- unsigned int reconstructionLines = m_Controls.Lines->value();
- unsigned int apodizatonArraySize = m_Controls.Lines->value();
- float angle = m_Controls.Angle->value(); // [deg]
- bool useGPU = m_Controls.UseGPUBf->isChecked();
-
- float timeSpacing;
- if (m_Controls.UseImageSpacing->isChecked())
- {
- timeSpacing = image->GetGeometry()->GetSpacing()[1] / 1000000.0f;
- MITK_INFO << "Calculated Scan Depth of " << (image->GetDimension(1)*image->GetGeometry()->GetSpacing()[1] /
- 1000000) * speedOfSound * 100 << "cm";
- }
- else
- {
- timeSpacing = (2 * m_Controls.ScanDepth->value() / 1000 / speedOfSound) / image->GetDimension(1);
- }
-
- bool isPAImage = true;
- if ("US Image" == m_Controls.ImageType->currentText())
- {
- isPAImage = false;
- }
- else if ("PA Image" == m_Controls.ImageType->currentText())
- {
- isPAImage = true;
- }
-
- float reconstructionDepth = m_Controls.ReconstructionDepth->value() / 1000.f; // [m]
-
- mitk::BeamformingSettings::ProbeGeometry geometry = mitk::BeamformingSettings::ProbeGeometry::Linear;
- if ("Linear" == m_Controls.Geometry->currentText())
- {
- geometry = mitk::BeamformingSettings::ProbeGeometry::Linear;
- }
- else if ("Concave" == m_Controls.Geometry->currentText())
- {
- geometry = mitk::BeamformingSettings::ProbeGeometry::Concave;
- }
- float probeRadius = m_Controls.ProbeRadius->value()/1000.f; // [m]
-
- return mitk::BeamformingSettings::New(pitchInMeters,
- speedOfSound, timeSpacing, angle, isPAImage, samplesPerLine, reconstructionLines,
- image->GetDimensions(), reconstructionDepth, useGPU, GPU_BATCH_SIZE, apod,
- apodizatonArraySize, algorithm, geometry, probeRadius);
-}
-
-void PAImageProcessing::EnableControls()
-{
- m_Controls.BatchProcessing->setEnabled(true);
- m_Controls.StepBeamforming->setEnabled(true);
- m_Controls.StepBandpass->setEnabled(true);
- m_Controls.StepCropping->setEnabled(true);
- m_Controls.StepBMode->setEnabled(true);
-
- UpdateSaveBoxes();
-
- m_Controls.DoResampling->setEnabled(true);
- UseResampling();
- m_Controls.Logfilter->setEnabled(true);
- m_Controls.BModeMethod->setEnabled(true);
- m_Controls.buttonApplyBModeFilter->setEnabled(true);
-
- m_Controls.CutoffAbove->setEnabled(true);
- m_Controls.CutoffBelow->setEnabled(true);
- m_Controls.buttonApplyCropFilter->setEnabled(true);
- m_Controls.BPSpeedOfSound->setEnabled(true);
- m_Controls.buttonApplyBandpass->setEnabled(true);
-
- m_Controls.Partial->setEnabled(true);
- m_Controls.boundHigh->setEnabled(true);
- m_Controls.boundLow->setEnabled(true);
- m_Controls.BFAlgorithm->setEnabled(true);
- m_Controls.ReconstructionDepth->setEnabled(true);
- m_Controls.ImageType->setEnabled(true);
- m_Controls.Apodization->setEnabled(true);
-
-#ifdef PHOTOACOUSTICS_USE_GPU
- m_Controls.UseGPUBf->setEnabled(true);
- m_Controls.UseGPUBmode->setEnabled(true);
-#endif
-
- m_Controls.BPhigh->setEnabled(true);
- m_Controls.BPlow->setEnabled(true);
- m_Controls.BPFalloffLow->setEnabled(true);
- m_Controls.BPFalloffHigh->setEnabled(true);
- m_Controls.UseImageSpacing->setEnabled(true);
- UseImageSpacing();
- m_Controls.Pitch->setEnabled(true);
- m_Controls.ElementCount->setEnabled(true);
- m_Controls.SpeedOfSound->setEnabled(true);
- m_Controls.Samples->setEnabled(true);
- m_Controls.Lines->setEnabled(true);
- m_Controls.Angle->setEnabled(true);
- m_Controls.buttonApplyBeamforming->setEnabled(true);
- m_Controls.UseSignalDelay->setEnabled(true);
- m_Controls.SignalDelay->setEnabled(true);
-}
-
-void PAImageProcessing::DisableControls()
-{
- m_Controls.BatchProcessing->setEnabled(false);
- m_Controls.StepBeamforming->setEnabled(false);
- m_Controls.StepBandpass->setEnabled(false);
- m_Controls.StepCropping->setEnabled(false);
- m_Controls.StepBMode->setEnabled(false);
- m_Controls.SaveBeamforming->setEnabled(false);
- m_Controls.SaveBandpass->setEnabled(false);
- m_Controls.SaveCropping->setEnabled(false);
- m_Controls.SaveBMode->setEnabled(false);
-
- m_Controls.DoResampling->setEnabled(false);
- m_Controls.ResamplingValue->setEnabled(false);
- m_Controls.Logfilter->setEnabled(false);
- m_Controls.BModeMethod->setEnabled(false);
- m_Controls.buttonApplyBModeFilter->setEnabled(false);
-
- m_Controls.CutoffAbove->setEnabled(false);
- m_Controls.CutoffBelow->setEnabled(false);
- m_Controls.buttonApplyCropFilter->setEnabled(false);
- m_Controls.BPSpeedOfSound->setEnabled(false);
- m_Controls.buttonApplyBandpass->setEnabled(false);
-
- m_Controls.Partial->setEnabled(false);
- m_Controls.boundHigh->setEnabled(false);
- m_Controls.boundLow->setEnabled(false);
- m_Controls.BFAlgorithm->setEnabled(false);
- m_Controls.ReconstructionDepth->setEnabled(false);
- m_Controls.ImageType->setEnabled(false);
- m_Controls.Apodization->setEnabled(false);
-
-#ifdef PHOTOACOUSTICS_USE_GPU
- m_Controls.UseGPUBf->setEnabled(false);
- m_Controls.UseGPUBmode->setEnabled(false);
-#endif
-
- m_Controls.BPhigh->setEnabled(false);
- m_Controls.BPlow->setEnabled(false);
- m_Controls.BPFalloffLow->setEnabled(false);
- m_Controls.BPFalloffHigh->setEnabled(false);
- m_Controls.UseImageSpacing->setEnabled(false);
- m_Controls.ScanDepth->setEnabled(false);
- m_Controls.Pitch->setEnabled(false);
- m_Controls.ElementCount->setEnabled(false);
- m_Controls.SpeedOfSound->setEnabled(false);
- m_Controls.Samples->setEnabled(false);
- m_Controls.Lines->setEnabled(false);
- m_Controls.Angle->setEnabled(false);
- m_Controls.buttonApplyBeamforming->setEnabled(false);
- m_Controls.UseSignalDelay->setEnabled(false);
- m_Controls.SignalDelay->setEnabled(false);
-}
-
-void PAImageProcessing::UseImageSpacing()
-{
- if (m_Controls.UseImageSpacing->isChecked())
- {
- m_Controls.ScanDepth->setDisabled(true);
- }
- else
- {
- m_Controls.ScanDepth->setEnabled(true);
- }
-}
-
-#include <mitkImageReadAccessor.h>
-
-void BeamformingThread::run()
-{
- if (m_SignalDelay != 0)
- {
- int cropPixels = std::round(m_SignalDelay / m_BFconfig->GetTimeSpacing() / 1000000);
- MITK_INFO << cropPixels;
- int errCode = 0;
- m_InputImage = m_FilterBank->ApplyCropping(m_InputImage, cropPixels, 0, 0, 0, 0, 0, &errCode);
-
- m_BFconfig = mitk::BeamformingSettings::New(m_BFconfig->GetPitchInMeters(), m_BFconfig->GetSpeedOfSound(),
- m_BFconfig->GetTimeSpacing(), m_BFconfig->GetAngle(), m_BFconfig->GetIsPhotoacousticImage(), m_BFconfig->GetSamplesPerLine(),
- m_BFconfig->GetReconstructionLines(), m_InputImage->GetDimensions(), m_BFconfig->GetReconstructionDepth(),
- m_BFconfig->GetUseGPU(), m_BFconfig->GetGPUBatchSize(), m_BFconfig->GetApod(),
- m_BFconfig->GetApodizationArraySize(), m_BFconfig->GetAlgorithm(), m_BFconfig->GetGeometry(), m_BFconfig->GetProbeRadius());
- }
-
- mitk::Image::Pointer resultImage;
- std::function<void(int, std::string)> progressHandle = [this](int progress, std::string progressInfo) {
- emit updateProgress(progress, progressInfo);
- };
- resultImage = m_FilterBank->ApplyBeamforming(m_InputImage, m_BFconfig, progressHandle);
- emit result(resultImage, "_bf");
-}
-
-void BeamformingThread::setConfig(mitk::BeamformingSettings::Pointer BFconfig)
-{
- m_BFconfig = BFconfig;
-}
-
-void BeamformingThread::setSignalDelay(float delay)
-{
- m_SignalDelay = delay;
-}
-
-void BeamformingThread::setInputImage(mitk::Image::Pointer image)
-{
- m_InputImage = image;
-}
-
-void BmodeThread::run()
-{
- mitk::Image::Pointer resultImage = m_FilterBank->ApplyBmodeFilter(m_InputImage,
- m_Method, m_UseLogfilter);
-
- if (m_ResampleSpacing != 0)
- {
- double desiredSpacing[2]{ m_InputImage->GetGeometry()->GetSpacing()[0], m_ResampleSpacing };
- resultImage = m_FilterBank->ApplyResampling(resultImage, desiredSpacing);
- }
- emit result(resultImage, "_bmode");
-}
-
-void BmodeThread::setConfig(bool useLogfilter, double resampleSpacing, mitk::PhotoacousticFilterService::BModeMethod method, bool useGPU)
-{
- m_UseLogfilter = useLogfilter;
- m_ResampleSpacing = resampleSpacing;
- m_Method = method;
- m_UseGPU = useGPU;
-}
-
-void BmodeThread::setInputImage(mitk::Image::Pointer image)
-{
- m_InputImage = image;
-}
-
-void CropThread::run()
-{
- mitk::Image::Pointer resultImage;
-
- int errCode = 0;
-
- resultImage = m_FilterBank->ApplyCropping(m_InputImage, m_CutAbove, m_CutBelow, m_CutRight, m_CutLeft, m_CutSliceFirst, (m_InputImage->GetDimension(2) - 1) - m_CutSliceLast, &errCode);
- if (errCode == -1)
- {
- emit result(nullptr, "_cropped");
- return;
- }
- emit result(resultImage, "_cropped");
-}
-
-void CropThread::setConfig(unsigned int CutAbove, unsigned int CutBelow, unsigned int CutRight, unsigned int CutLeft, unsigned int CutSliceFirst, unsigned int CutSliceLast)
-{
- m_CutAbove = CutAbove;
- m_CutBelow = CutBelow;
- m_CutRight = CutRight;
- m_CutLeft = CutLeft;
-
- m_CutSliceLast = CutSliceLast;
- m_CutSliceFirst = CutSliceFirst;
-}
-
-void CropThread::setInputImage(mitk::Image::Pointer image)
-{
- m_InputImage = image;
-}
-
-void BandpassThread::run()
-{
- mitk::Image::Pointer resultImage = m_FilterBank->ApplyBandpassFilter(m_InputImage, m_BPHighPass, m_BPLowPass, m_TukeyAlphaHighPass, m_TukeyAlphaLowPass, m_TimeSpacing, m_SpeedOfSound, m_IsBFImage);
- emit result(resultImage, "_bandpassed");
-}
-
-void BandpassThread::setConfig(float BPHighPass, float BPLowPass, float TukeyAlphaHighPass, float TukeyAlphaLowPass, float TimeSpacing, float SpeedOfSound, bool IsBFImage)
-{
- m_BPHighPass = BPHighPass;
- m_BPLowPass = BPLowPass;
- m_TukeyAlphaHighPass = TukeyAlphaHighPass;
- m_TukeyAlphaLowPass = TukeyAlphaLowPass;
- m_TimeSpacing = TimeSpacing;
- m_SpeedOfSound = SpeedOfSound;
- m_IsBFImage = IsBFImage;
-}
-
-void BandpassThread::setInputImage(mitk::Image::Pointer image)
-{
- m_InputImage = image;
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h
deleted file mode 100644
index e0b3172f56..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessing.h
+++ /dev/null
@@ -1,243 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef PAImageProcessing_h
-#define PAImageProcessing_h
-
-#include <mitkPhotoacousticFilterService.h>
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-#include <qthread.h>
-
-#include "ui_PAImageProcessingControls.h"
-
-#include "mitkBeamformingFilter.h"
-#include "mitkBeamformingSettings.h"
-
-Q_DECLARE_METATYPE(mitk::Image::Pointer)
-Q_DECLARE_METATYPE(std::string)
-
-/*!
-* \brief Plugin implementing an interface for the Photoacoustic Algorithms Module
-*
-* Beamforming, Image processing as B-Mode filtering, cropping, resampling, as well as batch processing can be performed using this plugin.
-*/
-
-class PAImageProcessing : public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- PAImageProcessing();
-
- protected slots:
-
- void UpperSliceBoundChanged();
- void LowerSliceBoundChanged();
- void SliceBoundsEnabled();
-
- void ChangedProbe();
- void UseResampling();
- void UseLogfilter();
- void SetResampling();
- void UseImageSpacing();
- void UpdateImageInfo();
- void UseSignalDelay();
-
- /** \brief Beamforming is being performed in a separate thread to keep the workbench from freezing.
- */
- void StartBeamformingThread();
-
- /** \brief B-mode filtering is being performed in a separate thread to keep the workbench from freezing.
- */
- void StartBmodeThread();
-
- /** \brief Cropping is being performed in a separate thread to keep the workbench from freezing.
- */
- void StartCropThread();
-
- /** \brief Method called when the bandpass thread finishes;
- * it adds the image to a new data node and registers it to the worbench's data storage
- */
- void HandleResults(mitk::Image::Pointer image, std::string nameExtension);
-
- /** \brief Bandpassing is being performed in a separate thread to keep the workbench from freezing.
- */
- void StartBandpassThread();
-
- void UpdateProgress(int progress, std::string progressInfo);
- void PAMessageBox(std::string message);
-
- void BatchProcessing();
- void UpdateSaveBoxes();
-
- void ChangedSOSBandpass();
- void ChangedSOSBeamforming();
-
-protected:
- void CreateQtPartControl(QWidget *parent) override;
-
- void SetFocus() override;
-
- /** \brief called by QmitkFunctionality when DataManager's selection has changed.
- * On a change some parameters are internally updated to calculate bounds for GUI elements as the slice selector for beamforming or
- * the bandpass filter settings.
- */
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,
- const QList<mitk::DataNode::Pointer>& nodes) override;
-
- /** \brief Instance of the GUI controls
- */
- Ui::PAImageProcessingControls m_Controls;
-
- float m_ResampleSpacing;
- bool m_UseLogfilter;
- std::string m_OldNodeName;
-
- /** \brief Method for updating the BFconfig by using a selected image and the GUI configuration.
- */
- mitk::BeamformingSettings::Pointer CreateBeamformingSettings(mitk::Image::Pointer image);
-
- void EnableControls();
- void DisableControls();
-
- /** \brief Class through which the filters are called.
- */
- mitk::PhotoacousticFilterService::Pointer m_FilterBank;
-};
-
-class BeamformingThread : public QThread
-{
- Q_OBJECT
- void run() Q_DECL_OVERRIDE;
-
-signals:
- void result(mitk::Image::Pointer, std::string nameExtension);
- void updateProgress(int, std::string);
- void message(std::string);
-
-public:
- BeamformingThread() : m_SignalDelay(0) {}
-
- void setConfig(mitk::BeamformingSettings::Pointer BFconfig);
- void setSignalDelay(float delay);
- void setInputImage(mitk::Image::Pointer image);
- void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank)
- {
- m_FilterBank = filterBank;
- }
-
-protected:
- mitk::BeamformingSettings::Pointer m_BFconfig;
- mitk::Image::Pointer m_InputImage;
- int m_Cutoff;
- float m_SignalDelay; // [us]
-
- mitk::PhotoacousticFilterService::Pointer m_FilterBank;
-};
-
-class BmodeThread : public QThread
-{
- Q_OBJECT
- void run() Q_DECL_OVERRIDE;
-
-signals:
- void result(mitk::Image::Pointer, std::string nameExtension);
-
-public:
- enum BModeMethod { ShapeDetection, Abs };
-
- void setConfig(bool useLogfilter, double resampleSpacing, mitk::PhotoacousticFilterService::BModeMethod method, bool useGPU);
- void setInputImage(mitk::Image::Pointer image);
- void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank)
- {
- m_FilterBank = filterBank;
- }
-
-protected:
- mitk::Image::Pointer m_InputImage;
-
- mitk::PhotoacousticFilterService::BModeMethod m_Method;
- bool m_UseLogfilter;
- double m_ResampleSpacing;
- bool m_UseGPU;
-
- mitk::PhotoacousticFilterService::Pointer m_FilterBank;
-};
-
-class CropThread : public QThread
-{
- Q_OBJECT
- void run() Q_DECL_OVERRIDE;
-
-signals:
- void result(mitk::Image::Pointer, std::string nameExtension);
-
-public:
- void setConfig(unsigned int CutAbove, unsigned int CutBelow, unsigned int CutRight, unsigned int CutLeft, unsigned int CutSliceFirst, unsigned int CutSliceLast);
- void setInputImage(mitk::Image::Pointer image);
- void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank)
- {
- m_FilterBank = filterBank;
- }
-
-protected:
- mitk::Image::Pointer m_InputImage;
-
- unsigned int m_CutAbove;
- unsigned int m_CutBelow;
- unsigned int m_CutRight;
- unsigned int m_CutLeft;
- unsigned int m_CutSliceLast;
- unsigned int m_CutSliceFirst;
-
- mitk::PhotoacousticFilterService::Pointer m_FilterBank;
-};
-
-class BandpassThread : public QThread
-{
- Q_OBJECT
- void run() Q_DECL_OVERRIDE;
-
-signals:
- void result(mitk::Image::Pointer, std::string nameExtension);
-
-public:
- void setConfig(float BPHighPass, float BPLowPass, float TukeyAlphaHighPass, float TukeyAlphaLowPass, float TimeSpacing, float SpeedOfSound, bool IsBFImage);
- void setInputImage(mitk::Image::Pointer image);
- void setFilterBank(mitk::PhotoacousticFilterService::Pointer filterBank)
- {
- m_FilterBank = filterBank;
- }
-
-protected:
- mitk::Image::Pointer m_InputImage;
-
- float m_BPHighPass;
- float m_BPLowPass;
- float m_TukeyAlphaHighPass;
- float m_TukeyAlphaLowPass;
- float m_TimeSpacing;
- float m_SpeedOfSound;
- bool m_IsBFImage;
-
- mitk::PhotoacousticFilterService::Pointer m_FilterBank;
-};
-
-#endif // PAImageProcessing_h
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessingControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessingControls.ui
deleted file mode 100644
index 6ec9decbac..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/PAImageProcessingControls.ui
+++ /dev/null
@@ -1,1317 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>PAImageProcessingControls</class>
- <widget class="QWidget" name="PAImageProcessingControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>601</width>
- <height>890</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <widget class="QToolBox" name="toolBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="currentIndex">
- <number>1</number>
- </property>
- <widget class="QWidget" name="pageBandpass">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>98</width>
- <height>28</height>
- </rect>
- </property>
- <attribute name="label">
- <string>Bandpass</string>
- </attribute>
- <widget class="QWidget" name="layoutWidget">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>0</y>
- <width>301</width>
- <height>529</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout_2" rowstretch="0,0,0,0,0,0,0,0,0,0,0,0" rowminimumheight="0,0,0,0,0,0,0,0,0,0,0,0">
- <property name="sizeConstraint">
- <enum>QLayout::SetDefaultConstraint</enum>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <item row="4" column="0">
- <widget class="QDoubleSpinBox" name="BPlow">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>200.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>8.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QLabel" name="BPHighLabel">
- <property name="text">
- <string>[MHz] f High Pass</string>
- </property>
- </widget>
- </item>
- <item row="4" column="1">
- <widget class="QLabel" name="BPLowLabel">
- <property name="text">
- <string>[MHz] f Low Pass</string>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QDoubleSpinBox" name="BPhigh">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="maximum">
- <double>200.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>0.100000000000000</double>
- </property>
- </widget>
- </item>
- <item row="9" column="0">
- <widget class="QDoubleSpinBox" name="BPSpeedOfSound">
- <property name="decimals">
- <number>1</number>
- </property>
- <property name="minimum">
- <double>200.000000000000000</double>
- </property>
- <property name="maximum">
- <double>3000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>5.000000000000000</double>
- </property>
- <property name="value">
- <double>1500.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="9" column="1">
- <widget class="QLabel" name="label_11">
- <property name="text">
- <string>[m/s] Speed of Sound</string>
- </property>
- </widget>
- </item>
- <item row="6" column="0">
- <widget class="QDoubleSpinBox" name="BPFalloffHigh">
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>0.500000000000000</double>
- </property>
- </widget>
- </item>
- <item row="6" column="1">
- <widget class="QLabel" name="label_19">
- <property name="toolTip">
- <string><html><head/><body><p><span style=" font-family:'sans-serif'; font-size:14px; color:#222222; background-color:#ffffff;">At </span><span style=" font-family:'sans-serif'; font-size:14px; font-style:italic; color:#222222; background-color:#ffffff;">α</span><span style=" font-family:'sans-serif'; font-size:14px; color:#222222; background-color:#ffffff;"> = 0 it's rectangular, at </span><span style=" font-family:'sans-serif'; font-size:14px; font-style:italic; color:#222222; background-color:#ffffff;">α</span><span style=" font-family:'sans-serif'; font-size:14px; color:#222222; background-color:#ffffff;"> = 1 it's a Hann window. Both flanks can be set independently.</span></p></body></html></string>
- </property>
- <property name="text">
- <string>Tukey Window α High Pass</string>
- </property>
- </widget>
- </item>
- <item row="7" column="0">
- <widget class="QDoubleSpinBox" name="BPFalloffLow">
- <property name="decimals">
- <number>2</number>
- </property>
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>0.500000000000000</double>
- </property>
- </widget>
- </item>
- <item row="7" column="1">
- <widget class="QLabel" name="label_13">
- <property name="toolTip">
- <string><html><head/><body><p><span style=" font-family:'sans-serif'; font-size:14px; color:#222222; background-color:#ffffff;">At </span><span style=" font-family:'sans-serif'; font-size:14px; font-style:italic; color:#222222; background-color:#ffffff;">α</span><span style=" font-family:'sans-serif'; font-size:14px; color:#222222; background-color:#ffffff;"> = 0 it's rectangular, at </span><span style=" font-family:'sans-serif'; font-size:14px; font-style:italic; color:#222222; background-color:#ffffff;">α</span><span style=" font-family:'sans-serif'; font-size:14px; color:#222222; background-color:#ffffff;"> = 1 it's a Hann window. Both flanks can be set independently.</span></p></body></html></string>
- </property>
- <property name="text">
- <string>Tukey Window α Low Pass</string>
- </property>
- </widget>
- </item>
- <item row="2" column="0" colspan="2">
- <widget class="QLabel" name="labelWarning2">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string><html><head/><body><p><span style=" font-size:10pt; font-weight:600; color:#ff0000;">Select input data in datamanager!</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="10" column="0" colspan="2">
- <widget class="QPushButton" name="buttonApplyBandpass">
- <property name="text">
- <string>Apply Bandpass</string>
- </property>
- </widget>
- </item>
- <item row="8" column="0" colspan="2">
- <widget class="QCheckBox" name="IsBFImage">
- <property name="toolTip">
- <string><html><head/><body><p>If not checked, treat input as raw US/PA data with Y-axis as a time coordinate in microseconds</p></body></html></string>
- </property>
- <property name="text">
- <string>Assume Spatial Coordinates</string>
- </property>
- </widget>
- </item>
- <item row="11" column="0" colspan="2">
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="pageBeamforming">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>583</width>
- <height>732</height>
- </rect>
- </property>
- <attribute name="label">
- <string>Beamforming</string>
- </attribute>
- <widget class="QWidget" name="layoutWidget">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>0</y>
- <width>306</width>
- <height>661</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <property name="spacing">
- <number>5</number>
- </property>
- <item row="6" column="0">
- <widget class="QComboBox" name="ImageType">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>PA Image</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>US Image</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="6" column="1">
- <widget class="QLabel" name="label_10">
- <property name="toolTip">
- <string><html><head/><body><p>which type of image do you plan to reconstruct?</p></body></html></string>
- </property>
- <property name="text">
- <string>Raw Data Type</string>
- </property>
- </widget>
- </item>
- <item row="5" column="0">
- <widget class="QComboBox" name="BFAlgorithm">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>DAS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>DMAS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>sDMAS</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="7" column="0">
- <widget class="QComboBox" name="Apodization">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <item>
- <property name="text">
- <string>Von Hann</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Hamming</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Box</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="24" column="1">
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>[mm] Transducer Pitch</string>
- </property>
- </widget>
- </item>
- <item row="7" column="1">
- <widget class="QLabel" name="label_16">
- <property name="text">
- <string>Apodization Function</string>
- </property>
- </widget>
- </item>
- <item row="5" column="1">
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>Beamforming Algorithm</string>
- </property>
- </widget>
- </item>
- <item row="18" column="0">
- <widget class="QLabel" name="label_14">
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item row="24" column="0">
- <widget class="QDoubleSpinBox" name="Pitch">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>9.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.050000000000000</double>
- </property>
- <property name="value">
- <double>0.340000000000000</double>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QLabel" name="label_20">
- <property name="text">
- <string>Probe Geomentry</string>
- </property>
- </widget>
- </item>
- <item row="8" column="0">
- <widget class="QDoubleSpinBox" name="Angle">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>1.000000000000000</double>
- </property>
- <property name="maximum">
- <double>180.000000000000000</double>
- </property>
- <property name="value">
- <double>45.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="8" column="1">
- <widget class="QLabel" name="label_9">
- <property name="toolTip">
- <string><html><head/><body><p>... of the transducer elements.</p></body></html></string>
- </property>
