diff --git a/CMake/BuildConfigurations/All.cmake b/CMake/BuildConfigurations/All.cmake
index 2e65fd8460..d9f0845fcf 100644
--- a/CMake/BuildConfigurations/All.cmake
+++ b/CMake/BuildConfigurations/All.cmake
@@ -1,44 +1,43 @@
set(MITK_CONFIG_PACKAGES )
set(_apple_package_excludes)
set(_package_excludes
${_apple_package_excludes}
- OpenCL
OpenMP
SYSTEM_Boost
Boost_LIBRARIES
SYSTEM_PYTHON
SUPERBUILD
POLHEMUS_TRACKER
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
)
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 ${_package})
endif()
endif()
endforeach()
set(MITK_BUILD_ALL_APPS ON CACHE BOOL "Build all MITK applications" FORCE)
set(MITK_BUILD_ALL_PLUGINS ON CACHE BOOL "Build all MITK plugins" FORCE)
set(MITK_BUILD_EXAMPLES ON CACHE BOOL "Build the MITK examples" FORCE)
set(BLUEBERRY_BUILD_ALL_PLUGINS ON CACHE BOOL "Build all BlueBerry plugins" FORCE)
diff --git a/CMake/FindOpenCL.cmake b/CMake/FindOpenCL.cmake
deleted file mode 100644
index 551d768b13..0000000000
--- a/CMake/FindOpenCL.cmake
+++ /dev/null
@@ -1,88 +0,0 @@
-# - Try to find OpenCL
-# This module tries to find an OpenCL implementation on your system. It supports
-# AMD / ATI, Apple and NVIDIA implementations, but should work, too.
-#
-# To set manually the paths, define these environment variables:
-# OpenCL_INCPATH - Include path (e.g. OpenCL_INCPATH=/opt/cuda/4.0/cuda/include)
-# OpenCL_LIBPATH - Library path (e.h. OpenCL_LIBPATH=/usr/lib64/nvidia)
-#
-# Once done this will define
-# OPENCL_FOUND - system has OpenCL
-# OPENCL_INCLUDE_DIRS - the OpenCL include directory
-# OPENCL_LIBRARIES - link these to use OpenCL
-#
-# WIN32 should work, but is untested
-
-FIND_PACKAGE(PackageHandleStandardArgs)
-
-SET (OPENCL_VERSION_STRING "0.1.0")
-SET(OPENCL_VERSION_MAJOR 0)
-SET(OPENCL_VERSION_MINOR 1)
-SET(OPENCL_VERSION_PATCH 0)
-
-IF(APPLE)
-
- FIND_LIBRARY(OPENCL_LIBRARIES OpenCL DOC "OpenCL lib for OSX")
- FIND_PATH(OPENCL_INCLUDE_DIRS OpenCL/cl.h DOC "Include for OpenCL on OSX")
- FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS OpenCL/cl.hpp DOC "Include for OpenCL CPP bindings on OSX")
-
-ELSE()
- IF (WIN32)
-
- FIND_PATH(OPENCL_INCLUDE_DIRS CL/cl.h)
- FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS CL/cl.hpp)
-
- IF(CMAKE_SIZEOF_VOID_P MATCHES "8")
- SET(OPENCL_LIB_DIR "$ENV{ATISTREAMSDKROOT}/lib/x86_64")
- if(NOT IS_DIRECTORY ${OPENCL_LIB_DIR})
- SET(OPENCL_LIB_DIR "$ENV{CUDA_PATH}/lib/x64")
- endif()
- ELSE()
- SET(OPENCL_LIB_DIR "$ENV{ATISTREAMSDKROOT}/lib/x86")
- if(NOT IS_DIRECTORY ${OPENCL_LIB_DIR}) # need to convert path in the cmake style ?