- <property name="text">
- <string>[°] Sensitive Angle</string>
- </property>
- </widget>
- </item>
- <item row="23" column="1">
- <widget class="QLabel" name="ReconstructionDepthLabel">
- <property name="text">
- <string>[mm] Reconstruction Depth</string>
- </property>
- </widget>
- </item>
- <item row="23" column="0">
- <widget class="QDoubleSpinBox" name="ReconstructionDepth">
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>300.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>60.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QComboBox" name="Geometry">
- <property name="currentText">
- <string>Linear</string>
- </property>
- <item>
- <property name="text">
- <string>Linear</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Concave</string>
- </property>
- </item>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QDoubleSpinBox" name="ProbeRadius">
- <property name="decimals">
- <number>2</number>
- </property>
- <property name="minimum">
- <double>0.000000000000000</double>
- </property>
- <property name="maximum">
- <double>999.990000000000009</double>
- </property>
- <property name="value">
- <double>40.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QLabel" name="label_23">
- <property name="text">
- <string>[mm] Concave Probe Radius</string>
- </property>
- </widget>
- </item>
- <item row="48" column="1">
- <widget class="QCheckBox" name="UseSignalDelay">
- <property name="toolTip">
- <string><html><head/><body><p>Some setups' hardware produces signal delays that need to be cropped out of the image before performing beamforming. To do this, select this box.</p></body></html></string>
- </property>
- <property name="text">
- <string>Consider Hardware Delay [µs]</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="48" column="0">
- <widget class="QDoubleSpinBox" name="SignalDelay">
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>1.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="49" column="0" colspan="2">
- <widget class="QCheckBox" name="UseImageSpacing">
- <property name="toolTip">
- <string><html><head/><body><p>... from y-spacing in the selected raw data. If this is switched of &quot;Manual Scan Depth&quot; is used.</p></body></html></string>
- </property>
- <property name="text">
- <string>Automatic Get Depth</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="50" column="1">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>[mm] Manual Scan Depth</string>
- </property>
- </widget>
- </item>
- <item row="44" column="0" colspan="2">
- <widget class="QCheckBox" name="UseGPUBf">
- <property name="toolTip">
- <string><html><head/><body><p>Using GPU is recommended - It is so much faster.</p></body></html></string>
- </property>
- <property name="text">
- <string>Compute On GPU</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="27" column="0">
- <widget class="QSpinBox" name="Lines">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimum">
- <number>64</number>
- </property>
- <property name="maximum">
- <number>2048</number>
- </property>
- <property name="singleStep">
- <number>128</number>
- </property>
- <property name="value">
- <number>512</number>
- </property>
- </widget>
- </item>
- <item row="51" column="0">
- <widget class="QSpinBox" name="ElementCount">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimum">
- <number>2</number>
- </property>
- <property name="maximum">
- <number>2048</number>
- </property>
- <property name="singleStep">
- <number>64</number>
- </property>
- <property name="value">
- <number>256</number>
- </property>
- </widget>
- </item>
- <item row="27" column="1">
- <widget class="QLabel" name="label_7">
- <property name="text">
- <string>Reconstructed Lines</string>
- </property>
- </widget>
- </item>
- <item row="42" column="0" colspan="2">
- <widget class="QLabel" name="label_22">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Advanced Options</string>
- </property>
- </widget>
- </item>
- <item row="50" column="0">
- <widget class="QDoubleSpinBox" name="ScanDepth">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>300.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>60.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="19" column="0">
- <widget class="QDoubleSpinBox" name="SpeedOfSound">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="decimals">
- <number>1</number>
- </property>
- <property name="minimum">
- <double>200.000000000000000</double>
- </property>
- <property name="maximum">
- <double>3000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>5.000000000000000</double>
- </property>
- <property name="value">
- <double>1500.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="52" column="1">
- <widget class="QLabel" name="label_6">
- <property name="toolTip">
- <string><html><head/><body><p>... Good default - change only if you know what you are doing.</p></body></html></string>
- </property>
- <property name="text">
- <string>Samples</string>
- </property>
- </widget>
- </item>
- <item row="19" column="1">
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>[m/s] Speed of Sound</string>
- </property>
- </widget>
- </item>
- <item row="52" column="0">
- <widget class="QSpinBox" name="Samples">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimum">
- <number>256</number>
- </property>
- <property name="maximum">
- <number>16384</number>
- </property>
- <property name="singleStep">
- <number>256</number>
- </property>
- <property name="value">
- <number>2048</number>
- </property>
- </widget>
- </item>
- <item row="51" column="1">
- <widget class="QLabel" name="label_5">
- <property name="toolTip">
- <string><html><head/><body><p>Set automatically from selected raw data x-Geometry.</p></body></html></string>
- </property>
- <property name="text">
- <string>Transducer Elements</string>
- </property>
- </widget>
- </item>
- <item row="41" column="0">
- <widget class="QLabel" name="label_24">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item row="1" column="0" colspan="2">
- <widget class="QLabel" name="labelWarning4">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string><html><head/><body><p><span style=" font-size:10pt; font-weight:600; color:#ff0000;">Select input data in datamanager!</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="28" column="1">
- <widget class="QLabel" name="ProgressInfo">
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item row="28" column="0">
- <widget class="QProgressBar" name="progressBar">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="maximum">
- <number>100</number>
- </property>
- <property name="value">
- <number>0</number>
- </property>
- </widget>
- </item>
- <item row="53" column="0" colspan="2">
- <spacer name="verticalSpacer_3">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item row="40" column="0" colspan="2">
- <widget class="QPushButton" name="buttonApplyBeamforming">
- <property name="text">
- <string>Apply Beamforming</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="pageCrop">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>98</width>
- <height>28</height>
- </rect>
- </property>
- <attribute name="label">
- <string>Cropping</string>
- </attribute>
- <widget class="QWidget" name="layoutWidget">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>0</y>
- <width>330</width>
- <height>301</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout_5">
- <item row="4" column="0">
- <widget class="QSpinBox" name="CutoffLeft">
- <property name="maximum">
- <number>999999999</number>
- </property>
- </widget>
- </item>
- <item row="4" column="1">
- <widget class="QLabel" name="label_8">
- <property name="text">
- <string>Left</string>
- </property>
- </widget>
- </item>
- <item row="3" column="3">
- <widget class="QLabel" name="label_21">
- <property name="text">
- <string>Bottom</string>
- </property>
- </widget>
- </item>
- <item row="8" column="1">
- <widget class="QLabel" name="label_17">
- <property name="toolTip">
- <string>minimal beamformed slice</string>
- </property>
- <property name="text">
- <string>First Slice</string>
- </property>
- </widget>
- </item>
- <item row="4" column="2">
- <widget class="QSpinBox" name="CutoffRight">
- <property name="maximum">
- <number>999999999</number>
- </property>
- </widget>
- </item>
- <item row="4" column="3">
- <widget class="QLabel" name="label_12">
- <property name="text">
- <string>Right</string>
- </property>
- </widget>
- </item>
- <item row="5" column="0" colspan="2">
- <widget class="QCheckBox" name="Partial">
- <property name="text">
- <string>Select Slices</string>
- </property>
- </widget>
- </item>
- <item row="9" column="0" colspan="4">
- <widget class="QPushButton" name="buttonApplyCropFilter">
- <property name="text">
- <string>Apply Crop Filer</string>
- </property>
- </widget>
- </item>
- <item row="0" column="0" colspan="4">
- <widget class="QLabel" name="labelWarning3">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string><html><head/><body><p><span style=" font-size:10pt; font-weight:600; color:#ff0000;">Select input data in datamanager!</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QLabel" name="label_203">
- <property name="text">
- <string>Top</string>
- </property>
- </widget>
- </item>
- <item row="8" column="0">
- <widget class="QSpinBox" name="boundLow">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="maximum">
- <number>99999</number>
- </property>
- </widget>
- </item>
- <item row="1" column="0" colspan="2">
- <widget class="QLabel" name="label_204">
- <property name="text">
- <string>Cut N Pixels from ...</string>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QSpinBox" name="CutoffAbove">
- <property name="maximum">
- <number>999999999</number>
- </property>
- <property name="singleStep">
- <number>1</number>
- </property>
- <property name="value">
- <number>0</number>
- </property>
- </widget>
- </item>
- <item row="3" column="2">
- <widget class="QSpinBox" name="CutoffBelow">
- <property name="maximum">
- <number>999999999</number>
- </property>
- <property name="value">
- <number>0</number>
- </property>
- </widget>
- </item>
- <item row="8" column="2">
- <widget class="QSpinBox" name="boundHigh">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="maximum">
- <number>99999</number>
- </property>
- <property name="value">
- <number>10</number>
- </property>
- </widget>
- </item>
- <item row="8" column="3">
- <widget class="QLabel" name="label_18">
- <property name="toolTip">
- <string>Maximal beamformed slice</string>
- </property>
- <property name="text">
- <string>Last Slice</string>
- </property>
- </widget>
- </item>
- <item row="10" column="0" colspan="4">
- <spacer name="verticalSpacer_5">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="pageBmode">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>98</width>
- <height>28</height>
- </rect>
- </property>
- <attribute name="label">
- <string>B-mode Generation</string>
- </attribute>
- <widget class="QWidget" name="layoutWidget">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>0</y>
- <width>301</width>
- <height>261</height>
- </rect>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QLabel" name="labelWarning">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string><html><head/><body><p><span style=" font-size:10pt; font-weight:600; color:#ff0000;">Select input data in datamanager!</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="BModeMethod">
- <property name="currentText">
- <string>Envelope Detection</string>
- </property>
- <item>
- <property name="text">
- <string>Envelope Detection</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>Absolute Filter</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_5">
- <item>
- <widget class="QCheckBox" name="DoResampling">
- <property name="toolTip">
- <string><html><head/><body><p>The image will still be oversampled after B-Mode generation. This default performs a sensible downsampling.</p></body></html></string>
- </property>
- <property name="text">
- <string>Resample Image after B-mode</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QDoubleSpinBox" name="ResamplingValue">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>13</width>
- <height>0</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- </font>
- </property>
- <property name="decimals">
- <number>3</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>0.050000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="ResamplingLabel">
- <property name="text">
- <string>[mm] Resampled y-Spacing </string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QCheckBox" name="Logfilter">
- <property name="toolTip">
- <string><html><head/><body><p>Adds a log() filter after the B-mode filter. Often used in US B-mode images.</p></body></html></string>
- </property>
- <property name="text">
- <string>Logarithmic Compression</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="UseGPUBmode">
- <property name="text">
- <string>Use GPU</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonApplyBModeFilter">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string>Do image processing</string>
- </property>
- <property name="text">
- <string>Apply B-mode Filter</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_4">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="pageLegacyBatch">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>98</width>
- <height>28</height>
- </rect>
- </property>
- <attribute name="label">
- <string>Legacy Batch Processing</string>
- </attribute>
- <widget class="QWidget" name="layoutWidget">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>0</y>
- <width>309</width>
- <height>231</height>
- </rect>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_7" stretch="0,0">
- <item>
- <widget class="QLabel" name="label_15">
- <property name="maximumSize">
- <size>
- <width>300</width>
- <height>100</height>
- </size>
- </property>
- <property name="text">
- <string><html><head/><body><p><span style=" font-weight:600;">Note:</span> This batch processing tool is depricated <br/>and is no longer tested. It is recommended to <br/>use the PA command line tool to process large <br/>amounts of files with consistent settings.</p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QGridLayout" name="gridLayout_3">
- <item row="2" column="2">
- <widget class="QCheckBox" name="StepBandpass">
- <property name="text">
- <string>Bandpass</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QCheckBox" name="StepCropping">
- <property name="text">
- <string>Crop</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QCheckBox" name="SaveBeamforming">
- <property name="text">
- <string>Save</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="3" column="2">
- <widget class="QCheckBox" name="SaveBandpass">
- <property name="text">
- <string>Save</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QCheckBox" name="SaveCropping">
- <property name="text">
- <string>Save</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QCheckBox" name="StepBeamforming">
- <property name="text">
- <string>Beamform</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="2" column="3">
- <widget class="QCheckBox" name="StepBMode">
- <property name="text">
- <string>B-Mode</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="3" column="3">
- <widget class="QCheckBox" name="SaveBMode">
- <property name="text">
- <string>Save</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="4" column="0" colspan="4">
- <widget class="QPushButton" name="BatchProcessing">
- <property name="text">
- <string>Start Batch Processing</string>
- </property>
- </widget>
- </item>
- <item row="5" column="0" colspan="4">
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </widget>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.cpp
deleted file mode 100644
index 5546ab5a81..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.h"
-#include "PAImageProcessing.h"
-
-void mitk::org_mitk_gui_qt_photoacoustics_imageprocessing_Activator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(PAImageProcessing, context)
-}
-
-void mitk::org_mitk_gui_qt_photoacoustics_imageprocessing_Activator::stop(ctkPluginContext*)
-{
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.h b/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.h
deleted file mode 100644
index fe6d9ea9aa..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.imageprocessing/src/internal/org_mitk_gui_qt_photoacoustics_imageprocessing_Activator.h
+++ /dev/null
@@ -1,32 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef org_mitk_gui_qt_photoacoustics_imageprocessing_Activator_h
-#define org_mitk_gui_qt_photoacoustics_imageprocessing_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk
-{
- class org_mitk_gui_qt_photoacoustics_imageprocessing_Activator : public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_photoacoustics_imageprocessing")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
- };
-}
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/CMakeLists.txt b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/CMakeLists.txt
deleted file mode 100644
index ec72937f68..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_photoacoustics_pausmotioncompensation)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE PAUSMOTIONCOMPENSATION_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt MitkPhotoacousticsAlgorithms
-)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/files.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/files.cmake
deleted file mode 100644
index 8641eb6e78..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/files.cmake
+++ /dev/null
@@ -1,42 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.cpp
- PAUSMotionCompensation.cpp
-)
-
-set(UI_FILES
- src/internal/PAUSMotionCompensationControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.h
- src/internal/PAUSMotionCompensation.h
-)
-
-# list of resource files which can be used by the plug-in
-# system without loading the plug-ins shared library,
-# for example the icon used in the menu and tabs for the
-# plug-in views in the workbench
-set(CACHED_RESOURCE_FILES
- resources/pai.svg
- plugin.xml
-)
-
-# list of Qt .qrc files which contain additional resources
-# specific to this plugin
-set(QRC_FILES
-
-)
-
-set(CPP_FILES )
-
-foreach(file ${SRC_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/${file})
-endforeach(file ${SRC_CPP_FILES})
-
-foreach(file ${INTERNAL_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/internal/${file})
-endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/manifest_headers.cmake
deleted file mode 100644
index 7a507c2915..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Pausmotioncompensation")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "DKFZ")
-set(Plugin-ContactAddress "")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/plugin.xml b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/plugin.xml
deleted file mode 100644
index 36c99db51c..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/plugin.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.pausmotioncompensation"
- name="PAUS Motion Compensation"
- category="Photoacoustics"
- class="PAUSMotionCompensation"
- icon="resources/pai.svg" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/resources/icon.xpm b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/resources/icon.xpm
deleted file mode 100644
index 9057c20bc6..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/resources/icon.xpm
+++ /dev/null
@@ -1,21 +0,0 @@
-/* XPM */
-static const char * icon_xpm[] = {
-"16 16 2 1",
-" c #FF0000",
-". c #000000",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" ",
-" "};
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/resources/pai.svg b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/resources/pai.svg
deleted file mode 100644
index d6f03a56da..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/resources/pai.svg
+++ /dev/null
@@ -1,286 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<svg
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://creativecommons.org/ns#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:svg="http://www.w3.org/2000/svg"
- xmlns="http://www.w3.org/2000/svg"
- xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
- xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- xml:space="preserve"
- enable-background="new 0 0 1792 1792"
- viewBox="0 0 1792 1792"
- height="1792px"
- width="1792px"
- y="0px"
- x="0px"
- id="Layer_1"
- version="1.1"
- inkscape:version="0.91 r13725"
- sodipodi:docname="pai.svg"><sodipodi:namedview
- pagecolor="#ffffff"
- bordercolor="#666666"
- borderopacity="1"
- objecttolerance="10"
- gridtolerance="10"
- guidetolerance="10"
- inkscape:pageopacity="0"
- inkscape:pageshadow="2"
- inkscape:window-width="1676"
- inkscape:window-height="1011"
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- showgrid="true"
- inkscape:zoom="0.26339286"
- inkscape:cx="500.8735"
- inkscape:cy="627.03137"
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- inkscape:window-y="18"
- inkscape:window-maximized="0"
- inkscape:current-layer="Layer_1"><inkscape:grid
- type="xygrid"
- id="grid8657" /></sodipodi:namedview><metadata
- id="metadata11"><rdf:RDF><cc:Work
- rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
- rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title /></cc:Work></rdf:RDF></metadata><defs
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diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.cpp
deleted file mode 100644
index a747f6651f..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.cpp
+++ /dev/null
@@ -1,208 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// Qmitk
-#include "PAUSMotionCompensation.h"
-
-// Qt
-#include <QMessageBox>
-
-// mitk image
-#include <mitkImage.h>
-
-const std::string PAUSMotionCompensation::VIEW_ID = "org.mitk.views.pausmotioncompensation";
-
-void PAUSMotionCompensation::SetFocus()
-{
- m_Controls.buttonPerformImageProcessing->setFocus();
-}
-
-void PAUSMotionCompensation::CreateQtPartControl(QWidget *parent)
-{
- // create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi(parent);
- connect(
- m_Controls.buttonPerformImageProcessing, &QPushButton::clicked, this, &PAUSMotionCompensation::DoImageProcessing);
- connect(
- m_Controls.buttonUpdateParameters, &QPushButton::clicked, this, &PAUSMotionCompensation::DoUpdateParameters);
-}
-
-void PAUSMotionCompensation::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer> &nodes)
-{
- // Clear the combo box where we choose the photoacoustic image
- m_Controls.comboBoxPA->clear();
-
- // Make sure that there are exactle 2 nodes selected
- if (nodes.size() != 2) {
- m_Controls.labelWarning->setVisible(true);
- m_Controls.buttonPerformImageProcessing->setEnabled(false);
- return;
- }
-
- // Make sure that the image data is okay
- foreach (mitk::DataNode::Pointer node, nodes) {
- if (node.IsNull() || !dynamic_cast<mitk::Image *>(node->GetData())) {
- m_Controls.labelWarning->setVisible(true);
- m_Controls.buttonPerformImageProcessing->setEnabled(false);
- return;
- }
-
- // Add the image names to the combo box
- m_Controls.comboBoxPA->addItem(QString::fromStdString(node->GetName()));
- }
-
- m_Controls.labelWarning->setVisible(false);
- m_Controls.buttonPerformImageProcessing->setEnabled(true);
-
-}
-
-void PAUSMotionCompensation::DoImageProcessing()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
-
- // Make sure that there are two images selected
- if (nodes.empty() || nodes.size() != 2)
- {
- QMessageBox::information(nullptr, "Warning", "Please select two images before starting image processing.");
- return;
- }
-
- mitk::DataNode::Pointer paNode, usNode;
-
- foreach (mitk::DataNode::Pointer node, nodes) {
- if(m_Controls.comboBoxPA->itemText(m_Controls.comboBoxPA->currentIndex()) == QString::fromStdString(node->GetName())) {
- paNode = node;
- } else {
- usNode = node;
- }
- }
-
- if(paNode.IsNull() || usNode.IsNull()) {
- MITK_INFO << "One of the nodes is empty. This may happen, if the two images have the same name. Please rename one of them.";
- QMessageBox::information(nullptr, "Template", "One of the nodes is empty. This may happen, if the two images have the same name. Please rename one of them.");
- return;
- }
-
- // here we have a valid mitk::DataNode
-
- // a node itself is not very useful, we need its data item (the image)
- mitk::BaseData *paData = paNode->GetData();
- mitk::BaseData *usData = usNode->GetData();
- if (paData && usData)
- {
- // test if this data item is an image or not (could also be a surface or something totally different)
- mitk::Image *paImage = dynamic_cast<mitk::Image *>(paData);
- mitk::Image *usImage = dynamic_cast<mitk::Image *>(usData);
- if (paImage && usImage)
- {
- std::stringstream message;
- std::string name;
- message << "Performing motion compensation for image ";
- if (paNode->GetName(name))
- {
- // a property called "name" was found for this DataNode
- message << "'" << name << "'";
- }
- message << " and ";
- if (usNode->GetName(name)) {
- message << "'" << name << "'";
- }
- message << ".";
- MITK_INFO << message.str();
-
- // actually do something here...
- m_Filter->SetPaInput(paImage);
- m_Filter->SetUsInput(usImage);
- try{
- m_Filter->Update();
- }
- catch (const std::exception& ) {
- QMessageBox::information(nullptr, "Warning", "Please make sure that both input images have the same dimension(s).");
- }
- mitk::Image::Pointer paOutput = m_Filter->GetPaOutput();
- mitk::Image::Pointer usOutput = m_Filter->GetUsOutput();
-
- auto paOutNode = mitk::DataNode::New();
- paOutNode->SetData(paOutput);
- paOutNode->SetName(paNode->GetName() + " compensated");
-
- this->GetDataStorage()->Add(paOutNode);
-
- auto usOutNode = mitk::DataNode::New();
- usOutNode->SetData(usOutput);
- usOutNode->SetName(usNode->GetName() + " compensated");
-
- this->GetDataStorage()->Add(usOutNode);
-
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
- }
- }
-}
-
-void PAUSMotionCompensation::DoUpdateParameters() {
-
- bool ok;
-
- unsigned int batchSize = m_Controls.lineBatchSize->text().toInt(&ok);
- if(!ok) {
- QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
- return;
- }
- m_Filter->SetBatchSize(batchSize);
-
- double pyrScale = m_Controls.linePyrScale->text().toDouble(&ok);
- if(!ok) {
- QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
- return;
- }
- m_Filter->SetPyrScale(pyrScale);
-
- unsigned int levels = m_Controls.lineLevels->text().toInt(&ok);
- if(!ok) {
- QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
- return;
- }
- m_Filter->SetLevels(levels);
-
- unsigned int winSize = m_Controls.lineWinSize->text().toInt(&ok);
- if(!ok) {
- QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
- return;
- }
- m_Filter->SetWinSize(winSize);
-
- unsigned int iterations = m_Controls.lineIterations->text().toInt(&ok);
- if(!ok) {
- QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
- return;
- }
- m_Filter->SetIterations(iterations);
-
- unsigned int polyN = m_Controls.linePolyN->text().toInt(&ok);
- if(!ok) {
- QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
- return;
- }
- m_Filter->SetPolyN(polyN);
-
- double polySigma = m_Controls.linePolySigma->text().toDouble(&ok);
- if(!ok) {
- QMessageBox::information(nullptr, "Warning", "Invalid parameter.");
- return;
- }
- m_Filter->SetPolySigma(polySigma);
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.h b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.h
deleted file mode 100644
index 7834097528..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensation.h
+++ /dev/null
@@ -1,58 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef PAUSMotionCompensation_h
-#define PAUSMotionCompensation_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-
-#include "ui_PAUSMotionCompensationControls.h"
-
-#include "mitkPhotoacousticMotionCorrectionFilter.h"
-
-/**
- \brief PAUSMotionCompensation
-
- Photoacoustic and ultrasound image motion correction can be performed with this plugin. Internally OpenCV2 calc OpticalFlowFarneback is used.
- \sa QmitkAbstractView
- \ingroup ${plugin_target}_internal
-*/
-class PAUSMotionCompensation : public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
-
-public:
- static const std::string VIEW_ID;
-
-protected:
- void CreateQtPartControl(QWidget *parent) override;
-
- void SetFocus() override;
-
- /// \brief called by QmitkFunctionality when DataManager's selection has changed
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,
- const QList<mitk::DataNode::Pointer> &nodes) override;
-
- /// \brief Called when the user clicks the GUI button
- void DoImageProcessing();
- void DoUpdateParameters();
-
- Ui::PAUSMotionCompensationControls m_Controls;
- mitk::PhotoacousticMotionCorrectionFilter::Pointer m_Filter = mitk::PhotoacousticMotionCorrectionFilter::New();
-};
-
-#endif // PAUSMotionCompensation_h
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensationControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensationControls.ui
deleted file mode 100644
index 8afd79a28c..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/PAUSMotionCompensationControls.ui
+++ /dev/null
@@ -1,179 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>PAUSMotionCompensationControls</class>
- <widget class="QWidget" name="PAUSMotionCompensationControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>242</width>
- <height>555</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QLabel" name="labelWarning">
- <property name="styleSheet">
- <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
- </property>
- <property name="text">
- <string>Please select 2 images!</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_8">
- <property name="text">
- <string>Photoacoustic image</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="comboBoxPA"/>
- </item>
- <item>
- <widget class="QPushButton" name="buttonPerformImageProcessing">
- <property name="toolTip">
- <string>Do image processing</string>
- </property>
- <property name="text">
- <string>Start processing</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_7">
- <property name="text">
- <string>Batch size</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineBatchSize">
- <property name="text">
- <string>5</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Pyramid scale:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="linePyrScale">
- <property name="text">
- <string>0.5</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Levels:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineLevels">
- <property name="text">
- <string>3</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Averaging window size:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineWinSize">
- <property name="text">
- <string>15</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string>Iterations:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineIterations">
- <property name="text">
- <string>3</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_5">
- <property name="text">
- <string>Pixel neighborhood for poly-expan:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="linePolyN">
- <property name="text">
- <string>5</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_6">
- <property name="text">
- <string>Standard deviation:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="linePolySigma">
- <property name="text">
- <string>1.1</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonUpdateParameters">
- <property name="text">
- <string>Update Parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="spacer1">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>220</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.cpp
deleted file mode 100644
index ee5313cc7b..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#include "org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.h"
-#include "PAUSMotionCompensation.h"
-
-namespace mitk
-{
- void org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator::start(ctkPluginContext *context)
- {
- BERRY_REGISTER_EXTENSION_CLASS(PAUSMotionCompensation, context)
- }
-
- void org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator::stop(ctkPluginContext *context) { Q_UNUSED(context) }
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.h b/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.h
deleted file mode 100644
index 50bacd7c85..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausmotioncompensation/src/internal/org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator.h
+++ /dev/null
@@ -1,34 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator_h
-#define org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk
-{
- class org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator : public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_photoacoustics_pausmotioncompensation")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
- void start(ctkPluginContext *context) override;
- void stop(ctkPluginContext *context) override;
-
- }; // org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator
-}
-
-#endif // org_mitk_gui_qt_photoacoustics_pausmotioncompensation_Activator_h
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/CMakeLists.txt b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/CMakeLists.txt
deleted file mode 100644
index 5c420ea0f4..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/CMakeLists.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-# The project name must correspond to the directory name of your plug-in
-# and must not contain periods.
-project(org_mitk_gui_qt_photoacoustics_pausviewer)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE PHOTOACOUSTICS_PAUSVIEWER_EXPORTS
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgets MitkAnnotation
-)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/files.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/files.cmake
deleted file mode 100644
index eabd5d2d68..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/files.cmake
+++ /dev/null
@@ -1,29 +0,0 @@
-set(SRC_CPP_FILES
- QmitkPAUSViewerView.cpp
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_photoacoustics_pausviewer_Activator.cpp
-)
-
-set(UI_FILES
- src/internal/QmitkPAUSViewerViewControls.ui
-)
-
-set(MOC_H_FILES
- src/QmitkPAUSViewerView.h
- src/internal/org_mitk_gui_qt_photoacoustics_pausviewer_Activator.h
-)
-
-set(CACHED_RESOURCE_FILES
- resources/iconPAUSViewer.svg
- plugin.xml
-)
-
-foreach(file ${SRC_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/${file})
-endforeach(file ${SRC_CPP_FILES})
-
-foreach(file ${INTERNAL_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/internal/${file})
-endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/manifest_headers.cmake
deleted file mode 100644
index bd3c813501..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "PA US Viewer")
-set(Plugin-Version "0.9")
-set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
-set(Plugin-ContactAddress "http://www.mitk.org")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/plugin.xml b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/plugin.xml
deleted file mode 100644
index 841dacc1b8..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/plugin.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.photoacoustics.pausviewer"
- name="PA US Viewer"
- category="Photoacoustics"
- class="QmitkPAUSViewerView"
- icon="resources/iconPAUSViewer.svg" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/resources/PAUSViewer.png b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/resources/PAUSViewer.png
deleted file mode 100644
index 8c0e9f9c88..0000000000
Binary files a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/resources/PAUSViewer.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/resources/iconPAUSViewer.svg b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/resources/iconPAUSViewer.svg
deleted file mode 100644
index fa91872af4..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/resources/iconPAUSViewer.svg
+++ /dev/null
@@ -1,62 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<svg
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://creativecommons.org/ns#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:svg="http://www.w3.org/2000/svg"
- xmlns="http://www.w3.org/2000/svg"
- xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
- xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- xml:space="preserve"
- enable-background="new 0 0 1792 1792"
- viewBox="0 0 1792 1792"
- height="128"
- width="128"
- y="0px"
- x="0px"
- id="Layer_1"
- version="1.1"
- inkscape:version="0.91 r13725"
- sodipodi:docname="iconPAUSViewer.svg"><sodipodi:namedview
- pagecolor="#ffffff"
- bordercolor="#666666"
- borderopacity="1"
- objecttolerance="10"
- gridtolerance="10"
- guidetolerance="10"
- inkscape:pageopacity="0"
- inkscape:pageshadow="2"
- inkscape:window-width="1549"
- inkscape:window-height="1176"
- id="namedview7"
- showgrid="false"
- inkscape:zoom="0.26339286"
- inkscape:cx="247.61536"
- inkscape:cy="845.87763"
- inkscape:window-x="51"
- inkscape:window-y="24"
- inkscape:window-maximized="1"
- inkscape:current-layer="Layer_1" /><metadata
- id="metadata11"><rdf:RDF><cc:Work
- rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
- rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title /></cc:Work></rdf:RDF></metadata><defs
- id="defs9" /><path
- id="path3"
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diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.cpp
deleted file mode 100644
index c5952656d8..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.cpp
+++ /dev/null
@@ -1,155 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-#include "mitkScaleLegendAnnotation.h"
-#include "mitkLayoutAnnotationRenderer.h"
-#include "mitkManualPlacementAnnotationRenderer.h"
-#include "mitkTextAnnotation2D.h"
-
-#include "QmitkPAUSViewerView.h"
-
-const std::string QmitkPAUSViewerView::VIEW_ID = "org.mitk.views.photoacoustics.pausviewer";
-
-QmitkPAUSViewerView::QmitkPAUSViewerView() : m_PADataStorage(mitk::StandaloneDataStorage::New()), m_USDataStorage(mitk::StandaloneDataStorage::New()), m_UltrasoundReference(nullptr)
-{
-}
-
-QmitkPAUSViewerView::~QmitkPAUSViewerView()
-{
- if(m_UltrasoundReference != nullptr)
- *m_UltrasoundReference = nullptr;
-}
-
-void QmitkPAUSViewerView::InitWindows()
-{
- AddOverlays();
-}
-
-void QmitkPAUSViewerView::SetFocus()
-{
-}
-
-void QmitkPAUSViewerView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer>& /*nodes*/)
-{
-}
-
-void QmitkPAUSViewerView::CreateQtPartControl(QWidget *parent)
-{
- m_Controls = new Ui::QmitkPAUSViewerViewControls;
- m_Controls->setupUi(parent);
-
- m_Controls->m_PARenderWindow->GetRenderer()->SetDataStorage(m_PADataStorage);
- m_Controls->m_USRenderWindow->GetRenderer()->SetDataStorage(m_USDataStorage);
-}
-
-void QmitkPAUSViewerView::SetPADataStorage(mitk::StandaloneDataStorage::Pointer paStore)
-{
- if (m_Controls == nullptr)
- return;
-
- m_PADataStorage = paStore;
- m_Controls->m_PARenderWindow->GetRenderer()->SetDataStorage(m_PADataStorage);
- m_Controls->m_PALevelWindow->SetDataStorage(m_PADataStorage);
-}
-
-void QmitkPAUSViewerView::SetUSDataStorage(mitk::StandaloneDataStorage::Pointer usStore)
-{
- if (m_Controls == nullptr)
- return;
-
- m_USDataStorage = usStore;
- m_Controls->m_USRenderWindow->GetRenderer()->SetDataStorage(m_USDataStorage);
- m_Controls->m_USLevelWindow->SetDataStorage(m_USDataStorage);
-}
-
-vtkRenderWindow* QmitkPAUSViewerView::GetPARenderWindow()
-{
- if (m_Controls == nullptr)
- return nullptr;
-
- return m_Controls->m_PARenderWindow->renderWindow();
-}
-
-vtkRenderWindow* QmitkPAUSViewerView::GetUSRenderWindow()
-{
- if (m_Controls == nullptr)
- return nullptr;
-
- return m_Controls->m_USRenderWindow->renderWindow();
-}
-
-
-void QmitkPAUSViewerView::AddOverlays()
-{
- //if (m_PARenderer == nullptr || /*m_PAOverlayController == nullptr||*/ m_USRenderer == nullptr /*|| m_USOverlayController == nullptr*/)
- //{
- m_PARenderer = mitk::BaseRenderer::GetInstance(GetPARenderWindow());
- m_USRenderer = mitk::BaseRenderer::GetInstance(GetUSRenderWindow());
- //}
- MITK_INFO << "1111111111111111111111";
- mitk::ScaleLegendAnnotation::Pointer scaleAnnotation = mitk::ScaleLegendAnnotation::New();
- //scaleAnnotation->SetLeftAxisVisibility(true);
- //scaleAnnotation->SetRightAxisVisibility(false);
- //scaleAnnotation->SetRightAxisVisibility(false);
- //scaleAnnotation->SetTopAxisVisibility(false);
- //scaleAnnotation->SetCornerOffsetFactor(0);
- MITK_INFO << "1111111111111111111111";
-
- // Add Overlays
- //![TextAnnotation2D]
- // Create a textAnnotation2D
- mitk::TextAnnotation2D::Pointer textAnnotation = mitk::TextAnnotation2D::New();
-
- textAnnotation->SetText("Test!"); // set UTF-8 encoded text to render
- textAnnotation->SetFontSize(40);
- textAnnotation->SetColor(1, 0, 0); // Set text color to red
- textAnnotation->SetOpacity(0.5);
- MITK_INFO << "1111111111111111111111";
-
- // The position of the Annotation can be set to a fixed coordinate on the display.
- mitk::Point2D pos;
- pos[0] = 10;
- pos[1] = 20;
- textAnnotation->SetPosition2D(pos);
- MITK_INFO << "1111111111111111111111";
-
- std::string rendererID = m_PARenderer->GetName();
-
- // The LayoutAnnotationRenderer can place the TextAnnotation2D at some defined corner positions
- mitk::LayoutAnnotationRenderer::AddAnnotation(
- textAnnotation, rendererID, mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1);
- mitk::LayoutAnnotationRenderer::AddAnnotation(
- textAnnotation, m_PARenderer.GetPointer(), mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1);
- mitk::ManualPlacementAnnotationRenderer::AddAnnotation(
- textAnnotation, m_PARenderer.GetPointer());
- MITK_INFO << "1111111111111111111111";
-
-
- mitk::LayoutAnnotationRenderer::AddAnnotation(scaleAnnotation.GetPointer(), m_PARenderer->GetName(), mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1);
- mitk::LayoutAnnotationRenderer::AddAnnotation(scaleAnnotation.GetPointer(), m_USRenderer, mitk::LayoutAnnotationRenderer::TopLeft, 5, 5, 1);
- MITK_INFO << "1111111111111111111111";
-
-}
-
-void QmitkPAUSViewerView::RemoveOverlays()
-{
- // m_PAOverlayManager->RemoveAllOverlays();
-}
-
-void QmitkPAUSViewerView::SetUltrasoundReference(QmitkPAUSViewerView** ultrasoundReference)
-{
- m_UltrasoundReference = ultrasoundReference;
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.h b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.h
deleted file mode 100644
index f8aaa5d4ee..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/QmitkPAUSViewerView.h
+++ /dev/null
@@ -1,70 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef QMITKPAUSVIEWERVIEW_H_INCLUDED
-#define QMITKPAUSVIEWERVIEW_H_INCLUDED
-
-#include <berryISelectionListener.h>
-#include <QmitkAbstractView.h>
-#include <mitkStandaloneDataStorage.h>
-#include <mitkBaseRenderer.h>
-#include "QmitkRenderWindow.h"
-
-#include "ui_QmitkPAUSViewerViewControls.h"
-#include "org_mitk_gui_qt_photoacoustics_pausviewer_Export.h"
-
-#include "mitkCommon.h"
-
-class PHOTOACOUSTICS_PAUSVIEWER_EXPORTS QmitkPAUSViewerView : public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- QmitkPAUSViewerView();
- ~QmitkPAUSViewerView() override;
-
- void CreateQtPartControl(QWidget *parent) override;
- void InitWindows();
-
- void SetPADataStorage(mitk::StandaloneDataStorage::Pointer paStore);
- void SetUSDataStorage(mitk::StandaloneDataStorage::Pointer usStore);
-
- vtkRenderWindow* GetPARenderWindow();
- vtkRenderWindow* GetUSRenderWindow();
-
- void SetUltrasoundReference(QmitkPAUSViewerView** ultrasoundReference);
-
-protected:
-
- void AddOverlays();
- void RemoveOverlays();
-
- mitk::StandaloneDataStorage::Pointer m_PADataStorage;
- mitk::StandaloneDataStorage::Pointer m_USDataStorage;
- mitk::BaseRenderer::Pointer m_PARenderer;
- mitk::BaseRenderer::Pointer m_USRenderer;
-
- void SetFocus() override;
-
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList<mitk::DataNode::Pointer>&) override;
-
- Ui::QmitkPAUSViewerViewControls* m_Controls;
- QmitkPAUSViewerView** m_UltrasoundReference;
-};
-
-#endif // QMITKPAUSVIEWERVIEW_H_INCLUDED
-
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/QmitkPAUSViewerViewControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/QmitkPAUSViewerViewControls.ui
deleted file mode 100644
index 8d192e8de4..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/QmitkPAUSViewerViewControls.ui
+++ /dev/null
@@ -1,129 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkPAUSViewerViewControls</class>
- <widget class="QWidget" name="QmitkPAUSViewerViewControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>1086</width>
- <height>744</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <property name="autoFillBackground">
- <bool>false</bool>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QmitkRenderWindow" name="m_USRenderWindow">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Ultrasound</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2">
- <widget class="QmitkRenderWindow" name="m_PARenderWindow">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <widget class="QLabel" name="label_2">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Photoacoustics</string>
- </property>
- </widget>
- </item>
- <item row="0" column="3">
- <widget class="QmitkLevelWindowWidget" name="m_PALevelWindow" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QmitkLevelWindowWidget" name="m_USLevelWindow" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <customwidgets>
- <customwidget>
- <class>QmitkRenderWindow</class>
- <extends>QListView</extends>
- <header>QmitkRenderWindow.h</header>
- </customwidget>
- <customwidget>
- <class>QmitkLevelWindowWidget</class>
- <extends>QWidget</extends>
- <header>QmitkLevelWindowWidget.h</header>
- <container>1</container>
- </customwidget>
- </customwidgets>
- <includes>
- <include location="local">QmitkDataStorageComboBox.h</include>
- </includes>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/org_mitk_gui_qt_photoacoustics_pausviewer_Activator.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/org_mitk_gui_qt_photoacoustics_pausviewer_Activator.cpp
deleted file mode 100644
index e8add31500..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/org_mitk_gui_qt_photoacoustics_pausviewer_Activator.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "org_mitk_gui_qt_photoacoustics_pausviewer_Activator.h"
-#include "QmitkPAUSViewerView.h"
-
-
-namespace mitk {
-
- void org_mitk_gui_qt_photoacoustics_pausviewer_Activator::start(ctkPluginContext* context)
- {
- BERRY_REGISTER_EXTENSION_CLASS(QmitkPAUSViewerView, context)
- }
-
- void org_mitk_gui_qt_photoacoustics_pausviewer_Activator::stop(ctkPluginContext* context)
- {
- Q_UNUSED(context)
- }
-
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/org_mitk_gui_qt_photoacoustics_pausviewer_Activator.h b/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/org_mitk_gui_qt_photoacoustics_pausviewer_Activator.h
deleted file mode 100644
index aae45490d2..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.pausviewer/src/internal/org_mitk_gui_qt_photoacoustics_pausviewer_Activator.h
+++ /dev/null
@@ -1,35 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-#ifndef _MITKPAUSVIEWERPLUGINACTIVATOR_H
-#define _MITKPAUSVIEWERPLUGINACTIVATOR_H
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
- class org_mitk_gui_qt_photoacoustics_pausviewer_Activator :
- public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_photoacoustics_pausviewer")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
-
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
- };
-
-}
-
-#endif // _MITKPAUSVIEWERPLUGINACTIVATOR_H
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/CMakeLists.txt b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/CMakeLists.txt
deleted file mode 100644
index e481678c85..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/CMakeLists.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-project(org_mitk_gui_qt_photoacoustics_simulation)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE PHOTOACOUSTICSIMULATION_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkPhotoacousticsLib MitkQtWidgetsExt
- PACKAGE_DEPENDS PUBLIC ITK
-)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/files.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/files.cmake
deleted file mode 100644
index 1d8c9f11f8..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/files.cmake
+++ /dev/null
@@ -1,42 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_photoacousticsimulation_Activator.cpp
- PASimulator.cpp
-)
-
-set(UI_FILES
- src/internal/PASimulatorControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_photoacousticsimulation_Activator.h
- src/internal/PASimulator.h
-)
-
-# list of resource files which can be used by the plug-in
-# system without loading the plug-ins shared library,
-# for example the icon used in the menu and tabs for the
-# plug-in views in the workbench
-set(CACHED_RESOURCE_FILES
- resources/pai_simulation.svg
- plugin.xml
-)
-
-# list of Qt .qrc files which contain additional resources
-# specific to this plugin
-set(QRC_FILES
-
-)
-
-set(CPP_FILES )
-
-foreach(file ${SRC_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/${file})
-endforeach(file ${SRC_CPP_FILES})
-
-foreach(file ${INTERNAL_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/internal/${file})
-endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/manifest_headers.cmake
deleted file mode 100644
index 4580c5bd1b..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Photoacousticsimulation")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "DKFZ")
-set(Plugin-ContactAddress "")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/plugin.xml b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/plugin.xml
deleted file mode 100644
index 1e47858a91..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/plugin.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.pasimulator"
- name="Photoacoustic tissue generator"
- class="PASimulator"
- icon="resources/pai_simulation.svg" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/resources/pai_simulation.svg b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/resources/pai_simulation.svg
deleted file mode 100644
index 23e71640e5..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/resources/pai_simulation.svg
+++ /dev/null
@@ -1,74 +0,0 @@
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-<svg
- xmlns:dc="http://purl.org/dc/elements/1.1/"
- xmlns:cc="http://creativecommons.org/ns#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:svg="http://www.w3.org/2000/svg"
- xmlns="http://www.w3.org/2000/svg"
- xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
- xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
- xml:space="preserve"
- enable-background="new 0 0 1792 1792"
- viewBox="0 0 1792 1792"
- height="128"
- width="128"
- y="0px"
- x="0px"
- id="Layer_1"
- version="1.1"
- sodipodi:docname="pai_simulation.svg"
- inkscape:version="0.92.1 r15371"><sodipodi:namedview
- pagecolor="#ffffff"
- bordercolor="#666666"
- borderopacity="1"
- objecttolerance="10"
- gridtolerance="10"
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- inkscape:pageopacity="0"
- inkscape:pageshadow="2"
- inkscape:window-width="1600"
- inkscape:window-height="1125"
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- inkscape:window-x="-9"
- inkscape:window-y="-9"
- inkscape:window-maximized="1"
- inkscape:current-layer="Layer_1" /><metadata
- id="metadata11"><rdf:RDF><cc:Work
- rdf:about=""><dc:format>image/svg+xml</dc:format><dc:type
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diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.cpp
deleted file mode 100644
index bc0de72a49..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.cpp
+++ /dev/null
@@ -1,252 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// Qmitk
-#include "PASimulator.h"
-
-// Qt
-#include <QMessageBox>
-#include <QCheckBox>
-#include <QFileDialog>
-
-// mitk
-#include <mitkImage.h>
-#include <mitkDataNode.h>
-#include <mitkIOUtil.h>
-
-#include <iostream>
-#include <fstream>
-
-const std::string PASimulator::VIEW_ID = "org.mitk.views.pasimulator";
-
-void PASimulator::SetFocus()
-{
- m_Controls.pushButtonShowRandomTissue->setFocus();
-}
-
-void PASimulator::CreateQtPartControl(QWidget *parent)
-{
- m_Controls.setupUi(parent);
- connect(m_Controls.pushButtonShowRandomTissue, SIGNAL(clicked()), this, SLOT(DoImageProcessing()));
- connect(m_Controls.pushButtonOpenPath, SIGNAL(clicked()), this, SLOT(OpenFolder()));
- connect(m_Controls.pushButtonOpenBinary, SIGNAL(clicked()), this, SLOT(OpenBinary()));
- connect(m_Controls.checkBoxGenerateBatch, SIGNAL(clicked()), this, SLOT(UpdateVisibilityOfBatchCreation()));
- connect(m_Controls.pushButtonAjustWavelength, SIGNAL(clicked()), this, SLOT(UpdateParametersAccordingToWavelength()));
- connect(m_Controls.checkBoxRngSeed, SIGNAL(clicked()), this, SLOT(ClickedCheckboxFixedSeed()));
- connect(m_Controls.checkBoxRandomizeParameters, SIGNAL(clicked()), this, SLOT(ClickedRandomizePhysicalParameters()));
-
- auto home = std::getenv("HOME");
- std::string home_env = "";
- if (home != nullptr)
- {
- home_env = std::string(home);
- }