- SET(OPENCL_LIB_DIR "$ENV{CUDA_PATH}/lib/Win32")
- endif()
- ENDIF()
- file(TO_CMAKE_PATH ${OPENCL_LIB_DIR} OPENCL_LIB_DIR)
- GET_FILENAME_COMPONENT(OPENCL_LIB_DIR ${OPENCL_LIB_DIR} ABSOLUTE)
-
- FIND_LIBRARY(OPENCL_LIBRARIES OpenCL.lib PATHS ${OPENCL_LIB_DIR} ENV OpenCL_LIBPATH)
-
- GET_FILENAME_COMPONENT(_OPENCL_INC_CAND ${OPENCL_LIB_DIR}/../../include ABSOLUTE)
-
- # On Win32 search relative to the library
- FIND_PATH(OPENCL_INCLUDE_DIRS CL/cl.h PATHS "${_OPENCL_INC_CAND}" ENV OpenCL_INCPATH)
- FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS CL/cl.hpp PATHS "${_OPENCL_INC_CAND}" ENV OpenCL_INCPATH)
-
- ELSE ()
-
- # Unix style platforms
- FIND_LIBRARY(OPENCL_LIBRARIES libOpenCL.so
- PATHS "/usr/local/cuda/lib64" "/opt/AMDAPP/lib64" ENV LD_LIBRARY_PATH ENV OpenCL_LIBPATH
- )
- GET_FILENAME_COMPONENT(OPENCL_LIB_DIR ${OPENCL_LIBRARIES} PATH)
- GET_FILENAME_COMPONENT(_OPENCL_INC_CAND ${OPENCL_LIB_DIR}/../../include ABSOLUTE)
-
- # The AMD SDK currently does not place its headers
- # in /usr/include, therefore also search relative
- # to the library
- FIND_PATH(OPENCL_INCLUDE_DIRS CL/cl.h PATHS ${_OPENCL_INC_CAND} "/usr/local/cuda/include" "/opt/AMDAPP/include" ENV OpenCL_INCPATH)
- FIND_PATH(_OPENCL_CPP_INCLUDE_DIRS CL/cl.hpp PATHS ${_OPENCL_INC_CAND} "/usr/local/cuda/include" "/opt/AMDAPP/include" ENV OpenCL_INCPATH)
-
- ENDIF ()
-
-ENDIF ()
-
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(OpenCL DEFAULT_MSG OPENCL_LIBRARIES OPENCL_INCLUDE_DIRS)
-
-IF(_OPENCL_CPP_INCLUDE_DIRS)
- SET( OPENCL_HAS_CPP_BINDINGS TRUE )
- LIST( APPEND OPENCL_INCLUDE_DIRS ${_OPENCL_CPP_INCLUDE_DIRS} )
- # This is often the same, so clean up
- LIST( REMOVE_DUPLICATES OPENCL_INCLUDE_DIRS )
-ENDIF()
-
-MARK_AS_ADVANCED(
- OPENCL_INCLUDE_DIRS
- )
-
diff --git a/CMake/PackageDepends/MITK_OpenCL_Config.cmake b/CMake/PackageDepends/MITK_OpenCL_Config.cmake
deleted file mode 100644
index 8d84d53174..0000000000
--- a/CMake/PackageDepends/MITK_OpenCL_Config.cmake
+++ /dev/null
@@ -1,7 +0,0 @@
-list(APPEND ALL_LIBRARIES ${OPENCL_LIBRARIES})
-list(APPEND ALL_INCLUDE_DIRECTORIES ${OPENCL_INCLUDE_DIRS})
-
-# on OS X the linker needs a flag pointing to the OpenCL.framework
-if(APPLE)
- set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -framework OpenCL")
-endif(APPLE)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 22c9334cf1..5d08edbc5d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,1408 +1,1403 @@
#[[ When increasing the minimum required version, check if Boost_ADDITIONAL_VERSIONS
in CMake/PackageDepends/MITK_Boost_Config.cmake can be removed. See the first
long comment in CMakeExternals/Boost.cmake for details. ]]
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()
#-----------------------------------------------------------------------------
# Policies
#-----------------------------------------------------------------------------
#[[ 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)
if(POLICY CMP0135)
cmake_policy(SET CMP0135 NEW) # https://cmake.org/cmake/help/v3.24/policy/CMP0135.html
endif()
#-----------------------------------------------------------------------------
# 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 2023.12.99)
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()
if(CMAKE_COMPILER_IS_GNUCXX)
mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION)
else()
set(GCC_VERSION 0)
endif()
set(MITK_CXX_STANDARD 17)
set(CMAKE_CXX_EXTENSIONS 0)
set(CMAKE_CXX_STANDARD ${MITK_CXX_STANDARD})
set(CMAKE_CXX_STANDARD_REQUIRED 1)