- else
- {
- home = std::getenv("HOMEPATH");
- if (home != nullptr)
- {
- home_env = std::string(home);
- }
- }
- m_Controls.label_NrrdFilePath->setText(home_env.c_str());
-
- m_PhotoacousticPropertyCalculator = mitk::pa::PropertyCalculator::New();
-
- UpdateVisibilityOfBatchCreation();
- ClickedRandomizePhysicalParameters();
- ClickedCheckboxFixedSeed();
-}
-
-void PASimulator::ClickedRandomizePhysicalParameters()
-{
- m_Controls.spinboxRandomizeParameters->setEnabled(m_Controls.checkBoxRandomizeParameters->isChecked());
-}
-
-void PASimulator::ClickedCheckboxFixedSeed()
-{
- m_Controls.spinBoxRngSeed->setEnabled(m_Controls.checkBoxRngSeed->isChecked());
-}
-
-void PASimulator::UpdateParametersAccordingToWavelength()
-{
- int wavelength = m_Controls.spinboxWavelength->value();
- double bloodOxygenation = m_Controls.spinboxBloodOxygenSaturation->value() / 100;
-
- auto result = m_PhotoacousticPropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::BLOOD, wavelength, bloodOxygenation);
- m_Controls.spinboxMaxAbsorption->setValue(result.mua);
- m_Controls.spinboxMinAbsorption->setValue(result.mua);
- m_Controls.spinboxBloodVesselScatteringMinimum->setValue(result.mus);
- m_Controls.spinboxBloodVesselScatteringMaximum->setValue(result.mus);
- m_Controls.spinboxBloodVesselAnisotropyMinimum->setValue(result.g);
- m_Controls.spinboxBloodVesselAnisotropyMaximum->setValue(result.g);
-
- result = m_PhotoacousticPropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::EPIDERMIS, wavelength, bloodOxygenation);
- m_Controls.spinboxSkinAbsorption->setValue(result.mua);
- m_Controls.spinboxSkinScattering->setValue(result.mus);
- m_Controls.spinboxSkinAnisotropy->setValue(result.g);
-
- result = m_PhotoacousticPropertyCalculator->CalculatePropertyForSpecificWavelength(
- mitk::pa::PropertyCalculator::TissueType::STANDARD_TISSUE, wavelength, bloodOxygenation);
- m_Controls.spinboxBackgroundAbsorption->setValue(result.mua);
- m_Controls.spinboxBackgroundScattering->setValue(result.mus);
- m_Controls.spinboxBackgroundAnisotropy->setValue(result.g);
-}
-
-void PASimulator::UpdateVisibilityOfBatchCreation()
-{
- m_Controls.widgetBatchFile->setVisible(m_Controls.checkBoxGenerateBatch->isChecked());
-}
-
-mitk::pa::TissueGeneratorParameters::Pointer PASimulator::GetParametersFromUIInput()
-{
- auto parameters = mitk::pa::TissueGeneratorParameters::New();
-
- // Getting settings from UI
- // General settings
- parameters->SetXDim(m_Controls.spinboxXDim->value());
- parameters->SetYDim(m_Controls.spinboxYDim->value());
- parameters->SetZDim(m_Controls.spinboxZDim->value());
- parameters->SetDoPartialVolume(m_Controls.checkBoxPartialVolume->isChecked());
- parameters->SetRandomizePhysicalProperties(m_Controls.checkBoxRandomizeParameters->isChecked());
- parameters->SetRandomizePhysicalPropertiesPercentage(m_Controls.spinboxRandomizeParameters->value());
- parameters->SetVoxelSpacingInCentimeters(m_Controls.spinboxSpacing->value());
- parameters->SetUseRngSeed(m_Controls.checkBoxRngSeed->isChecked());
- parameters->SetRngSeed(m_Controls.spinBoxRngSeed->value());
-
- // Monte Carlo simulation parameters
- parameters->SetMCflag(m_Controls.spinboxMcFlag->value());
- parameters->SetMCLaunchflag(m_Controls.spinboxLaunchFlag->value());
- parameters->SetMCBoundaryflag(m_Controls.spinboxboundaryFlag->value());
- parameters->SetMCLaunchPointX(m_Controls.spinboxLaunchpointX->value());
- parameters->SetMCLaunchPointY(m_Controls.spinboxLaunchpointY->value());
- parameters->SetMCLaunchPointZ(m_Controls.spinboxLaunchpointZ->value());
- parameters->SetMCFocusPointX(m_Controls.spinboxFocuspointX->value());
- parameters->SetMCFocusPointY(m_Controls.spinboxFocuspointY->value());
- parameters->SetMCFocusPointZ(m_Controls.spinboxFocuspointZ->value());
- parameters->SetMCTrajectoryVectorX(m_Controls.spinboxTrajectoryVectorX->value());
- parameters->SetMCTrajectoryVectorY(m_Controls.spinboxTrajectoryVectorY->value());
- parameters->SetMCTrajectoryVectorZ(m_Controls.spinboxTrajectoryVectorZ->value());
- parameters->SetMCRadius(m_Controls.spinboxRadius->value());
- parameters->SetMCWaist(m_Controls.spinboxWaist->value());
-
- // Vessel settings
- parameters->SetMaxVesselAbsorption(m_Controls.spinboxMaxAbsorption->value());
- parameters->SetMinVesselAbsorption(m_Controls.spinboxMinAbsorption->value());
- parameters->SetMaxVesselBending(m_Controls.spinboxMaxBending->value());
- parameters->SetMinVesselBending(m_Controls.spinboxMinBending->value());
- parameters->SetMaxVesselRadiusInMillimeters(m_Controls.spinboxMaxDiameter->value());
- parameters->SetMinVesselRadiusInMillimeters(m_Controls.spinboxMinDiameter->value());
- parameters->SetMaxNumberOfVessels(m_Controls.spinboxMaxVessels->value());
- parameters->SetMinNumberOfVessels(m_Controls.spinboxMinVessels->value());
- parameters->SetMinVesselScattering(m_Controls.spinboxBloodVesselScatteringMinimum->value());
- parameters->SetMaxVesselScattering(m_Controls.spinboxBloodVesselScatteringMaximum->value());
- parameters->SetMinVesselAnisotropy(m_Controls.spinboxBloodVesselAnisotropyMinimum->value());
- parameters->SetMaxVesselAnisotropy(m_Controls.spinboxBloodVesselAnisotropyMaximum->value());
- parameters->SetVesselBifurcationFrequency(m_Controls.spinboxBifurcationFrequency->value());
- parameters->SetMinVesselZOrigin(m_Controls.spinboxMinSpawnDepth->value());
- parameters->SetMaxVesselZOrigin(m_Controls.spinboxMaxSpawnDepth->value());
-
- // Background tissue settings
- parameters->SetMinBackgroundAbsorption(m_Controls.spinboxBackgroundAbsorption->value());
- parameters->SetMaxBackgroundAbsorption(m_Controls.spinboxBackgroundAbsorption->value());
- parameters->SetBackgroundScattering(m_Controls.spinboxBackgroundScattering->value());
- parameters->SetBackgroundAnisotropy(m_Controls.spinboxBackgroundAnisotropy->value());
-
- // Air settings
- parameters->SetAirThicknessInMillimeters(m_Controls.spinboxAirThickness->value());
-
- //Skin tissue settings
- parameters->SetSkinThicknessInMillimeters(m_Controls.spinboxSkinThickness->value());
- parameters->SetSkinAbsorption(m_Controls.spinboxSkinAbsorption->value());
- parameters->SetSkinScattering(m_Controls.spinboxSkinScattering->value());
- parameters->SetSkinAnisotropy(m_Controls.spinboxSkinAnisotropy->value());
-
- parameters->SetCalculateNewVesselPositionCallback(&mitk::pa::VesselMeanderStrategy::CalculateNewRandomlyDivergingDirectionVector);
-
- return parameters;
-}
-
-void PASimulator::DoImageProcessing()
-{
- int numberOfVolumes = 1;
-
- if (m_Controls.checkBoxGenerateBatch->isChecked())
- {
- if (m_Controls.labelBinarypath->text().isNull() || m_Controls.labelBinarypath->text().isEmpty())
- {
- QMessageBox::warning(nullptr, QString("Warning"), QString("You need to specify the binary first!"));
- return;
- }
-
- numberOfVolumes = m_Controls.spinboxNumberVolumes->value();
-
- if (numberOfVolumes < 1)
- {
- QMessageBox::warning(nullptr, QString("Warning"), QString("You need to create at least one volume!"));
- return;
- }
- }
-
- auto tissueParameters = GetParametersFromUIInput();
-
- for (int volumeIndex = 0; volumeIndex < numberOfVolumes; volumeIndex++)
- {
- mitk::pa::InSilicoTissueVolume::Pointer volume =
- mitk::pa::InSilicoTissueGenerator::GenerateInSilicoData(tissueParameters);
-
- mitk::Image::Pointer tissueVolume = volume->ConvertToMitkImage();
-
- if (m_Controls.checkBoxGenerateBatch->isChecked())
- {
- std::string nrrdFilePath = m_Controls.label_NrrdFilePath->text().toStdString();
- std::string tissueName = m_Controls.lineEditTissueName->text().toStdString();
- std::string binaryPath = m_Controls.labelBinarypath->text().toStdString();
- long numberOfPhotons = m_Controls.spinboxNumberPhotons->value() * 1000L;
-
- auto batchParameters = mitk::pa::SimulationBatchGeneratorParameters::New();
- batchParameters->SetBinaryPath(binaryPath);
- batchParameters->SetNrrdFilePath(nrrdFilePath);
- batchParameters->SetNumberOfPhotons(numberOfPhotons);
- batchParameters->SetTissueName(tissueName);
- batchParameters->SetVolumeIndex(volumeIndex);
- batchParameters->SetYOffsetLowerThresholdInCentimeters(m_Controls.spinboxFromValue->value());
- batchParameters->SetYOffsetUpperThresholdInCentimeters(m_Controls.spinboxToValue->value());
- batchParameters->SetYOffsetStepInCentimeters(m_Controls.spinboxStepValue->value());
- mitk::pa::SimulationBatchGenerator::WriteBatchFileAndSaveTissueVolume(batchParameters, tissueVolume);
- }
- else
- {
- mitk::DataNode::Pointer dataNode = mitk::DataNode::New();
- dataNode->SetData(tissueVolume);
- dataNode->SetName(m_Controls.lineEditTissueName->text().toStdString());
- this->GetDataStorage()->Add(dataNode);
- mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage());
- }
- }
-}
-
-void PASimulator::OpenFolder()
-{
- m_Controls.label_NrrdFilePath->setText(QFileDialog::getExistingDirectory().append("/"));
-}
-
-void PASimulator::OpenBinary()
-{
- m_Controls.labelBinarypath->setText(QFileDialog::getOpenFileName());
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.h b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.h
deleted file mode 100644
index 60dc6b4dd2..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.h
+++ /dev/null
@@ -1,72 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef PASimulator_h
-#define PASimulator_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-
-#include "ui_PASimulatorControls.h"
-
-#include "mitkPATissueGenerator.h"
-#include "mitkPATissueGeneratorParameters.h"
-#include "mitkPAInSilicoTissueVolume.h"
-#include "mitkPAPropertyCalculator.h"
-#include "mitkPASimulationBatchGenerator.h"
-
-/**
- \brief PASimulator
-
- \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation.
-
- \sa QmitkAbstractView
- \ingroup ${plugin_target}_internal
-*/
-class PASimulator : public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- protected slots:
-
- /// \brief Called when the user clicks the GUI button
- void DoImageProcessing();
- void ClickedCheckboxFixedSeed();
- void ClickedRandomizePhysicalParameters();
- void OpenFolder();
- void OpenBinary();
- void UpdateVisibilityOfBatchCreation();
- void UpdateParametersAccordingToWavelength();
-
-protected:
-
- void CreateQtPartControl(QWidget *parent) override;
-
- void SetFocus() override;
-
- Ui::PASimulatorControls m_Controls;
-
- mitk::pa::PropertyCalculator::Pointer m_PhotoacousticPropertyCalculator;
-
-private:
-
- mitk::pa::TissueGeneratorParameters::Pointer GetParametersFromUIInput();
-};
-
-#endif // PASimulator_h
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulatorControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulatorControls.ui
deleted file mode 100644
index 4187e1e967..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulatorControls.ui
+++ /dev/null
@@ -1,4728 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>PASimulatorControls</class>
- <widget class="QWidget" name="PASimulatorControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>437</width>
- <height>655</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="font">
- <font>
- <family>Ubuntu</family>
- </font>
- </property>
- <property name="contextMenuPolicy">
- <enum>Qt::NoContextMenu</enum>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <property name="windowIcon">
- <iconset>
- <normaloff>:/org.mitk.gui.qt.photoacousticsimulation/resources/icon.xpm</normaloff>:/org.mitk.gui.qt.photoacousticsimulation/resources/icon.xpm</iconset>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QTabWidget" name="tabWidget">
- <property name="sizePolicy">
- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>415</width>
- <height>600</height>
- </size>
- </property>
- <property name="font">
- <font>
- <family>Ubuntu</family>
- </font>
- </property>
- <property name="currentIndex">
- <number>0</number>
- </property>
- <widget class="QWidget" name="tabGenerator">
- <attribute name="title">
- <string>Generator</string>
- </attribute>
- <widget class="QWidget" name="verticalWidget_2" native="true">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>10</y>
- <width>391</width>
- <height>581</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>391</width>
- <height>581</height>
- </size>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="label_16">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Volume parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_17">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_26">
- <item>
- <widget class="QLabel" name="label_55">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Tissue name:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_18">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Size x:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_15">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>Spacing:</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_25">
- <item>
- <widget class="QLineEdit" name="lineEditTissueName">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>PhotoacousticTissue</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_6">
- <item>
- <widget class="QSpinBox" name="spinboxXDim">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>35</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_19">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>y:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinboxYDim">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>50</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_20">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>z:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinboxZDim">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximum">
- <number>9999</number>
- </property>
- <property name="value">
- <number>50</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="labelSigma_5">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>voxels</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_6">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_7">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxSpacing">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>0.120000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_17">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_7">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_18">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_27">
- <item>
- <widget class="QLabel" name="label_99">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Randomize:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_40">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Custom seed:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_59">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Partial volume effects:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_58">
- <property name="text">
- <string>Generate batch file output:</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_29">
- <item>
- <widget class="QCheckBox" name="checkBoxRandomizeParameters">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxRngSeed">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxPartialVolume">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxGenerateBatch">
- <property name="text">
- <string/>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_28">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_53">
- <item>
- <widget class="QLabel" name="labelSigma_2">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>sigma: </string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxRandomizeParameters">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>0</number>
- </property>
- <property name="maximum">
- <double>100.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>2.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="labelSigma_3">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>%</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_48">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_16">
- <item>
- <widget class="QSpinBox" name="spinBoxRngSeed">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximum">
- <number>999999999</number>
- </property>
- <property name="value">
- <number>1337</number>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_18">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_29">
- <item>
- <spacer name="horizontalSpacer_17">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_15">
- <item>
- <spacer name="horizontalSpacer_15">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QWidget" name="widgetBatchFile" native="true">
- <layout class="QVBoxLayout" name="verticalLayout_5">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_24">
- <item>
- <widget class="QLabel" name="label_53">
- <property name="text">
- <string>Number of volumes to generate:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinboxNumberVolumes">
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="maximum">
- <number>9999999</number>
- </property>
- <property name="value">
- <number>1</number>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_23">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_28">
- <item>
- <widget class="QLabel" name="label_57">
- <property name="text">
- <string>Save generated tissue path:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButtonOpenPath">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>50</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>open</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_NrrdFilePath">
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_31">
- <item>
- <widget class="QLabel" name="label_60">
- <property name="text">
- <string>Path to MitkMcxyz binary:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButtonOpenBinary">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>50</width>
- <height>0</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>50</width>
- <height>16777215</height>
- </size>
- </property>
- <property name="text">
- <string>open</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="labelBinarypath">
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_30">
- <item>
- <widget class="QLabel" name="label_61">
- <property name="text">
- <string>From (cm):</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxFromValue">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="minimum">
- <double>-100000.000000000000000</double>
- </property>
- <property name="maximum">
- <double>100000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>-1.800000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_62">
- <property name="text">
- <string>To (cm):</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxToValue">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="minimum">
- <double>-10000.000000000000000</double>
- </property>
- <property name="maximum">
- <double>10000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>1.800000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_63">
- <property name="text">
- <string>Step:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxStepValue">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="minimum">
- <double>-10000.000000000000000</double>
- </property>
- <property name="maximum">
- <double>10000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>0.120000000000000</double>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_23">
- <item>
- <widget class="QLabel" name="label_51">
- <property name="text">
- <string>Number of Photons (x1000):</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinboxNumberPhotons">
- <property name="minimum">
- <number>0</number>
- </property>
- <property name="maximum">
- <number>999999999</number>
- </property>
- <property name="singleStep">
- <number>1</number>
- </property>
- <property name="value">
- <number>100000</number>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="pushButtonShowRandomTissue">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Generate Tissue</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="tabTissue">
- <attribute name="title">
- <string>Tissue</string>
- </attribute>
- <widget class="QWidget" name="verticalWidget_3" native="true">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>10</y>
- <width>391</width>
- <height>581</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>391</width>
- <height>581</height>
- </size>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_82">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_17">
- <item>
- <widget class="QLabel" name="label_101">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <italic>false</italic>
- <bold>true</bold>
- <underline>false</underline>
- </font>
- </property>
- <property name="text">
- <string>Air Parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_104">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>Thickness:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_103">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>10</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>10</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_65">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>75</weight>
- <italic>false</italic>
- <bold>true</bold>
- <underline>false</underline>
- </font>
- </property>
- <property name="text">
- <string>Background Parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_66">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Absorption coefficient:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_68">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Scattering coefficient:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_70">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Anisotropy facor:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_107">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>10</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>10</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_76">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>75</weight>
- <italic>false</italic>
- <bold>true</bold>
- <underline>false</underline>
- </font>
- </property>
- <property name="text">
- <string>Skin Parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_95">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Thickness:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_71">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Absorption coefficient:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_73">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Scattering coefficient:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_75">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Anisotropy facor:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_109">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>10</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>10</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_16">
- <item>
- <widget class="QLabel" name="label_102">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_57">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxAirThickness">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximum">
- <double>999.990000000000009</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>12.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_105">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>mm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_52">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_106">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>10</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>10</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_77">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_32">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBackgroundAbsorption">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>0.100000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_67">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>per cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_27">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_33">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBackgroundScattering">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.500000000000000</double>
- </property>
- <property name="value">
- <double>15.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_69">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>per cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_28">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_34">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBackgroundAnisotropy">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>0.900000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_29">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_108">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>10</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>10</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_78">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_51">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxSkinThickness">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_96">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>mm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_46">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_35">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxSkinAbsorption">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>3.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_72">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>per cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_30">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_36">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxSkinScattering">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1000.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.500000000000000</double>
- </property>
- <property name="value">
- <double>20.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_74">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>per cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_31">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_37">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxSkinAnisotropy">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>0.900000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_32">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_110">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>10</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>10</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>11</pointsize>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer_4">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="tabVessels">
- <attribute name="title">
- <string>Vessels</string>
- </attribute>
- <widget class="QWidget" name="widgetAdvancedSettings" native="true">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>10</y>
- <width>391</width>
- <height>581</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>391</width>
- <height>581</height>
- </size>
- </property>
- <layout class="QVBoxLayout" name="layoutAdvancedParameters">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="label_13">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="toolTip">
- <string/>
- </property>
- <property name="text">
- <string>Vessel Parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_81">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_15">
- <item>
- <widget class="QLabel" name="label_2">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The number of bloos vessels to generate</string>
- </property>
- <property name="text">
- <string>Count: </string>
- </property>
- <property name="alignment">
- <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_5">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The radius of the blood vessels in mm</string>
- </property>
- <property name="text">
- <string>Radius:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_7">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>the absorption coefficient refers to the number of absorption events per centimeter.</string>
- </property>
- <property name="text">
- <string>Absorption: </string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_48">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The reduced scattering coefficient.
-It refers to the amount of scattering events per centimeter.</string>
- </property>
- <property name="text">
- <string>Scattering: </string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_52">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The anisotropy factor is the probability of a photon to not change its direction after a scattering event.</string>
- </property>
- <property name="text">
- <string>Anisotropy factor: </string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_47">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The bifurcation frequency determines how often the vessel should bifurcate.
-The vessel will bifurcate after meandering a mean of the specified amount of voxels.
-When given a value of 0, the vessel will never bifurcate.</string>
- </property>
- <property name="text">
- <string>Bifurcation frequency:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_10">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The curvedness it a setting to determine how much the vessel is allowed to bend during creation.
-A value of 0 refers to no bending at all and a value of 5 is the maximum.</string>
- </property>
- <property name="text">
- <string>Curvedness: </string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_43">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The spawn depth defines the depth range in which the vessels enter the volume.</string>
- </property>
- <property name="text">
- <string>Spawn depth:</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QSpinBox" name="spinboxMinVessels">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimum number of blood vessels</string>
- </property>
- <property name="minimum">
- <number>0</number>
- </property>
- <property name="value">
- <number>1</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>to</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="spinboxMaxVessels">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The maximum number of blood vessels</string>
- </property>
- <property name="value">
- <number>1</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_6">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Vessels</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_26">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMinDiameter">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimum radius</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="value">
- <double>2.250000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_3">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>to</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMaxDiameter">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The maximum radius</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="value">
- <double>4.050000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_4">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>mm </string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_25">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMinAbsorption">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimum absorption coefficient</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>2.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_8">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>to</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMaxAbsorption">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The maximum absorption coefficient</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>8.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_9">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>per cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_24">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_21">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBloodVesselScatteringMinimum">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimum scattering</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>999.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>1.000000000000000</double>
- </property>
- <property name="value">
- <double>15.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_14">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>to</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBloodVesselScatteringMaximum">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimum scattering</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>999.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>1.000000000000000</double>
- </property>
- <property name="value">
- <double>15.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_50">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>per cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_21">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_22">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBloodVesselAnisotropyMinimum">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimum anisotropy factor</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>0.900000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_11">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>to</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBloodVesselAnisotropyMaximum">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The maximum anisotropy factor</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="maximum">
- <double>1.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.100000000000000</double>
- </property>
- <property name="value">
- <double>0.900000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_20">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_20">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBifurcationFrequency">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The bifurcation frequency determines how often the vessel should bifurcate.
-The vessel will bifurcate after meandering a mean of the specified amount of voxels.
-When given a value of 0, the vessel will never bifurcate.</string>
- </property>
- <property name="decimals">
- <number>0</number>
- </property>
- <property name="minimum">
- <double>1.000000000000000</double>
- </property>
- <property name="maximum">
- <double>999999999.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>5.000000000000000</double>
- </property>
- <property name="value">
- <double>50.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_49">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>voxels</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_19">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMinBending">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimal curvedness of the vessel.
-A value of 0 refers to no bending at all and a value of 5 is the maximum.</string>
- </property>
- <property name="maximum">
- <double>5.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_42">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>to</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMaxBending">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The maximal curvedness of the vessel.
-A value of 0 refers to no bending at all and a value of 5 is the maximum.</string>
- </property>
- <property name="maximum">
- <double>5.000000000000000</double>
- </property>
- <property name="singleStep">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>0.200000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_12">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>A.U.</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_16">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_27">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMinSpawnDepth">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>The minimum spawn depth</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>2.200000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_44">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>to</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxMaxSpawnDepth">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="toolTip">
- <string>the maximum spawn depth</string>
- </property>
- <property name="decimals">
- <number>5</number>
- </property>
- <property name="minimum">
- <double>0.010000000000000</double>
- </property>
- <property name="value">
- <double>4.200000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_45">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>cm</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_35">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>60</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="tabMonteCarlo">
- <attribute name="title">
- <string>Monte Carlo</string>
- </attribute>
- <widget class="QWidget" name="widgetAdvancedSettings_2" native="true">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>10</y>
- <width>391</width>
- <height>581</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>391</width>
- <height>581</height>
- </size>
- </property>
- <layout class="QVBoxLayout" name="layoutAdvancedParameters_2">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="label_21">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Monte Carlo Parameters</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_39">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>General:</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_25">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_33">
- <item>
- <widget class="QLabel" name="label_22">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Mcflag: </string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_25">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Launchflag:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_28">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Boundaryflag:</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_32">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_5">
- <item>
- <widget class="QSpinBox" name="spinboxMcFlag">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="value">
- <number>4</number>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_8">
- <item>
- <widget class="QSpinBox" name="spinboxLaunchFlag">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="minimum">
- <number>0</number>
- </property>
- <property name="value">
- <number>0</number>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_8">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_9">
- <item>
- <widget class="QSpinBox" name="spinboxboundaryFlag">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="minimum">
- <number>1</number>
- </property>
- <property name="value">
- <number>2</number>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_9">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_31">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>Initial launch point:</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_10">
- <item>
- <widget class="QLabel" name="label_23">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>x</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxLaunchpointX">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_24">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>y</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxLaunchpointY">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_26">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>z</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxLaunchpointZ">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_10">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_32">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>Focus point:</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_11">
- <item>
- <widget class="QLabel" name="label_27">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>x</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxFocuspointX">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_29">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>y</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxFocuspointY">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_30">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>z</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxFocuspointZ">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_11">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QLabel" name="label_36">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>Trajectory vector:</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_12">
- <item>
- <widget class="QLabel" name="label_33">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>x</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxTrajectoryVectorX">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_34">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>y</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxTrajectoryVectorY">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.342000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_35">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>z</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QDoubleSpinBox" name="spinboxTrajectoryVectorZ">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.939700000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_12">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_26">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_35">
- <item>
- <widget class="QLabel" name="label_37">
- <property name="text">
- <string>radius:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_38">
- <property name="text">
- <string>waist:</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_34">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_13">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxRadius">
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.500000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_13">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_14">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxWaist">
- <property name="decimals">
- <number>4</number>
- </property>
- <property name="maximum">
- <double>1000.000000000000000</double>
- </property>
- <property name="value">
- <double>0.010000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_14">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <spacer name="verticalSpacer_3">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- <widget class="QWidget" name="tabWavelength">
- <attribute name="title">
- <string>Wavelength</string>
- </attribute>
- <widget class="QWidget" name="widgetAdvancedSettings_3" native="true">
- <property name="geometry">
- <rect>
- <x>10</x>
- <y>10</y>
- <width>391</width>
- <height>581</height>
- </rect>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="MinimumExpanding" vsizetype="MinimumExpanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>391</width>
- <height>581</height>
- </size>
- </property>
- <property name="contextMenuPolicy">
- <enum>Qt::NoContextMenu</enum>
- </property>
- <layout class="QVBoxLayout" name="layoutAdvancedParameters_3">
- <property name="leftMargin">
- <number>0</number>
- </property>
- <property name="topMargin">
- <number>0</number>
- </property>
- <property name="rightMargin">
- <number>0</number>
- </property>
- <property name="bottomMargin">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="label_41">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Adjust physical properties by wavelength</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QTextEdit" name="textEdit">
- <property name="enabled">
- <bool>false</bool>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>250</height>
- </size>
- </property>
- <property name="html">
- <string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
-<html><head><meta name="qrichtext" content="1" /><style type="text/css">
-p, li { white-space: pre-wrap; }
-</style></head><body style=" font-family:'Ubuntu'; font-size:7.8pt; font-weight:400; font-style:normal;">
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">This widget enables the adjustment of the physical properties of the tissue according to a selected wavelength of the light and the oxygen saturation of the blood.</span></p>
-<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
-<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">The algorithm and measurements were provided by the publication </span><span style=" font-size:11pt; font-weight:600;">Optical properties of biological tissues: a review </span><span style=" font-size:11pt;">by Steve L. Jacques.</span></p></body></html></string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_19">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_31">
- <item>
- <widget class="QLabel" name="label_80">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Wavelength:</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_81">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>Vessel oxygen saturation:</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_30">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_38">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxWavelength">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>0</number>
- </property>
- <property name="minimum">
- <double>300.000000000000000</double>
- </property>
- <property name="maximum">
- <double>1000.000000000000000</double>
- </property>
- <property name="value">
- <double>650.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_33">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_39">
- <item>
- <widget class="QDoubleSpinBox" name="spinboxBloodOxygenSaturation">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="decimals">
- <number>0</number>
- </property>
- <property name="maximum">
- <double>100.000000000000000</double>
- </property>
- <property name="value">
- <double>75.000000000000000</double>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_82">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>25</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>25</height>
- </size>
- </property>
- <property name="text">
- <string>%</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_34">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>40</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QPushButton" name="pushButtonAjustWavelength">
- <property name="text">
- <string>Adjust tissue properties</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_5">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- </widget>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/org_mitk_gui_qt_photoacousticsimulation_Activator.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/org_mitk_gui_qt_photoacousticsimulation_Activator.cpp
deleted file mode 100644
index aa825b7358..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/org_mitk_gui_qt_photoacousticsimulation_Activator.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "org_mitk_gui_qt_photoacousticsimulation_Activator.h"
-#include "PASimulator.h"
-
-void mitk::org_mitk_gui_qt_photoacousticsimulation_Activator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(PASimulator, context)
-}
-
-void mitk::org_mitk_gui_qt_photoacousticsimulation_Activator::stop(ctkPluginContext*)
-{
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/org_mitk_gui_qt_photoacousticsimulation_Activator.h b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/org_mitk_gui_qt_photoacousticsimulation_Activator.h
deleted file mode 100644
index 7a0804c507..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/org_mitk_gui_qt_photoacousticsimulation_Activator.h
+++ /dev/null
@@ -1,32 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef org_mitk_gui_qt_photoacousticsimulation_Activator_h
-#define org_mitk_gui_qt_photoacousticsimulation_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk
-{
- class org_mitk_gui_qt_photoacousticsimulation_Activator : public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_photoacousticsimulation")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
- };
-}
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/CMakeLists.txt b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/CMakeLists.txt
deleted file mode 100644
index ac2049cb04..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_photoacoustics_spectralunmixing)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE SPECTRALUNMIXING_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt MitkPhotoacousticsLib
-)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/GUI.PNG b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/GUI.PNG
deleted file mode 100644
index 23c2c5cdd0..0000000000
Binary files a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/GUI.PNG and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/Manual.dox
deleted file mode 100644
index f0c5887d21..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/Manual.dox
+++ /dev/null
@@ -1,32 +0,0 @@
-/**
-\page org_mitk_gui_qt_photoacoustics_spectralunmixing The spectral unmixing (SU) plugin
-
-\imageMacro{photoacoustics_spectralunmixing-dox.png,"Icon of Spectralunmixing",2.00}
-
-\tableofcontents
-
-\section org_mitk_gui_qt_photoacoustics_spectralunmixingIntroduction
-The spectral unmixing plugin provides a GUI tool to perform spectral unmixing of multispectral MITK images. It was designed to unmix beamformed photoacoustic images. The outputs are MITK images for every chosen absorber (endmember). Furthermore it is possible to calculate the oxygen saturation of the multispectral input if the endmembers oxy- and deoxyhemoglobin are selected in the GUI as well as an output image that contains the information about the relative error between unmixing result and the input image.
-Detailed information about the Plugin, the baseclass and its subclasses can be found in their header files. If you want to call the SU filter from your own class have a look at the �mitkSpectralUnmixingTest.cpp�. There you find information about which functions are callable or have to be called from your class to guarantee the promised functionality of the SU filter.
-
-\section org_mitk_gui_qt_photoacoustics_spectralunmixingOverview
-<ul>
-<li> supports several linear Eigen solvers collected in the �mitkPALinearSpectralUnmixingFilter�
-<li> supports several linear Vigra solvers collected in the �mitkPASpectralUnmixingVigraFilter�
-<li> calculates oxygen saturation with the �mitkPASpectralUnmixingSO2�
-</ul>
-
-\section How to add an additional algorithm:
-If the algorithm fits in one of the existing classes you can ignore steps 0. � 3.
-0. Have a look at the commit rMITK36cfd1731089: implement three empty classes for Simplex, Lagrange and Vigra SU algorithms. Which actually are exactly the first (not all!) steps to implement a new algorithm.
-1. Add your future header and cpp file to files.cmake
-2. Create a header file which needs at least the methods shown in header.PNG
-\imageMacro{header.PNG,"empty header for a new SU algorithm",2.00}
-3. Create a cpp file which takes an Eigen endmember matrix and an Eigen input vector as inputs and returns an Eigen vector as result. A structure like in the cpp.PNG is recommended. If your class will consist of more than one algorithm you should have an if/else decision between them with an enum like in the cpp.PNG otherwise you can directly return your result.
-\imageMacro{cpp.PNG,"example cpp file for a new SU algorithm",2.00}
-4. In the Plugin you just have to add another �else if� like in the plugin.PNG. The string in the else if has to be the same then selectable in the GUI(step 5).
-\imageMacro{plugin.PNG,"changes of Plugin for a new SU algorithm",2.00}
-5. To make you algorithm selectable you have to add to the GUI Combobox. Klick at 1. (GUI.PNG), then at 2. and then name your algorithm 3. like in step 4.
-\imageMacro{GUI.PNG,"changes of GUI for a new SU algorithm",2.00}
-
-*/
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/cpp.PNG b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/cpp.PNG
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diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/plugin.PNG b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/UserManual/plugin.PNG
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diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/doxygen/modules.dox
deleted file mode 100644
index de1394cc0e..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/documentation/doxygen/modules.dox