# This is necessary to avoid problems with compile feature checks.
# CMAKE_CXX_STANDARD seems to only set the -std=c++<std> flag for targets.
# However, compile flag checks also need to be done with -std=c++<std>.
# The MITK_CXX<std>_FLAG variable is also used for external projects
# build during the MITK super-build.
mitkFunctionCheckCompilerFlags("-std=c++${MITK_CXX_STANDARD}" MITK_CXX${MITK_CXX_STANDARD}_FLAG)
#-----------------------------------------------------------------------------
# Warn if source or build path is too long
#-----------------------------------------------------------------------------
if(WIN32)
set(_src_dir_length_max 50)
set(_bin_dir_length_max 50)
if(MITK_USE_SUPERBUILD)
set(_src_dir_length_max 34) # _src_dir_length_max - strlen(ep/src/ITK-build)
set(_bin_dir_length_max 40) # _bin_dir_length_max - strlen(MITK-build)
endif()
string(LENGTH "${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)
mark_as_advanced(
MITK_XVFB_TESTING
MITK_FAST_TESTING
MITK_BUILD_ALL_APPS
)
#-----------------------------------------------------------------------------
# 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 ${_buildConfigs})
mitkFunctionEnableBuildConfiguration()
mitkFunctionCreateWhitelistPaths(MITK)
mitkFunctionFindWhitelists(MITK)
# -----------------------------------------
# Qt version related variables
option(MITK_USE_Qt6 "Use Qt 6 library" ON)
if(MITK_USE_Qt6)
set(MITK_QT6_MINIMUM_VERSION 6.6)
set(MITK_QT6_COMPONENTS
Concurrent
Core
Core5Compat
CoreTools
Designer
DesignerComponentsPrivate
Gui
Help
LinguistTools
Network
OpenGL
OpenGLWidgets
Qml
Sql
StateMachine
Svg
ToolsTools
UiTools
WebEngineCore
WebEngineWidgets
Widgets
Xml
)
if(APPLE)
list(APPEND MITK_QT6_COMPONENTS DBus)
endif()
# Hint at default install locations of Qt
if(NOT Qt6_DIR)
if(MSVC)
set(_dir_candidates "C:/Qt")
if(CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)")
set(_compilers "msvc${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 2022)
list(APPEND _compilers "msvc2019") # Binary compatible
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()
if(APPLE)
list(APPEND _compilers macos)
endif()
foreach(_dir_candidate ${_dir_candidates})
get_filename_component(_dir_candidate ${_dir_candidate} REALPATH)
foreach(_compiler ${_compilers})
set(_glob_expression "${_dir_candidate}/6.*/${_compiler}")
file(GLOB _hints ${_glob_expression})
list(SORT _hints)
list(APPEND MITK_QT6_HINTS ${_hints})
endforeach()
endforeach()
endif()
find_package(Qt6 ${MITK_QT6_MINIMUM_VERSION} COMPONENTS ${MITK_QT6_COMPONENTS} REQUIRED HINTS ${MITK_QT6_HINTS})
get_target_property(QT_QMAKE_EXECUTABLE Qt6::qmake LOCATION)
get_target_property(QT_HELPGENERATOR_EXECUTABLE Qt6::qhelpgenerator LOCATION)
endif()
if(Qt6_DIR)
list(APPEND CMAKE_PREFIX_PATH "${Qt6_DIR}/../../..")
list(REMOVE_DUPLICATES CMAKE_PREFIX_PATH)
endif()
# -----------------------------------------
# Custom dependency logic
if(WIN32 AND Qt6_DIR)
set(_dir_candidate "${Qt6_DIR}/../../../../../Tools/OpenSSLv3/Win_x64")
get_filename_component(_dir_candidate ${_dir_candidate} ABSOLUTE)
if(EXISTS "${_dir_candidate}")
set(OPENSSL_ROOT_DIR "${_dir_candidate}")
endif()
endif()
find_package(OpenSSL 3)
if(NOT OpenSSL_FOUND)
find_package(OpenSSL 1.1.1)
endif()
option(MITK_USE_SYSTEM_Boost "Use the system Boost" OFF)
set(MITK_USE_Boost_LIBRARIES "" CACHE STRING "A semi-colon separated list of required Boost libraries")
if(MITK_USE_cpprestsdk)
if(NOT OpenSSL_FOUND)
set(openssl_message "Could not find OpenSSL (dependency of C++ REST SDK).\n")
if(UNIX)
if(APPLE)
set(openssl_message "${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)
set(python3_mininum_version 3.11)
else()
set(python3_mininum_version 3.8)
endif()
find_package(Python3 ${python3_mininum_version} REQUIRED COMPONENTS Interpreter Development NumPy)
if(WIN32)
string(REPLACE "\\" "/" Python3_STDARCH "${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(mitkFunctionAddManifest)
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( ${MITK_USE_MatchPoint} )
include(mitkFunctionCreateMatchPointDeployedAlgorithm)
endif()
include(mitkMacroConfigureItkPixelTypes)
include(mitkMacroCreateExecutable)
include(mitkMacroCreateModuleTests)
include(mitkMacroGenerateToolsLibrary)
include(mitkMacroGetLinuxDistribution)
include(mitkMacroGetPMDPlatformString)
include(mitkMacroInstall)
include(mitkMacroInstallHelperApp)
include(mitkMacroInstallTargets)
include(mitkMacroMultiplexPicType)
# Deprecated
include(mitkMacroCreateCTKPlugin)
#-----------------------------------------------------------------------------
# Global CMake variables
#-----------------------------------------------------------------------------
if(NOT DEFINED CMAKE_DEBUG_POSTFIX)