+++ /dev/null
@@ -1,16 +0,0 @@
-/**
- \defgroup org_mitk_gui_qt_photoacoustics_spectralunmixing org.mitk.gui.qt.photoacoustics.spectralunmixing
- \ingroup MITKPlugins
-
- \brief Describe your plugin here.
-
-*/
-
-/**
- \defgroup org_mitk_gui_qt_photoacoustics_spectralunmixing_internal Internal
- \ingroup org_mitk_gui_qt_photoacoustics_spectralunmixing
-
- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.photoacoustics.spectralunmixing plugin. Other
- plugins must not rely on these classes. They contain implementation details and their interface
- may change at any time. We mean it.
-*/
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/files.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/files.cmake
deleted file mode 100644
index 2940e51e6b..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/files.cmake
+++ /dev/null
@@ -1,42 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.cpp
- SpectralUnmixing.cpp
-)
-
-set(UI_FILES
- src/internal/SpectralUnmixingControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.h
- src/internal/SpectralUnmixing.h
-)
-
-# list of resource files which can be used by the plug-in
-# system without loading the plug-ins shared library,
-# for example the icon used in the menu and tabs for the
-# plug-in views in the workbench
-set(CACHED_RESOURCE_FILES
- resources/spectralunmixing.svg
- plugin.xml
-)
-
-# list of Qt .qrc files which contain additional resources
-# specific to this plugin
-set(QRC_FILES
-
-)
-
-set(CPP_FILES )
-
-foreach(file ${SRC_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/${file})
-endforeach(file ${SRC_CPP_FILES})
-
-foreach(file ${INTERNAL_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/internal/${file})
-endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/manifest_headers.cmake
deleted file mode 100644
index a537cfdfe3..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Spectralunmixing")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "DKFZ")
-set(Plugin-ContactAddress "")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/plugin.xml b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/plugin.xml
deleted file mode 100644
index 0e3fe22367..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/plugin.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.spectralunmixing"
- name="Spectral Unmixing"
- category="Photoacoustics"
- class="SpectralUnmixing"
- icon="resources/spectralunmixing.svg" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/resources/spectralunmixing.svg b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/resources/spectralunmixing.svg
deleted file mode 100644
index d021376ed0..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/resources/spectralunmixing.svg
+++ /dev/null
@@ -1,103 +0,0 @@
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diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp
deleted file mode 100644
index df041d4a4d..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.cpp
+++ /dev/null
@@ -1,479 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// Qmitk
-#include "SpectralUnmixing.h"
-
-// Qt
-#include <QMessageBox>
-
-// mitk image
-#include <mitkImage.h>
-
-// Include to perform Spectral Unmixing
-#include "mitkPASpectralUnmixingFilterBase.h"
-#include "mitkPALinearSpectralUnmixingFilter.h"
-#include "mitkPASpectralUnmixingSO2.h"
-#include "mitkPASpectralUnmixingFilterVigra.h"
-#include "mitkPASpectralUnmixingFilterLagrange.h"
-#include "mitkPASpectralUnmixingFilterSimplex.h"
-
-#include <chrono>
-#include <numeric>
-#include <QtConcurrentRun>
-
-const std::string SpectralUnmixing::VIEW_ID = "org.mitk.views.spectralunmixing";
-
-void SpectralUnmixing::SetFocus()
-{
- m_Controls.buttonPerformImageProcessing->setFocus();
-}
-
-void SpectralUnmixing::CreateQtPartControl(QWidget *parent)
-{
- // create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi(parent);
- connect(m_Controls.buttonPerformImageProcessing, &QPushButton::clicked, this, &SpectralUnmixing::DoImageProcessing);
- m_Controls.tableWeight->hide();
- m_Controls.tableSO2->hide();
- m_Controls.tableError->hide();
- connect((QObject*)(m_Controls.QComboBoxAlgorithm), SIGNAL(currentIndexChanged(int)), this, SLOT(EnableGUIWeight()));
- connect((QObject*)(m_Controls.checkBoxsO2), SIGNAL(clicked()), this, SLOT(EnableGUISO2()));
- connect((QObject*)(m_Controls.checkBoxError), SIGNAL(clicked()), this, SLOT(EnableGUIError()));
- this->connect(this, SIGNAL(finishSignal()), this, SLOT(storeOutputs()));
- this->connect(this, SIGNAL(crashSignal()), this, SLOT(crashInfo()));
- this->connect(this, SIGNAL(enableSignal()), this, SLOT(EnableGUIControl()));
-}
-
-void SpectralUnmixing::EnableGUIControl()
-{
- SwitchGUIControl(false);
-}
-
-void SpectralUnmixing::SwitchGUIControl(bool change)
-{
- m_Controls.inputtable->setEnabled(change);
- m_Controls.checkBoxOx->setEnabled(change);
- m_Controls.checkBoxDeOx->setEnabled(change);
- m_Controls.checkBoxMelanin->setEnabled(change);
- m_Controls.checkBoxAdd->setEnabled(change);
- m_Controls.QComboBoxAlgorithm->setEnabled(change);
- m_Controls.tableWeight->setEnabled(change);
- m_Controls.checkBoxsO2->setEnabled(change);
- m_Controls.tableSO2->setEnabled(change);
- m_Controls.checkBoxVerbose->setEnabled(change);
- m_Controls.checkBoxChrono->setEnabled(change);
- m_Controls.buttonPerformImageProcessing->setEnabled(change);
- m_Controls.checkBoxError->setEnabled(change);
-}
-
-void SpectralUnmixing::EnableGUIWeight()
-{
- auto qs = m_Controls.QComboBoxAlgorithm->currentText();
- std::string Algorithm = qs.toUtf8().constData();
- if (Algorithm == "weighted")
- m_Controls.tableWeight->show();
- else
- m_Controls.tableWeight->hide();
-}
-
-void SpectralUnmixing::EnableGUISO2()
-{
- if (m_Controls.checkBoxsO2->isChecked())
- m_Controls.tableSO2->show();
- else
- m_Controls.tableSO2->hide();
-}
-
-void SpectralUnmixing::EnableGUIError()
-{
- if (m_Controls.checkBoxError->isChecked())
- m_Controls.tableError->show();
- else
- m_Controls.tableError->hide();
-}
-
-void SpectralUnmixing::SetVerboseMode(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, bool PluginVerbose)
-{
- m_SpectralUnmixingFilter->Verbose(PluginVerbose);
-}
-
-void SpectralUnmixing::SetWavlength(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter)
-{
- int col = 0;
- int Wavelength = 1;
- while (m_Controls.inputtable->item(0, col) && Wavelength > 0)
- {
- QString Text = m_Controls.inputtable->item(0, col)->text();
- Wavelength = Text.toInt();
- if (Wavelength > 0)
- {
- m_SpectralUnmixingFilter->AddWavelength(Wavelength);
- MITK_INFO(PluginVerbose) << "Wavelength: " << Wavelength << "nm \n";
- }
- ++col;
- }
-}
-
-void SpectralUnmixing::SetChromophore(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector<bool> boolVec,
- std::vector<std::string> chromophoreNameVec)
-{
- unsigned int numberofChromophores = 0;
-
- std::vector<mitk::pa::PropertyCalculator::ChromophoreType> m_ChromoType = { mitk::pa::PropertyCalculator::ChromophoreType::OXYGENATED,
- mitk::pa::PropertyCalculator::ChromophoreType::DEOXYGENATED, mitk::pa::PropertyCalculator::ChromophoreType::MELANIN,
- mitk::pa::PropertyCalculator::ChromophoreType::ONEENDMEMBER};
-
- for (unsigned int chromo = 0; chromo < m_ChromoType.size(); ++chromo)
- {
- if (boolVec[chromo] == true)
- {
- MITK_INFO(PluginVerbose) << "Chromophore: " << chromophoreNameVec[chromo];
- m_SpectralUnmixingFilter->AddChromophore(m_ChromoType[chromo]);
- numberofChromophores += 1;
- }
- }
-
- if (numberofChromophores == 0)
- mitkThrow() << "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!";
-}
-
-void SpectralUnmixing::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer> &nodes)
-{
- // iterate all selected objects, adjust warning visibility
- foreach (mitk::DataNode::Pointer node, nodes)
- {
- if (node.IsNotNull() && dynamic_cast<mitk::Image *>(node->GetData()))
- {
- m_Controls.labelWarning->setVisible(false);
- m_Controls.buttonPerformImageProcessing->setEnabled(true);
- return;
- }
- }
-
- m_Controls.labelWarning->setVisible(true);
- m_Controls.buttonPerformImageProcessing->setEnabled(false);
-}
-
-mitk::pa::SpectralUnmixingFilterBase::Pointer SpectralUnmixing::GetFilterInstance(std::string algorithm)
-{
- mitk::pa::SpectralUnmixingFilterBase::Pointer spectralUnmixingFilter;
-
- if (algorithm == "householderQr")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::HOUSEHOLDERQR);
- }
-
- else if (algorithm == "ldlt")
- {
- MITK_WARN << "Unfortunaly algorithm is likley to fail!";
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LDLT);
- }
-
- else if (algorithm == "llt")
- {
- MITK_WARN << "Unfortunaly algorithm is likley to fail!";
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::LLT);
- }
-
- else if (algorithm == "colPivHouseholderQr")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::COLPIVHOUSEHOLDERQR);
- }
-
- else if (algorithm == "jacobiSvd")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::JACOBISVD);
- }
-
- else if (algorithm == "fullPivLu")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVLU);
- }
-
- else if (algorithm == "fullPivHouseholderQr")
- {
- spectralUnmixingFilter = mitk::pa::LinearSpectralUnmixingFilter::New();
- dynamic_cast<mitk::pa::LinearSpectralUnmixingFilter*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType::FULLPIVHOUSEHOLDERQR);
- }
-
- else if (algorithm == "NNLARS")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LARS);
- }
-
- else if (algorithm == "NNGoldfarb")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::GOLDFARB);
- }
-
- else if (algorithm == "weighted")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::WEIGHTED);
- //Tranfer GUI information(Weights) to filter
- unsigned int colunm = 0;
- int Weight = 1;
- while (m_Controls.tableWeight->item(0, colunm) && Weight > 0)
- {
- QString Text = m_Controls.tableWeight->item(0, colunm)->text();
- Weight = Text.toInt();
- if (Weight > 0)
- {
- MITK_INFO(PluginVerbose) << "Weight: " << Weight;
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra*>(spectralUnmixingFilter.GetPointer())
- ->AddWeight(Weight);
- }
- ++colunm;
- }
- }
-
- else if (algorithm == "LS")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterVigra::New();
- dynamic_cast<mitk::pa::SpectralUnmixingFilterVigra*>(spectralUnmixingFilter.GetPointer())
- ->SetAlgorithm(mitk::pa::SpectralUnmixingFilterVigra::VigraAlgortihmType::LS);
- }
-
- else if (algorithm == "SimplexMax")
- {
- spectralUnmixingFilter = mitk::pa::SpectralUnmixingFilterSimplex::New();
- }
-
- else
- mitkThrow() << "404 ALGORITHM NOT FOUND!";
-
- return spectralUnmixingFilter;
-}
-
-
-void SpectralUnmixing::SetSO2Settings(mitk::pa::SpectralUnmixingSO2::Pointer m_sO2)
-{
- for (unsigned int i = 0; i < 4; ++i)
- {
- if (m_Controls.tableSO2->item(0, i))
- {
- QString Text = m_Controls.tableSO2->item(0, i)->text();
- int value = Text.toInt();
- MITK_INFO(PluginVerbose) << "SO2 setting value: " << value;
- m_sO2->AddSO2Settings(value);
- }
- else
- m_sO2->AddSO2Settings(0);
- }
-}
-
-void SpectralUnmixing::SetRelativeErrorSettings(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter)
-{
- for (unsigned int i = 0; i < 2; ++i)
- {
- if (m_Controls.tableError->item(0, i))
- {
- QString Text = m_Controls.tableError->item(0, i)->text();
- int value = Text.toInt();
- MITK_INFO(PluginVerbose) << "Relative error setting value: " << value;
- m_SpectralUnmixingFilter->AddRelativeErrorSettings(value);
- }
- else
- m_SpectralUnmixingFilter->AddRelativeErrorSettings(0);
- }
-}
-
-void SpectralUnmixing::CalculateSO2(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector<bool> boolVec)
-{
- MITK_INFO(PluginVerbose) << "CALCULATE OXYGEN SATURATION ...";
-
- if (!boolVec[0])
- mitkThrow() << "SELECT CHROMOPHORE DEOXYHEMOGLOBIN!";
- if (!boolVec[1])
- mitkThrow() << "SELECT CHROMOPHORE OXYHEMOGLOBIN!";
- auto m_sO2 = mitk::pa::SpectralUnmixingSO2::New();
- m_sO2->Verbose(PluginVerbose);
- SetSO2Settings(m_sO2);
-
- // Initialize pipeline from SU filter class to SO2 class
- auto output1 = m_SpectralUnmixingFilter->GetOutput(0);
- auto output2 = m_SpectralUnmixingFilter->GetOutput(1);
- m_sO2->SetInput(0, output1);
- m_sO2->SetInput(1, output2);
-
- m_sO2->Update();
-
- mitk::Image::Pointer sO2 = m_sO2->GetOutput(0);
- sO2->SetSpacing(output1->GetGeometry()->GetSpacing());
- WriteOutputToDataStorage(sO2, "sO2");
- MITK_INFO(PluginVerbose) << "[DONE]";
-}
-
-void SpectralUnmixing::WriteOutputToDataStorage(mitk::Image::Pointer m_Image, std::string name)
-{
- mitk::DataNode::Pointer dataNodeOutput = mitk::DataNode::New();
- dataNodeOutput->SetData(m_Image);
- dataNodeOutput->SetName(name);
- this->GetDataStorage()->Add(dataNodeOutput);
-}
-
-void SpectralUnmixing::Settings(mitk::Image::Pointer image)
-{
- boolVec = { m_Controls.checkBoxOx->isChecked(), m_Controls.checkBoxDeOx->isChecked(),
- m_Controls.checkBoxMelanin->isChecked(), m_Controls.checkBoxAdd->isChecked() };
- outputNameVec = { "HbO2", "Hb", "Melanin", "Static Endmember" };
- sO2Bool = (m_Controls.checkBoxsO2->isChecked());
-
- //Read GUI information(algorithm)
- auto qs = m_Controls.QComboBoxAlgorithm->currentText();
- Algorithm = qs.toUtf8().constData();
-
- m_SpectralUnmixingFilter = GetFilterInstance(Algorithm);
- SetVerboseMode(m_SpectralUnmixingFilter, PluginVerbose);
- m_SpectralUnmixingFilter->RelativeError(m_Controls.checkBoxError->isChecked());
- m_SpectralUnmixingFilter->SetInput(image);
- SetWavlength(m_SpectralUnmixingFilter);
- SetChromophore(m_SpectralUnmixingFilter, boolVec, outputNameVec);
-
- boolVec.push_back(m_Controls.checkBoxError->isChecked());
- outputNameVec.push_back("Relative Error");
- if (m_Controls.checkBoxError->isChecked())
- SetRelativeErrorSettings(m_SpectralUnmixingFilter);
-
- m_SpectralUnmixingFilter->AddOutputs(std::accumulate(boolVec.begin(), boolVec.end(), 0));
- MITK_INFO(PluginVerbose) << "Number of indexed outputs: " << std::accumulate(boolVec.begin(), boolVec.end(), 0);
-}
-
-void SpectralUnmixing::storeOutputs()
-{
- int outputCounter = 0;
- mitk::Image::Pointer m_Output;
- for (unsigned int chromophore = 0; chromophore < outputNameVec.size(); ++chromophore)
- {
- if (boolVec[chromophore] != false)
- {
- m_Output = m_SpectralUnmixingFilter->GetOutput(outputCounter++);
- m_Output->SetSpacing(image->GetGeometry()->GetSpacing());
- WriteOutputToDataStorage(m_Output, outputNameVec[chromophore] + Algorithm);
- }
- }
-
- if (sO2Bool)
- CalculateSO2(m_SpectralUnmixingFilter, boolVec);
-
- mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage());
- MITK_INFO(PluginVerbose) << "Adding images to DataStorage...[DONE]";
-
- std::chrono::steady_clock::time_point _end(std::chrono::steady_clock::now());
- MITK_INFO(m_Controls.checkBoxChrono->isChecked()) << "Time for image Processing: "
- << std::chrono::duration_cast<std::chrono::duration<double>>(_end - _start).count();
- QApplication::setOverrideCursor(Qt::ArrowCursor);
- SwitchGUIControl(true);
-}
-
-void SpectralUnmixing::WorkingThreadUpdateFilter(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter)
-{
- //SwitchGUIControl(false);
- emit enableSignal();
- try
- {
- m_SpectralUnmixingFilter->Update();
- emit finishSignal();
- }
- catch (const mitk::Exception& e)
- {
- QApplication::setOverrideCursor(Qt::ArrowCursor);
- SwitchGUIControl(true);
- errorMessage = e.GetDescription();
- emit crashSignal();
- }
-}
-
-void SpectralUnmixing::crashInfo()
-{
- const char *error = errorMessage.c_str();
- QMessageBox::information(nullptr, "Template", error);
-}
-
-void SpectralUnmixing::DoImageProcessing()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- if (nodes.empty())
- return;
-
- mitk::DataNode *node = nodes.front();
-
- if (!node)
- {
- // Nothing selected. Inform the user and return
- QMessageBox::information(nullptr, "Template", "Please load and select an image before starting image processing.");
- return;
- }
-
- // here we have a valid mitk::DataNode
-
- // a node itself is not very useful, we need its data item (the image)
- mitk::BaseData *data = node->GetData();
- if (data)
- {
- // test if this data item is an image or not (could also be a surface or something totally different)
- image = dynamic_cast<mitk::Image *>(data);
- if (image)
- {
- std::stringstream message;
- std::string name;
- message << "PERFORMING SPECTRAL UNMIXING ";
- if (node->GetName(name))
- {
- // a property called "name" was found for this DataNode
- message << "'" << name << "'";
- }
- message << ".";
-
- _start = std::chrono::steady_clock::now();
- PluginVerbose = m_Controls.checkBoxVerbose->isChecked();
- MITK_INFO(PluginVerbose) << message.str();
-
- try
- {
- Settings(image);
- MITK_INFO(PluginVerbose) << "Updating Filter...";
- QApplication::setOverrideCursor(Qt::WaitCursor);
- QtConcurrent::run(this, &SpectralUnmixing::WorkingThreadUpdateFilter, m_SpectralUnmixingFilter);
- }
- catch (const mitk::Exception& e)
- {
- QApplication::setOverrideCursor(Qt::ArrowCursor);
- QMessageBox::information(nullptr, "Template", e.GetDescription());
- }
- }
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.h b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.h
deleted file mode 100644
index bb47e7f612..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixing.h
+++ /dev/null
@@ -1,197 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#ifndef SpectralUnmixing_h
-#define SpectralUnmixing_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-#include <mitkPASpectralUnmixingFilterBase.h>
-#include <mitkPASpectralUnmixingSO2.h>
-
-#include <chrono>
-#include "ui_SpectralUnmixingControls.h"
-
-/**
-* \brief The spectral unmixing plugin provides a GUI tool to perform spectral unmixing of multispectral MITK images.
-* It was designed to unmix beamformed photoacoustic imgaes. The outputs are as well MITK images for every chosen absorber
-* (endmember). Furthermore it is possible to calculate the oxygen saturation of the multispectral input if the endmembers
-* oxy- and deoxyhemoglobin are selected in the GUI.
-*
-* For further information look at the documentation of the mitkPASpectralUnmixingFilterBase.h
-*
-* @exeption if the GenerateOutput method throws a exception the plugin will show a QMessageBox with the exception
-* message at the GUI
-*/
-class SpectralUnmixing : public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
-
- public:
- static const std::string VIEW_ID;
-
- protected:
- void CreateQtPartControl(QWidget *parent) override;
- void SetFocus() override;
-
- /// \brief called by QmitkFunctionality when DataManager's selection has changed
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,
- const QList<mitk::DataNode::Pointer> &nodes) override;
-
-
- /**
- * \brief Called when the user clicks the GUI button. Checks if the selected data is an image. Then passen on the GUI
- * information using the Settings method. Afterwards it performs spectral unmixing via the WorkingThreadUpdateFilter
- * method in a own thread. The spectral unmixing is based on the spectral unmixing filter base and its subclasses.
- * @exception if nothing is selected. Inform the user and return
- * @exception if settings fails. Informs with the mitkthorw information of the filter as QMessageBox
- */
- void DoImageProcessing();
-
- /**
- * \brief slots are there to show/hide input tables for weights-, relative error and SO2 settings ig they are not needed
- */
- public slots:
- void EnableGUIWeight();
- void EnableGUISO2();
- void EnableGUIError();
-
- /**
- * \brief slot waits for finishSignal of the working thread and starts storeOutputs
- */
- public slots:
- /**
- * \brief slot does the image post processing
- * - GetOutput from m_SpectralUnmixingFilter
- * - calles WriteOutputToDataStorage
- * - if (true) calls CalculateSO2
- * - does the rendering
- * - if (true) shows the chrono result
- * - switches the GUI back on
- */
- void storeOutputs();
- signals:
- void finishSignal();
-
- public slots:
- void EnableGUIControl();
- signals:
- void enableSignal();
-
- /**
- * \brief slot waits for crashSignal and if neccessary ends working thread and shows QMessageBox with the error message
- */
- public slots:
- void crashInfo();
- signals:
- void crashSignal();
-
- protected:
- Ui::SpectralUnmixingControls m_Controls;
-
- /**
- * \brief passes the algorithm information from the GUI on to the spectral unmixing filter base subclass method
- * "SetAlgortihm" and initializes the subclassFilter::Pointer.
- * @param algorithm has to be a string which can be assigned to the mitk::pa::LinearSpectralUnmixingFilter::AlgortihmType
- * @throws if the algorithm string doesn't match to an implemented algorithm
- */
- mitk::pa::SpectralUnmixingFilterBase::Pointer GetFilterInstance(std::string algorithm);
-
- bool PluginVerbose = true;
- mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter;
- std::vector<std::string> outputNameVec;
- std::vector<bool> boolVec;
- std::string Algorithm;
- bool sO2Bool;
- mitk::Image *image;
- std::chrono::steady_clock::time_point _start;
- std::string errorMessage;
-
- private:
- /**
- * \brief thread
- * - disables GUI
- * - tries Filter->Update() method
- * - gives finishSignal which calls storeOutputs
- * - cathes by enables GUI and gives crashSignal
- */
- void WorkingThreadUpdateFilter(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter);
-
- /**
- * \brief takes an MITK image as input and performs spectral unmixing based on the spectral unmixing filter base and its subclasses.
- * Therefor it first passes all information from the GUI into the filter by using the "set"methods of the plugin, which then are calling
- * the "add" methods of the filter(base).
- * @param image has to be an MITK image (pointer). For the request on the image look at the docu of the mitkPASpectralUnmixngFilterBase.h
- */
- virtual void Settings(mitk::Image::Pointer image);
-
- /**
- * \brief The method takes a image pointer and a file name which then will get to the data storage.
- * @param m_Image is a mitk_::Image::Pointer pointing at the output which one wants to get stored
- * @param name has to be a string and will be the file name
- */
- virtual void WriteOutputToDataStorage(mitk::Image::Pointer m_Image, std::string name);
-
- /**
- * \brief passes the algorithm information if verbose mode is requested from the GUI on to the spectral unmixing filter
- * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base
- * @param PluginVerbose is the GUI information bool
- */
- virtual void SetVerboseMode(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, bool PluginVerbose);
-
- /**
- * \brief passes the wavelength information from the GUI on to the spectral unmixing filter base method "AddWavelength".
- * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base
- */
- virtual void SetWavlength(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter);
-
- /**
- * \brief passes the chromophore information from the GUI on to the spectral unmixing filter base method "AddChromophore".
- * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base
- * @param boolVec is a vector which contains the information which chromophore was checked in the GUI
- * @param chromophoreNameVec contains the names of all chromophores as strings
- * @throws "PRESS 'IGNORE' AND CHOOSE A CHROMOPHORE!" if no chromophore was chosen
- */
- virtual void SetChromophore(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector<bool> boolVec, std::vector<std::string> chromophoreNameVec);
-
- /**
- * \brief passes the SetRelativeErrorSettings information from the GUI on to the spectral unmixing filter base method "AddRelativeErrorSettings".
- * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base#
- */
- virtual void SetRelativeErrorSettings(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter);
-
- /**
- * \brief passes the SetSO2Settings information from the GUI on to the spectral unmixing SO2 filter method "AddSO2Settings".
- * @param m_sO2 is a pointer of the spectral unmixing SO2 filter
- */
- virtual void SetSO2Settings(mitk::pa::SpectralUnmixingSO2::Pointer m_sO2);
-
- /**
- * \brief calcultes out of two identical sized MITK images the oxygen saturation and stores the result in an image. Herein the two
- * input images are the output for oxy- and deoxyhemoglobin from the GenerateOutput method (spectral unmixing filter results).
- * @param m_SpectralUnmixingFilter is a pointer of the spectral unmixing filter base to get the filter output images as sO2 input
- * @param boolVec is a vector which contains the information which chromophore was checked in the GUI
- * @throws if oxy- or deoxyhemoglobin was not selected in the GUI
- */
- virtual void CalculateSO2(mitk::pa::SpectralUnmixingFilterBase::Pointer m_SpectralUnmixingFilter, std::vector<bool> boolVec);
-
- /**
- * \brief enables/disables GUI
- * @param change true means GUI buttons enabled, false disabled respectively
- */
- virtual void SwitchGUIControl(bool change);
-};
-
-#endif // SpectralUnmixing_h
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui
deleted file mode 100644
index aa90868457..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/SpectralUnmixingControls.ui
+++ /dev/null
@@ -1,1232 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>SpectralUnmixingControls</class>
- <widget class="QWidget" name="SpectralUnmixingControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>325</width>
- <height>742</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QLabel" name="labelWarning">
- <property name="styleSheet">
- <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
- </property>
- <property name="text">
- <string>Please select an image!</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="Line" name="line_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Wavelengths settings </string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QTableWidget" name="inputtable">
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>75</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>16777215</width>
- <height>75</height>
- </size>
- </property>
- <property name="font">
- <font>
- <pointsize>10</pointsize>
- </font>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>* \brief All values have to be intergers. They need to have the same order than the wavelength at the image.</p></body></html></string>
- </property>
- <property name="showGrid">
- <bool>true</bool>
- </property>
- <property name="gridStyle">
- <enum>Qt::SolidLine</enum>
- </property>
- <attribute name="horizontalHeaderDefaultSectionSize">
- <number>42</number>
- </attribute>
- <attribute name="horizontalHeaderMinimumSectionSize">
- <number>50</number>
- </attribute>
- <attribute name="verticalHeaderDefaultSectionSize">
- <number>30</number>
- </attribute>
- <attribute name="verticalHeaderMinimumSectionSize">
- <number>30</number>
- </attribute>
- <row>
- <property name="text">
- <string>λ [nm]</string>
- </property>
- </row>
- <column>
- <property name="text">
- <string>1</string>
- </property>
- </column>
- <column>
- <property name="text">
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- </item>
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- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_2">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p><span style=" font-weight:400;">* \brief Select as least one Absorber. It's not possible to select more absorbers then wavelengths.</span></p></body></html></string>
- </property>
- <property name="text">
- <string>Chromophore selection</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxOx">
- <property name="toolTip">
- <string><html><head/><body><p>* \brief One of the main absorbers in near infrared spectrum.</p></body></html></string>
- </property>
- <property name="text">
- <string>Oxyhemoglobin</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxDeOx">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>* \brief One of the main absorbers in near infrared spectrum.</p></body></html></string>
- </property>
- <property name="text">
- <string>Deoxygenated hemoglobin</string>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- <property name="tristate">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxMelanin">
- <property name="toolTip">
- <string><html><head/><body><p>* \brief One of the main absorbers in near infrared spectrum.</p></body></html></string>
- </property>
- <property name="text">
- <string>Melanin</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxAdd">
- <property name="toolTip">
- <string><html><head/><body><p>* \brief This endmember will be unmixed with 1 at all wavelgnths.</p></body></html></string>
- </property>
- <property name="text">
- <string>Static Endmember</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="Line" name="line_5">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_3">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p><span style=" font-weight:400;">* \brief One needs to choose an spectral unmixing algorithm.</span></p></body></html></string>
- </property>
- <property name="text">
- <string>Unmixing algorithm</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QComboBox" name="QComboBoxAlgorithm">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="font">
- <font>
- <family>MS Shell Dlg 2</family>
- </font>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>* \brief For detailed information about the algorithms please have a look at the documentation.</p></body></html></string>
- </property>
- <property name="editable">
- <bool>false</bool>
- </property>
- <property name="maxVisibleItems">
- <number>21</number>
- </property>
- <property name="maxCount">
- <number>2147483647</number>
- </property>
- <item>
- <property name="text">
- <string>==CHOSE ALGORITHM==</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>==QR decomposition==</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>householderQr</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>colPivHouseholderQr</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>fullPivHouseholderQr</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>==LU decompositon</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>fullPivLu</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>==Cholesky decompostion==</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>ldlt</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string comment="43" extracomment="ewrwer">llt</string>
- </property>
- <property name="icon">
- <iconset>
- <normaloff>.</normaloff>.</iconset>
- </property>
- </item>
- <item>
- <property name="text">
- <string>==Least squares==</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>LS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>jacobiSvd</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>NNLARS</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>NNGoldfarb</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>weighted</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>==Others==</string>
- </property>
- </item>
- <item>
- <property name="text">
- <string>SimplexMax</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <widget class="QTableWidget" name="tableWeight">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>75</height>
- </size>
- </property>
- <property name="maximumSize">
- <size>
- <width>380</width>
- <height>81</height>
- </size>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>* \brief the weights are at the same order as the wavelength</p></body></html></string>
- </property>
- <property name="autoFillBackground">
- <bool>false</bool>
- </property>
- <property name="dragEnabled">
- <bool>false</bool>
- </property>
- <row>
- <property name="text">
- <string>Weights [%]</string>
- </property>
- </row>
- <column>
- <property name="text">
- <string>1</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>2</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>3</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>4</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>5</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>6</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>7</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>8</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>9</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>10</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>11</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>12</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>13</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>14</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>15</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>16</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>17</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>18</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>19</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>20</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>21</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>22</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>23</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>24</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>25</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>26</string>
- </property>
- </column>
- <item row="0" column="0">
- <property name="text">
- <string>11</string>
- </property>
- </item>
- <item row="0" column="1">
- <property name="text">
- <string>10</string>
- </property>
- </item>
- <item row="0" column="2">
- <property name="text">
- <string>9</string>
- </property>
- </item>
- <item row="0" column="3">
- <property name="text">
- <string>8</string>
- </property>
- </item>
- <item row="0" column="4">
- <property name="text">
- <string>7</string>
- </property>
- </item>
- <item row="0" column="5">
- <property name="text">
- <string>7</string>
- </property>
- </item>
- <item row="0" column="6">
- <property name="text">
- <string>6</string>
- </property>
- </item>
- <item row="0" column="7">
- <property name="text">
- <string>6</string>
- </property>
- </item>
- <item row="0" column="8">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="9">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="10">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="11">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="12">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="13">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="14">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="15">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="16">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="17">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="18">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="19">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="20">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="21">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="22">
- <property name="text">
- <string>5</string>
- </property>
- </item>
- <item row="0" column="23">
- <property name="text">
- <string>6</string>
- </property>
- </item>
- <item row="0" column="24">
- <property name="text">
- <string>6</string>
- </property>
- </item>
- <item row="0" column="25">
- <property name="text">
- <string>6</string>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <widget class="Line" name="line_6">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_4">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Oxygen saturation</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxsO2">
- <property name="toolTip">
- <string><html><head/><body><p>* \brief calculates HbO2/(HbO2+Hb) if De- and oxyhemoglobin are selected.</p></body></html></string>
- </property>
- <property name="text">
- <string>calculate sO2</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QTableWidget" name="tableSO2">
- <property name="maximumSize">
- <size>
- <width>380</width>
- <height>82</height>
- </size>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>* \brief below threshold calculated sO2 value will set to zero</p></body></html></string>
- </property>
- <row>
- <property name="text">
- <string>Threshold</string>
- </property>
- </row>
- <column>
- <property name="text">
- <string>HbO2</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Hb</string>
- </property>
- <property name="toolTip">
- <string/>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Sum</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>SO2 %</string>
- </property>
- </column>
- <item row="0" column="0">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="1">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="2">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="3">
- <property name="text">
- <string/>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <widget class="Line" name="line">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label_5">
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Additional Settings</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxVerbose">
- <property name="toolTip">
- <string><html><head/><body><p>* \brief This mode will give additional console outputs for debugging.</p></body></html></string>
- </property>
- <property name="text">
- <string>Verbose Mode (additional console outputs)</string>
- </property>
- <property name="tristate">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxChrono">
- <property name="toolTip">
- <string><html><head/><body><p>* \brief This checkbox will start Chrono and takes the time between clicking of the &quot;Perform spectral unmixing&quot; button until the GUI enables again.</p></body></html></string>
- </property>
- <property name="text">
- <string>Chrono</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="checkBoxError">
- <property name="toolTip">
- <string><html><head/><body><p>* \brief Calculates the realtive error between unmixing result and the input image in the L2 norm.</p></body></html></string>
- </property>
- <property name="text">
- <string>Relative error image</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QTableWidget" name="tableError">
- <property name="maximumSize">
- <size>
- <width>307</width>
- <height>70</height>
- </size>
- </property>
- <property name="toolTip">
- <string><html><head/><body><p>* \brief below the threshold calculated relative error will set to zero</p></body></html></string>
- </property>
- <row>
- <property name="text">
- <string>Threshold</string>
- </property>
- </row>
- <column>
- <property name="text">
- <string>HbO2</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Hb</string>
- </property>
- </column>
- <item row="0" column="0">
- <property name="text">
- <string/>
- </property>
- </item>
- <item row="0" column="1">
- <property name="text">
- <string/>
- </property>
- </item>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonPerformImageProcessing">
- <property name="toolTip">
- <string>Do image processing</string>
- </property>
- <property name="text">
- <string>Perform spectral unmixing</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="Line" name="line_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>17</width>
- <height>54</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.cpp
deleted file mode 100644
index 6964b0ff61..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#include "org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.h"
-#include "SpectralUnmixing.h"
-
-namespace mitk
-{
- void org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator::start(ctkPluginContext *context)
- {
- BERRY_REGISTER_EXTENSION_CLASS(SpectralUnmixing, context)
- }
-
- void org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator::stop(ctkPluginContext *context) { Q_UNUSED(context) }
-}
diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.h b/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.h
deleted file mode 100644
index 42d07daaa1..0000000000
--- a/Plugins/org.mitk.gui.qt.photoacoustics.spectralunmixing/src/internal/org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator.h
+++ /dev/null
@@ -1,34 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator_h
-#define org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk
-{
- class org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator : public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_photoacoustics_spectralunmixing")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
- void start(ctkPluginContext *context) override;
- void stop(ctkPluginContext *context) override;
-
- }; // org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator
-}
-
-#endif // org_mitk_gui_qt_photoacoustics_spectralunmixing_Activator_h
diff --git a/Plugins/org.mitk.gui.qt.preprocessing.resampling/CMakeLists.txt b/Plugins/org.mitk.gui.qt.preprocessing.resampling/CMakeLists.txt
index cd46837ebb..87a2b09302 100644
--- a/Plugins/org.mitk.gui.qt.preprocessing.resampling/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.preprocessing.resampling/CMakeLists.txt
@@ -1,9 +1,7 @@
-
project(org_mitk_gui_qt_preprocessing_resampling)
mitk_create_plugin(
EXPORT_DIRECTIVE PREPROCESSING_RESAMPLING_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgetsExt MitkMapperExt MitkImageDenoising
- PACKAGE_DEPENDS ITK|ITKMathematicalMorphology
)
diff --git a/Plugins/org.mitk.gui.qt.radiomics/CMakeLists.txt b/Plugins/org.mitk.gui.qt.radiomics/CMakeLists.txt
index ff56114085..13a722be5a 100644
--- a/Plugins/org.mitk.gui.qt.radiomics/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.radiomics/CMakeLists.txt
@@ -1,9 +1,7 @@
-
project(org_mitk_gui_qt_radiomics)
mitk_create_plugin(
EXPORT_DIRECTIVE RADIOMICS_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS MitkQtWidgetsExt MitkCLUtilities MitkBasicImageProcessing MitkMultilabel
- PACKAGE_DEPENDS ITK|ITKMathematicalMorphology
)
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/CMakeLists.txt b/Plugins/org.mitk.gui.qt.spectrocamrecorder/CMakeLists.txt
deleted file mode 100644
index 34a55ab54c..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_spectrocamrecorder)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE SPECTROCAMRECORDER_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt MitkSpectroCam
-)
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/files.cmake b/Plugins/org.mitk.gui.qt.spectrocamrecorder/files.cmake
deleted file mode 100644
index 563aebf275..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/files.cmake
+++ /dev/null
@@ -1,42 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_spectrocamrecorder_Activator.cpp
- SpectroCamRecorder.cpp
-)
-
-set(UI_FILES
- src/internal/SpectroCamRecorderControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_spectrocamrecorder_Activator.h
- src/internal/SpectroCamRecorder.h
-)
-
-# list of resource files which can be used by the plug-in
-# system without loading the plug-ins shared library,
-# for example the icon used in the menu and tabs for the
-# plug-in views in the workbench
-set(CACHED_RESOURCE_FILES
- resources/icon.xpm
- plugin.xml
-)
-
-# list of Qt .qrc files which contain additional resources
-# specific to this plugin
-set(QRC_FILES
-
-)
-
-set(CPP_FILES )
-
-foreach(file ${SRC_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/${file})
-endforeach(file ${SRC_CPP_FILES})
-
-foreach(file ${INTERNAL_CPP_FILES})
- set(CPP_FILES ${CPP_FILES} src/internal/${file})
-endforeach(file ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.spectrocamrecorder/manifest_headers.cmake
deleted file mode 100644
index 8be1ce8a71..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Spectrocamrecorder")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "DKFZ")
-set(Plugin-ContactAddress "")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/plugin.xml b/Plugins/org.mitk.gui.qt.spectrocamrecorder/plugin.xml
deleted file mode 100644
index 028c1f5624..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/plugin.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.spectrocamrecorder"
- name="SpectroCam Recorder"
- class="SpectroCamRecorder"
- icon="resources/icon.xpm" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/resources/icon.xpm b/Plugins/org.mitk.gui.qt.spectrocamrecorder/resources/icon.xpm
deleted file mode 100644
index ea406d17e1..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/resources/icon.xpm
+++ /dev/null
@@ -1,1144 +0,0 @@
-/* XPM */
-static char * C:\m\MITK\Plugins\org_mitk_gui_qt_spectrocamrecorder\resources\icon_xpm[] = {
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-"; 4#'&)&!&~&{&%%]&^&/&(&_&:&<&w@e@Z$[&}&0+a+)+'+'.T w@=@].|&1&2&3&4&e@w@d@f@,+#.h@5&6&7&8&9&0&a&",
-"; ; b&c&d&e&f&g&h&i&j&k&l&P@)#P@h@|@g m&n&o&i%T p&T q&r&s&t&u&v&w&1.,+h@f@f@<@Q@r+x&y&z&A&B&C&D&",
-"; ; E&F&G&H&I&J&K&L&M&N&O&o.r+T l+P&Q&R&S&T&U&V&W&X&Y&Z&`& *.*+*@*#*$*G.[@}@'+f@%*&*****=*=*-*;*",
-"; ; ; >*,*'*`$)*!*~*{*]*^*L 8.l+L /*(*=@p+_*:*<*[*}*|*1*2*3*4*5*6*7*8*9$'+J.9*0*a*b*c*=*C&C&d*e*",
-"; ; ; f*g*h*-$i*j*k*l*m*n*W )+2.0.#.o*p*q*r*s*t*u*v*w*x*y*z*A*B*C*[@<@e@f@I%D*E*F*G*H*I*J*K*L*M*",
-"; ; ; ; N*O*P*Q*R*S*T*U*V*#.).E+W*P.X*Y*Z*F@_ `* =.=+=@=#=$=%=&=*===-=;=>=,='=)=!=~={=]=^=/=(=_=",
-"; ; ; ; : :=<=[=}=|=1=2=3=4=5=6=Y*7=8=[%[%D+9=0=a=b=c=d=e=f=g=h=i=j=k=l=m=n=o=p=q=r=s=t=u=v=w=x=",
-"; ; ; ; ; y=z=A=B=C=D=E=F=Z*U.U.[%[%D+G=H=< I=J=K=L=M=N=O=P=Q=R=S=T=U=V=W=X=Y=Z=`=`= -.-+-@-#-b ",
-"; ; ; ; b _ $-l.%-&-*-a _ F@[%c _ {.a =-..--;->-,-'-)-!-~-{-]-^-V=U=U=/-(-_-:-<-[-[-}-|-1-2-3-; ",
-"; ; ; ; r@G=4-5-6-7-F@a 8-a {.9-8-< t v#0-a-b-c-d-e-f-g-h-i-j-k-/-k-k-k-l-m-n-o-p-q-r-s-t-u-; ; ",
-"; ; ; ; r@a v-v-D+G=H=8-$ $ u-t ^@, n.w-x-y-z-A-B-C-D-E-F-G-H-/-k-k-k-I-J-K-L-M-N-O-P-Q-^@; ; ; ",
-"; ; ; ; r@.._ G==-8-< t E.> n.n.- % R-+ S-T-U-V-V-B-W-X-Y-Z-`- ;.;+;@;#;$;%;&;*;=;-;;;; ; ; ; ; ",
-"; ; ; ; : $ < ..t D.D.# E.b E.= /@> ##>;,;';);!;!;~;{;];^;/;(;_;:;<;[;};|;1;2;3;4;% ; ; ; ; ; ; ",
-"; ; ; ; ; /@# , n.$ $ % > b r@r@b : , 5;6;7;8;9;0;a;b;c;d;e;v#f;g;h;i;j;k;l;m;n;o;p;q;; ; ; ; ; ",
-"; ; ; ; : b = - = E./@> b : : : : ; r;s;t;u;v;w;x;y;z;A;B;C;D;E;F;G;H;I;J;J;K;L;M;N;O;P;> ; ; ; "};
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorder.cpp b/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorder.cpp
deleted file mode 100644
index 77b0e8d92f..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorder.cpp
+++ /dev/null
@@ -1,144 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// Qmitk
-#include "SpectroCamRecorder.h"
-
-// Qt
-#include <QMessageBox>
-
-//mitk image
-#include <mitkImage.h>
-
-// other
-#include <mitkSpectroCamController.h>
-
-const std::string SpectroCamRecorder::VIEW_ID = "org.mitk.views.spectrocamrecorder";
-
-void SpectroCamRecorder::SetFocus()
-{
- m_Controls.buttonPerformImageProcessing->setFocus();
-}
-
-void SpectroCamRecorder::CreateQtPartControl( QWidget *parent )
-{
- // create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi( parent );
- connect( m_Controls.buttonPerformImageProcessing, SIGNAL(clicked()), this, SLOT(DoImageProcessing()) );
- connect( m_Controls.buttonWhiteBalance, SIGNAL(clicked()), this, SLOT(SetWhiteBalance()) );
- connect( m_Controls.buttonSave, SIGNAL(clicked()), this, SLOT(SaveImage()) );
-
- // intialize the camera (!= start).
- m_Controller.Ini();
-}
-
-SpectroCamRecorder::~SpectroCamRecorder()
-{
- if (m_Controller.isCameraRunning())
- {
- m_Controller.CloseCameraConnection();
- }
-}
-
-void SpectroCamRecorder::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer>& nodes )
-{
- //// iterate all selected objects, adjust warning visibility
- //foreach( mitk::DataNode::Pointer node, nodes )
- //{
- // if( node.IsNotNull() && dynamic_cast<mitk::Image*>(node->GetData()) )
- // {
- // m_Controls.labelWarning->setVisible( false );
- // m_Controls.buttonPerformImageProcessing->setEnabled( true );
- // return;
- // }
- //}
-
- //m_Controls.labelWarning->setVisible( true );
- //m_Controls.buttonPerformImageProcessing->setEnabled( false );
-}
-
-
-void SpectroCamRecorder::SaveImage()
-{
- mitk::Image::Pointer imageToSave = m_Controller.GetCurrentImage();
- QString imageName = m_Controls.lineEdit->text();
-
-
- mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
- imageNode->SetData(imageToSave);
- imageNode->SetName(imageName.toStdString());
-
-
- GetDataStorage()->Add(imageNode);
-
-}
-
-void SpectroCamRecorder::SetWhiteBalance()
-{
- m_Controller.SetCurrentImageAsWhiteBalance();
-}
-
-void SpectroCamRecorder::DoImageProcessing()
-{
- //QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- //if (nodes.empty()) return;
-
- //mitk::DataNode* node = nodes.front();
-
- //if (!node)
- //{
- // // Nothing selected. Inform the user and return
- // QMessageBox::information( nullptr, "Template", "Please load and select an image before starting image processing.");
- // return;
- //}
-
- //// here we have a valid mitk::DataNode
-
- //// a node itself is not very useful, we need its data item (the image)
- //mitk::BaseData* data = node->GetData();
- //if (data)
- //{
- // // test if this data item is an image or not (could also be a surface or something totally different)
- // mitk::Image* image = dynamic_cast<mitk::Image*>( data );
- // if (image)
- // {
- // std::stringstream message;
- // std::string name;
- // message << "Performing image processing for image ";
- // if (node->GetName(name))
- // {
- // // a property called "name" was found for this DataNode
- // message << "'" << name << "'";
- // }
- // message << ".";
- // MITK_INFO << message.str();
-
- // // actually do something here...
-
- // }
- //}
-
- if (m_Controller.isCameraRunning())
- {
- m_Controller.CloseCameraConnection();
- }
- else
- {
- m_Controller.OpenCameraConnection();
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorder.h b/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorder.h
deleted file mode 100644
index 8b66e67852..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorder.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef SpectroCamRecorder_h
-#define SpectroCamRecorder_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-
-#include "ui_SpectroCamRecorderControls.h"
-
-#include <mitkSpectroCamController.h>
-
-
-/**
-\brief SpectroCamRecorder
-
-\warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation.
-
-\sa QmitkAbstractView
-\ingroup ${plugin_target}_internal
-*/
-class SpectroCamRecorder : public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a Qt meta-object
- // (everything that derives from QObject and wants to have signal/slots)
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- virtual ~SpectroCamRecorder();
-
-protected slots:
-
- /// \brief Called when the user clicks the GUI button
- void DoImageProcessing();
-
- void SetWhiteBalance();
-
- void SaveImage();
-
-protected:
-
- virtual void CreateQtPartControl(QWidget *parent);
-
- virtual void SetFocus();
-
- /// \brief called by QmitkFunctionality when DataManager's selection has changed
- virtual void OnSelectionChanged( berry::IWorkbenchPart::Pointer source,
- const QList<mitk::DataNode::Pointer>& nodes );
-
- Ui::SpectroCamRecorderControls m_Controls;
-
-private:
-
- mitk::SpectroCamController m_Controller;
-
-
-
-};
-
-#endif // SpectroCamRecorder_h
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorderControls.ui b/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorderControls.ui
deleted file mode 100644
index 6aeca09807..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/SpectroCamRecorderControls.ui
+++ /dev/null
@@ -1,82 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>SpectroCamRecorderControls</class>
- <widget class="QWidget" name="SpectroCamRecorderControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>222</width>
- <height>228</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QPushButton" name="buttonPerformImageProcessing">
- <property name="toolTip">
- <string>Do image processing</string>
- </property>
- <property name="text">
- <string>Start/Stop camera</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonWhiteBalance">
- <property name="text">
- <string>Use current stack as white balance</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="buttonSave">
- <property name="text">
- <string>Save current stack to datastorage</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="label">
- <property name="text">
- <string>stack name</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLineEdit" name="lineEdit">
- <property name="text">
- <string>stack_1</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="spacer1">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Expanding</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>220</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/org_mitk_gui_qt_spectrocamrecorder_Activator.cpp b/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/org_mitk_gui_qt_spectrocamrecorder_Activator.cpp
deleted file mode 100644
index 1f23f17995..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/org_mitk_gui_qt_spectrocamrecorder_Activator.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-#include "org_mitk_gui_qt_spectrocamrecorder_Activator.h"
-#include "SpectroCamRecorder.h"
-
-namespace mitk {
-
-void org_mitk_gui_qt_spectrocamrecorder_Activator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(SpectroCamRecorder, context)
-}
-
-void org_mitk_gui_qt_spectrocamrecorder_Activator::stop(ctkPluginContext* context)
-{
- Q_UNUSED(context)
-}
-
-}
diff --git a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/org_mitk_gui_qt_spectrocamrecorder_Activator.h b/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/org_mitk_gui_qt_spectrocamrecorder_Activator.h
deleted file mode 100644
index 150987c1d6..0000000000
--- a/Plugins/org.mitk.gui.qt.spectrocamrecorder/src/internal/org_mitk_gui_qt_spectrocamrecorder_Activator.h
+++ /dev/null
@@ -1,37 +0,0 @@
-/*============================================================================
-
-The Medical Imaging Interaction Toolkit (MITK)
-
-Copyright (c) German Cancer Research Center (DKFZ)
-All rights reserved.
-
-Use of this source code is governed by a 3-clause BSD license that can be
-found in the LICENSE file.
-
-============================================================================*/
-
-
-#ifndef org_mitk_gui_qt_spectrocamrecorder_Activator_h
-#define org_mitk_gui_qt_spectrocamrecorder_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
-class org_mitk_gui_qt_spectrocamrecorder_Activator :
- public QObject, public ctkPluginActivator
-{
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_spectrocamrecorder")
- Q_INTERFACES(ctkPluginActivator)
-
-public:
-
- void start(ctkPluginContext* context);
- void stop(ctkPluginContext* context);
-
-}; // org_mitk_gui_qt_spectrocamrecorder_Activator
-
-}
-
-#endif // org_mitk_gui_qt_spectrocamrecorder_Activator_h
diff --git a/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt b/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt
index df74ecb71c..480138e063 100644
--- a/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt
@@ -1,28 +1,26 @@
project(org_mitk_gui_qt_xnat)
-find_package(OpenSSL)
+if(WIN32)
+ set(MITK_OPENSSL_SSL_DLL "" CACHE FILEPATH "")
+ set(MITK_OPENSSL_CRYPTO_DLL "" CACHE FILEPATH "")
-if( NOT OPENSSL_FOUND AND NOT SSL_EAY_RELEASE AND NOT LIB_EAY_RELEASE )
- message( "Could not find OpenSSL, XNAT will not work for HTTPS connections. Please set the SSL_EAY_RELEASE and LIB_EAY_RELEASE CMake variables to the respective libraries." )
-endif()
-
-if( WIN32 AND EXISTS "${SSL_EAY_RELEASE}" AND EXISTS "${LIB_EAY_RELEASE}" )
- foreach(config_type ${CMAKE_CONFIGURATION_TYPES})
- execute_process(COMMAND "${CMAKE_COMMAND}" -E make_directory "${MITK_BINARY_DIR}/bin/${config_type}")
- endforeach()
-
- configure_file( ${SSL_EAY_RELEASE} ${MITK_BINARY_DIR}/bin/Release/ COPYONLY )
- configure_file( ${LIB_EAY_RELEASE} ${MITK_BINARY_DIR}/bin/Release/ COPYONLY )
- configure_file( ${SSL_EAY_RELEASE} ${MITK_BINARY_DIR}/bin/Debug/ COPYONLY )
- configure_file( ${LIB_EAY_RELEASE} ${MITK_BINARY_DIR}/bin/Debug/ COPYONLY )
+ if(MITK_OPENSSL_SSL_DLL AND EXISTS "${MITK_OPENSSL_SSL_DLL}" AND MITK_OPENSSL_CRYPTO_DLL AND EXISTS "${MITK_OPENSSL_CRYPTO_DLL}")
+ foreach(config_type ${CMAKE_CONFIGURATION_TYPES})
+ execute_process(COMMAND "${CMAKE_COMMAND}" -E make_directory "${MITK_BINARY_DIR}/bin/${config_type}")
+ configure_file("${MITK_OPENSSL_SSL_DLL}" "${MITK_BINARY_DIR}/bin/${config_type}/" COPYONLY)
+ configure_file("${MITK_OPENSSL_CRYPTO_DLL}" "${MITK_BINARY_DIR}/bin/${config_type}/" COPYONLY)
+ endforeach()
- MITK_INSTALL( FILES ${SSL_EAY_RELEASE})
- MITK_INSTALL( FILES ${LIB_EAY_RELEASE})
+ MITK_INSTALL(FILES
+ "${MITK_OPENSSL_SSL_DLL}"
+ "${MITK_OPENSSL_CRYPTO_DLL}"
+ )
+ endif()
endif()
mitk_create_plugin(
PACKAGE_DEPENDS Poco|Zip
MODULE_DEPENDS MitkXNAT
EXPORT_DIRECTIVE XNAT_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
)
diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index 9ca98ed3e1..b83484ef43 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -1,503 +1,499 @@
#-----------------------------------------------------------------------------
# Convenient macro allowing to download a file
#-----------------------------------------------------------------------------
if(NOT MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL)
set(MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL http://mitk.org/download/thirdparty)
endif()
macro(downloadFile url dest)
file(DOWNLOAD ${url} ${dest} STATUS status)
list(GET status 0 error_code)
list(GET status 1 error_msg)
if(error_code)
message(FATAL_ERROR "error: Failed to download ${url} - ${error_msg}")
endif()
endmacro()
#-----------------------------------------------------------------------------
# MITK Prerequisites
#-----------------------------------------------------------------------------
if(UNIX AND NOT APPLE)
include(mitkFunctionCheckPackageHeader)
# Check for libxt-dev
mitkFunctionCheckPackageHeader(StringDefs.h libxt-dev /usr/include/X11/)
# Check for libtiff4-dev
mitkFunctionCheckPackageHeader(tiff.h libtiff4-dev)
endif()
# We need a proper patch program. On Linux and MacOS, we assume
# that "patch" is available. On Windows, we download patch.exe
# if not patch program is found.
find_program(PATCH_COMMAND patch)
if((NOT PATCH_COMMAND OR NOT EXISTS ${PATCH_COMMAND}) AND WIN32)
downloadFile(${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/patch.exe
${CMAKE_CURRENT_BINARY_DIR}/patch.exe)
find_program(PATCH_COMMAND patch ${CMAKE_CURRENT_BINARY_DIR})
endif()
if(NOT PATCH_COMMAND)
message(FATAL_ERROR "No patch program found.")
endif()
#-----------------------------------------------------------------------------
# ExternalProjects
#-----------------------------------------------------------------------------
get_property(external_projects GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS)
if(MITK_CTEST_SCRIPT_MODE)
# Write a file containing the list of enabled external project targets.
# This file can be read by a ctest script to separately build projects.
set(SUPERBUILD_TARGETS )
foreach(proj ${external_projects})
if(MITK_USE_${proj})
list(APPEND SUPERBUILD_TARGETS ${proj})
endif()
endforeach()
file(WRITE "${CMAKE_BINARY_DIR}/SuperBuildTargets.cmake" "set(SUPERBUILD_TARGETS ${SUPERBUILD_TARGETS})")
endif()
# A list of "nice" external projects, playing well together with CMake
set(nice_external_projects ${external_projects})
list(REMOVE_ITEM nice_external_projects Boost)
foreach(proj ${nice_external_projects})
if(MITK_USE_${proj})
set(EXTERNAL_${proj}_DIR "${${proj}_DIR}" CACHE PATH "Path to ${proj} build directory")
mark_as_advanced(EXTERNAL_${proj}_DIR)
if(EXTERNAL_${proj}_DIR)
set(${proj}_DIR ${EXTERNAL_${proj}_DIR})
endif()
endif()
endforeach()
set(EXTERNAL_BOOST_ROOT "${BOOST_ROOT}" CACHE PATH "Path to Boost directory")
mark_as_advanced(EXTERNAL_BOOST_ROOT)
if(EXTERNAL_BOOST_ROOT)
set(BOOST_ROOT ${EXTERNAL_BOOST_ROOT})
endif()
if(BUILD_TESTING)
set(EXTERNAL_MITK_DATA_DIR "${MITK_DATA_DIR}" CACHE PATH "Path to the MITK data directory")
mark_as_advanced(EXTERNAL_MITK_DATA_DIR)
if(EXTERNAL_MITK_DATA_DIR)
set(MITK_DATA_DIR ${EXTERNAL_MITK_DATA_DIR})
endif()
endif()
#-----------------------------------------------------------------------------
# External project settings
#-----------------------------------------------------------------------------
include(ExternalProject)
include(mitkMacroQueryCustomEPVars)
include(mitkFunctionInstallExternalCMakeProject)
include(mitkFunctionCleanExternalProject)
-option(MITK_AUTOCLEAN_EXTERNAL_PROJECTS "Experimental: Clean external project builds if updated" OFF)
-mark_as_advanced(MITK_AUTOCLEAN_EXTERNAL_PROJECTS)
+option(MITK_AUTOCLEAN_EXTERNAL_PROJECTS "Experimental: Clean external project builds if updated" ON)
set(ep_prefix "${CMAKE_BINARY_DIR}/ep")
set_property(DIRECTORY PROPERTY EP_PREFIX ${ep_prefix})
# Compute -G arg for configuring external projects with the same CMake generator:
if(CMAKE_EXTRA_GENERATOR)
set(gen "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}")
else()
set(gen "${CMAKE_GENERATOR}")
endif()
set(gen_platform ${CMAKE_GENERATOR_PLATFORM})
# Use this value where semi-colons are needed in ep_add args:
set(sep "^^")
##
if(MSVC_VERSION)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /bigobj /MP")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj /MP")
endif()
-if(MITK_USE_Boost_LIBRARIES)
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_ALL_DYN_LINK")
-endif()
-
# This is a workaround for passing linker flags
# actually down to the linker invocation
set(_cmake_required_flags_orig ${CMAKE_REQUIRED_FLAGS})
set(CMAKE_REQUIRED_FLAGS "-Wl,-rpath")
mitkFunctionCheckCompilerFlags(${CMAKE_REQUIRED_FLAGS} _has_rpath_flag)
set(CMAKE_REQUIRED_FLAGS ${_cmake_required_flags_orig})
set(_install_rpath_linkflag )
if(_has_rpath_flag)
if(APPLE)
set(_install_rpath_linkflag "-Wl,-rpath,@loader_path/../lib")
else()
set(_install_rpath_linkflag "-Wl,-rpath='$ORIGIN/../lib'")
endif()
endif()
set(_install_rpath)
if(APPLE)
set(_install_rpath "@loader_path/../lib")
elseif(UNIX)
# this work for libraries as well as executables
set(_install_rpath "\$ORIGIN/../lib")
endif()
set(ep_common_args
+ -DCMAKE_POLICY_DEFAULT_CMP0091:STRING=OLD
-DCMAKE_CXX_EXTENSIONS:STRING=${CMAKE_CXX_EXTENSIONS}
-DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
-DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
-DCMAKE_MACOSX_RPATH:BOOL=TRUE
"-DCMAKE_INSTALL_RPATH:STRING=${_install_rpath}"
-DBUILD_TESTING:BOOL=OFF
-DCMAKE_INSTALL_PREFIX:PATH=<INSTALL_DIR>
-DBUILD_SHARED_LIBS:BOOL=ON
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
-DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
-DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
"-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} ${MITK_CXX14_FLAG}"
#debug flags
-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG}
-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG}
#release flags
-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE}
-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE}
#relwithdebinfo
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO}
#link flags
-DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS}
-DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS}
-DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS}
)
if(MSVC_VERSION)
list(APPEND ep_common_args
-DCMAKE_DEBUG_POSTFIX:STRING=d
)
set(DCMTK_CMAKE_DEBUG_POSTFIX d)
endif()
set(ep_common_cache_args
)
set(ep_common_cache_default_args
"-DCMAKE_PREFIX_PATH:PATH=<INSTALL_DIR>;${CMAKE_PREFIX_PATH}"
"-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}"
"-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}"
)
# Pass the CMAKE_OSX variables to external projects
if(APPLE)
set(MAC_OSX_ARCHITECTURE_ARGS
-DCMAKE_OSX_ARCHITECTURES:PATH=${CMAKE_OSX_ARCHITECTURES}
-DCMAKE_OSX_DEPLOYMENT_TARGET:PATH=${CMAKE_OSX_DEPLOYMENT_TARGET}
-DCMAKE_OSX_SYSROOT:PATH=${CMAKE_OSX_SYSROOT}
)
set(ep_common_args
${MAC_OSX_ARCHITECTURE_ARGS}
${ep_common_args}
)
endif()
set(mitk_superbuild_ep_args)
set(mitk_depends )
# Include external projects
include(CMakeExternals/MITKData.cmake)
foreach(p ${external_projects})
set(p_hash "")
set(p_file "${CMAKE_SOURCE_DIR}/CMakeExternals/${p}.cmake")
if(EXISTS ${p_file})
file(MD5 ${p_file} p_hash)
else()
foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS})
set(MITK_CMAKE_EXTERNALS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMakeExternals")
set(p_file "${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/${p}.cmake")
if(EXISTS "${p_file}")
file(MD5 "${p_file}" p_hash)
break()
endif()
endforeach()
endif()
if(p_hash)
set(p_hash_file "${ep_prefix}/tmp/${p}-hash.txt")
if(MITK_AUTOCLEAN_EXTERNAL_PROJECTS)
if(EXISTS "${p_hash_file}")
file(READ "${p_hash_file}" p_prev_hash)
if(NOT p_hash STREQUAL p_prev_hash)
mitkCleanExternalProject(${p})
endif()
endif()
endif()
file(WRITE "${p_hash_file}" ${p_hash})
endif()
include("${p_file}" OPTIONAL)
list(APPEND mitk_superbuild_ep_args
-DMITK_USE_${p}:BOOL=${MITK_USE_${p}}
)
get_property(_package GLOBAL PROPERTY MITK_${p}_PACKAGE)
if(_package)
list(APPEND mitk_superbuild_ep_args -D${p}_DIR:PATH=${${p}_DIR})
endif()
list(APPEND mitk_depends ${${p}_DEPENDS})
endforeach()
if (SWIG_EXECUTABLE)
list(APPEND mitk_superbuild_ep_args -DSWIG_EXECUTABLE=${SWIG_EXECUTABLE})
endif()
#-----------------------------------------------------------------------------
# Set superbuild boolean args
#-----------------------------------------------------------------------------
set(mitk_cmake_boolean_args
BUILD_SHARED_LIBS
WITH_COVERAGE
BUILD_TESTING
MITK_BUILD_ALL_PLUGINS
MITK_BUILD_ALL_APPS
MITK_BUILD_EXAMPLES
MITK_USE_Qt5
MITK_USE_SYSTEM_Boost
MITK_USE_BLUEBERRY
MITK_USE_OpenCL
MITK_USE_OpenMP
MITK_ENABLE_PIC_READER
)
#-----------------------------------------------------------------------------
# Create the final variable containing superbuild boolean args
#-----------------------------------------------------------------------------
set(mitk_superbuild_boolean_args)
foreach(mitk_cmake_arg ${mitk_cmake_boolean_args})
list(APPEND mitk_superbuild_boolean_args -D${mitk_cmake_arg}:BOOL=${${mitk_cmake_arg}})
endforeach()
if(MITK_BUILD_ALL_PLUGINS)
list(APPEND mitk_superbuild_boolean_args -DBLUEBERRY_BUILD_ALL_PLUGINS:BOOL=ON)
endif()
#-----------------------------------------------------------------------------
# MITK Utilities
#-----------------------------------------------------------------------------
set(proj MITK-Utilities)
ExternalProject_Add(${proj}
DOWNLOAD_COMMAND ""
CONFIGURE_COMMAND ""
BUILD_COMMAND ""
INSTALL_COMMAND ""
DEPENDS
${mitk_depends}
)
#-----------------------------------------------------------------------------
# Additional MITK CXX/C Flags
#-----------------------------------------------------------------------------
set(MITK_ADDITIONAL_C_FLAGS "" CACHE STRING "Additional C Flags for MITK")
set(MITK_ADDITIONAL_C_FLAGS_RELEASE "" CACHE STRING "Additional Release C Flags for MITK")
set(MITK_ADDITIONAL_C_FLAGS_DEBUG "" CACHE STRING "Additional Debug C Flags for MITK")
mark_as_advanced(MITK_ADDITIONAL_C_FLAGS MITK_ADDITIONAL_C_FLAGS_DEBUG MITK_ADDITIONAL_C_FLAGS_RELEASE)
set(MITK_ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CXX Flags for MITK")
set(MITK_ADDITIONAL_CXX_FLAGS_RELEASE "" CACHE STRING "Additional Release CXX Flags for MITK")
set(MITK_ADDITIONAL_CXX_FLAGS_DEBUG "" CACHE STRING "Additional Debug CXX Flags for MITK")
mark_as_advanced(MITK_ADDITIONAL_CXX_FLAGS MITK_ADDITIONAL_CXX_FLAGS_DEBUG MITK_ADDITIONAL_CXX_FLAGS_RELEASE)
set(MITK_ADDITIONAL_EXE_LINKER_FLAGS "" CACHE STRING "Additional exe linker flags for MITK")
set(MITK_ADDITIONAL_SHARED_LINKER_FLAGS "" CACHE STRING "Additional shared linker flags for MITK")
set(MITK_ADDITIONAL_MODULE_LINKER_FLAGS "" CACHE STRING "Additional module linker flags for MITK")
mark_as_advanced(MITK_ADDITIONAL_EXE_LINKER_FLAGS MITK_ADDITIONAL_SHARED_LINKER_FLAGS MITK_ADDITIONAL_MODULE_LINKER_FLAGS)
#-----------------------------------------------------------------------------
# MITK Configure
#-----------------------------------------------------------------------------
if(MITK_INITIAL_CACHE_FILE)
set(mitk_initial_cache_arg -C "${MITK_INITIAL_CACHE_FILE}")
endif()
set(mitk_optional_cache_args )
foreach(type RUNTIME ARCHIVE LIBRARY)
if(DEFINED CTK_PLUGIN_${type}_OUTPUT_DIRECTORY)
list(APPEND mitk_optional_cache_args -DCTK_PLUGIN_${type}_OUTPUT_DIRECTORY:PATH=${CTK_PLUGIN_${type}_OUTPUT_DIRECTORY})
endif()
endforeach()
# Optional python variables
if(MITK_USE_Python3)
list(APPEND mitk_optional_cache_args
-DMITK_USE_Python3:BOOL=${MITK_USE_Python3}
"-DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE}"
"-DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIRS}"
"-DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY}"
"-DPython3_STDLIB:FILEPATH=${Python3_STDLIB}"
"-DPython3_SITELIB:FILEPATH=${Python3_SITELIB}"
)
endif()
if(OPENSSL_ROOT_DIR)
list(APPEND mitk_optional_cache_args
"-DOPENSSL_ROOT_DIR:PATH=${OPENSSL_ROOT_DIR}"
)
endif()
if(CMAKE_FRAMEWORK_PATH)
list(APPEND mitk_optional_cache_args
"-DCMAKE_FRAMEWORK_PATH:PATH=${CMAKE_FRAMEWORK_PATH}"
)
endif()
if(Eigen_INCLUDE_DIR)
list(APPEND mitk_optional_cache_args
-DEigen_INCLUDE_DIR:PATH=${Eigen_INCLUDE_DIR}
)
endif()
# Optional pass through of Doxygen
if(DOXYGEN_EXECUTABLE)
list(APPEND mitk_optional_cache_args
-DDOXYGEN_EXECUTABLE:FILEPATH=${DOXYGEN_EXECUTABLE}
)
endif()
if(MITK_DOXYGEN_BUILD_ALWAYS)
list(APPEND mitk_optional_cache_args
-DMITK_DOXYGEN_BUILD_ALWAYS:BOOL=${MITK_DOXYGEN_BUILD_ALWAYS}
)
endif()
set(proj MITK-Configure)
ExternalProject_Add(${proj}
LIST_SEPARATOR ${sep}
DOWNLOAD_COMMAND ""
CMAKE_GENERATOR ${gen}
CMAKE_GENERATOR_PLATFORM ${gen_platform}
CMAKE_CACHE_ARGS
# --------------- Build options ----------------
-DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
-DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
"-DCMAKE_PREFIX_PATH:PATH=${ep_prefix};${CMAKE_PREFIX_PATH}"
"-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}"
"-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}"
# --------------- Compile options ----------------
-DCMAKE_CXX_EXTENSIONS:STRING=${CMAKE_CXX_EXTENSIONS}
-DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
-DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
-DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
"-DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS} ${MITK_ADDITIONAL_C_FLAGS}"
"-DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS} ${MITK_ADDITIONAL_CXX_FLAGS}"
# debug flags
"-DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG} ${MITK_ADDITIONAL_CXX_FLAGS_DEBUG}"
"-DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG} ${MITK_ADDITIONAL_C_FLAGS_DEBUG}"
# release flags
"-DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE} ${MITK_ADDITIONAL_CXX_FLAGS_RELEASE}"
"-DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE} ${MITK_ADDITIONAL_C_FLAGS_RELEASE}"
# relwithdebinfo
-DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO}
-DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO}
# link flags
"-DCMAKE_EXE_LINKER_FLAGS:STRING=${CMAKE_EXE_LINKER_FLAGS} ${MITK_ADDITIONAL_EXE_LINKER_FLAGS}"
"-DCMAKE_SHARED_LINKER_FLAGS:STRING=${CMAKE_SHARED_LINKER_FLAGS} ${MITK_ADDITIONAL_SHARED_LINKER_FLAGS}"
"-DCMAKE_MODULE_LINKER_FLAGS:STRING=${CMAKE_MODULE_LINKER_FLAGS} ${MITK_ADDITIONAL_MODULE_LINKER_FLAGS}"
# Output directories
-DMITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY}
-DMITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY}
-DMITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY}
# ------------- Boolean build options --------------
${mitk_superbuild_boolean_args}
${mitk_optional_cache_args}
-DMITK_USE_SUPERBUILD:BOOL=OFF
-DMITK_BUILD_CONFIGURATION:STRING=${MITK_BUILD_CONFIGURATION}
-DMITK_FAST_TESTING:BOOL=${MITK_FAST_TESTING}
-DMITK_XVFB_TESTING:BOOL=${MITK_XVFB_TESTING}
-DMITK_XVFB_TESTING_COMMAND:STRING=${MITK_XVFB_TESTING_COMMAND}
-DCTEST_USE_LAUNCHERS:BOOL=${CTEST_USE_LAUNCHERS}
# ----------------- Miscellaneous ---------------
-DCMAKE_LIBRARY_PATH:PATH=${CMAKE_LIBRARY_PATH}
-DCMAKE_INCLUDE_PATH:PATH=${CMAKE_INCLUDE_PATH}
-DMITK_CTEST_SCRIPT_MODE:STRING=${MITK_CTEST_SCRIPT_MODE}
-DMITK_SUPERBUILD_BINARY_DIR:PATH=${MITK_BINARY_DIR}
-DMITK_MODULES_TO_BUILD:INTERNAL=${MITK_MODULES_TO_BUILD}
-DMITK_WHITELIST:STRING=${MITK_WHITELIST}
-DMITK_WHITELISTS_EXTERNAL_PATH:STRING=${MITK_WHITELISTS_EXTERNAL_PATH}
-DMITK_WHITELISTS_INTERNAL_PATH:STRING=${MITK_WHITELISTS_INTERNAL_PATH}
-DMITK_EXTENSION_DIRS:STRING=${MITK_EXTENSION_DIRS}
-DMITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES}
-DMITK_ACCESSBYITK_FLOATING_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES}
-DMITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES}
-DMITK_ACCESSBYITK_VECTOR_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}
-DMITK_ACCESSBYITK_DIMENSIONS:STRING=${MITK_ACCESSBYITK_DIMENSIONS}
-DMITK_CUSTOM_REVISION_DESC:STRING=${MITK_CUSTOM_REVISION_DESC}
# --------------- External project options ---------------
-DMITK_DATA_DIR:PATH=${MITK_DATA_DIR}
-DMITK_EXTERNAL_PROJECT_PREFIX:PATH=${ep_prefix}
-DCppMicroServices_DIR:PATH=${CppMicroServices_DIR}
-DDCMTK_CMAKE_DEBUG_POSTFIX:STRING=${DCMTK_CMAKE_DEBUG_POSTFIX}
-DBOOST_ROOT:PATH=${BOOST_ROOT}
-DBOOST_LIBRARYDIR:PATH=${BOOST_LIBRARYDIR}
-DMITK_USE_Boost_LIBRARIES:STRING=${MITK_USE_Boost_LIBRARIES}
-DQt5_DIR:PATH=${Qt5_DIR}
CMAKE_ARGS
${mitk_initial_cache_arg}
${MAC_OSX_ARCHITECTURE_ARGS}
${mitk_superbuild_ep_args}
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
BINARY_DIR ${CMAKE_BINARY_DIR}/MITK-build
BUILD_COMMAND ""
INSTALL_COMMAND ""
DEPENDS
MITK-Utilities
)
mitkFunctionInstallExternalCMakeProject(${proj})
#-----------------------------------------------------------------------------
# MITK
#-----------------------------------------------------------------------------
if(CMAKE_GENERATOR MATCHES ".*Makefiles.*")
set(mitk_build_cmd "$(MAKE)")
else()
set(mitk_build_cmd ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/MITK-build --config ${CMAKE_CFG_INTDIR})
endif()
if(NOT DEFINED SUPERBUILD_EXCLUDE_MITKBUILD_TARGET OR NOT SUPERBUILD_EXCLUDE_MITKBUILD_TARGET)
set(MITKBUILD_TARGET_ALL_OPTION "ALL")
else()
set(MITKBUILD_TARGET_ALL_OPTION "")
endif()
add_custom_target(MITK-build ${MITKBUILD_TARGET_ALL_OPTION}
COMMAND ${mitk_build_cmd}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/MITK-build
DEPENDS MITK-Configure
)
#-----------------------------------------------------------------------------
# Custom target allowing to drive the build of the MITK project itself
#-----------------------------------------------------------------------------
add_custom_target(MITK
COMMAND ${mitk_build_cmd}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/MITK-build
)
diff --git a/Utilities/IpPic/CMakeLists.txt b/Utilities/IpPic/CMakeLists.txt
index c137311f03..718ec78ce8 100644
--- a/Utilities/IpPic/CMakeLists.txt
+++ b/Utilities/IpPic/CMakeLists.txt
@@ -1,22 +1,14 @@
-
set(_options NO_INIT GCC_DEFAULT_VISIBILITY)
+
if(MITK_WIN32_FORCE_STATIC)
list(APPEND _options FORCE_STATIC)
endif()
-set(_additional_libs)
-if(USE_ITKZLIB)
- list(APPEND _additional_libs itkzlib)
-else()
- list(APPEND _additional_libs z)
-endif(USE_ITKZLIB)
-
mitk_create_module(
- ADDITIONAL_LIBS ${_additional_libs}
- ${_options}
C_MODULE
WARNINGS_NO_ERRORS
+ ${_options}
+ PACKAGE_DEPENDS PRIVATE ITK|ZLIB
)
target_compile_definitions(${MODULE_TARGET} PRIVATE -DMITK_IPPIC_COMPILE)
-