# We can't do this yet because the CTK Plugin Framework
# cannot cope with a postfix yet.
#set(CMAKE_DEBUG_POSTFIX d)
endif()
#-----------------------------------------------------------------------------
# Output directories.
#-----------------------------------------------------------------------------
set(_default_LIBRARY_output_dir lib)
set(_default_RUNTIME_output_dir bin)
set(_default_ARCHIVE_output_dir lib)
foreach(type LIBRARY RUNTIME ARCHIVE)
# Make sure the directory exists
if(MITK_CMAKE_${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)
#-----------------------------------------------------------------------------
if(OpenSSL_FOUND AND WIN32)
#[[ On Windows, CMake is able to locate the link libraries for OpenSSL but it
does not look for the corresponding DLLs that we need to copy to our
binary directories and include in packaging.
Setting these paths manually is cumbersome so we try to use a simple
heuristic to automatically set them:
- Based on the link libraries (usually located in a lib folder),
try to find the "../bin" binary directory.
- Use the base file names of the link libraries to find corresponding
DLLs like "<base name>*.dll", that usually are named like
"<base name>-1_1-x64.dll" or similar.
]]
set(openssl_ssl_dll "")
set(openssl_crypto_dll "")
if(OPENSSL_SSL_LIBRARY AND EXISTS "${OPENSSL_SSL_LIBRARY}")
get_filename_component(openssl_bin_dir "${OPENSSL_SSL_LIBRARY}" DIRECTORY)
get_filename_component(openssl_bin_dir "${openssl_bin_dir}" DIRECTORY)
set(openssl_bin_dir "${openssl_bin_dir}/bin")
if(EXISTS "${openssl_bin_dir}")
get_filename_component(openssl_ssl_basename "${OPENSSL_SSL_LIBRARY}" NAME_WE)
file(GLOB openssl_ssl_dll "${openssl_bin_dir}/${openssl_ssl_basename}*.dll")
list(LENGTH openssl_ssl_dll num_findings)
if(num_findings GREATER 1)
set(openssl_ssl_dll "")
endif()
get_filename_component(openssl_crypto_basename "${OPENSSL_CRYPTO_LIBRARY}" NAME_WE)
file(GLOB openssl_crypto_dll "${openssl_bin_dir}/${openssl_crypto_basename}*.dll")
list(LENGTH openssl_crypto_dll num_findings)
if(num_findings GREATER 1)
set(openssl_crypto_dll "")
endif()
endif()
endif()
set(MITK_OPENSSL_SSL_DLL "${openssl_ssl_dll}" CACHE FILEPATH "")
if(DEFINED CACHE{MITK_OPENSSL_SSL_DLL} AND NOT MITK_OPENSSL_SSL_DLL AND openssl_ssl_dll)
set(MITK_OPENSSL_SSL_DLL "${openssl_ssl_dll}" CACHE FILEPATH "" FORCE)
endif()
set(MITK_OPENSSL_CRYPTO_DLL "${openssl_crypto_dll}" CACHE FILEPATH "")
if(DEFINED CACHE{MITK_OPENSSL_CRYPTO_DLL} AND NOT MITK_OPENSSL_CRYPTO_DLL AND openssl_crypto_dll)
set(MITK_OPENSSL_CRYPTO_DLL "${openssl_crypto_dll}" CACHE FILEPATH "" FORCE)
endif()
if(MITK_OPENSSL_SSL_DLL AND EXISTS "${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
"${MITK_OPENSSL_SSL_DLL}"
"${MITK_OPENSSL_CRYPTO_DLL}"
)
endif()
endif()
# 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)
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} ${MITK_CXX${MITK_CXX_STANDARD}_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 "${MITK_CXX_FLAGS} -DWIN32_LEAN_AND_MEAN -DNOMINMAX")
mitkFunctionCheckCompilerFlags("/wd4005" MITK_CXX_FLAGS) # warning C4005: macro redefinition
mitkFunctionCheckCompilerFlags("/wd4231" MITK_CXX_FLAGS) # warning C4231: nonstandard extension used : 'extern' before template explicit instantiation
# the following line should be removed after fixing bug 17637
mitkFunctionCheckCompilerFlags("/wd4316" MITK_CXX_FLAGS) # warning C4316: object alignment on heap
mitkFunctionCheckCompilerFlags("/wd4180" MITK_CXX_FLAGS) # warning C4180: qualifier applied to function type has no meaning
mitkFunctionCheckCompilerFlags("/wd4251" MITK_CXX_FLAGS) # warning C4251: 'identifier' : class 'type' needs to have dll-interface to be used by clients of class 'type2'
endif()
if(APPLE)
set(MITK_CXX_FLAGS "${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-deprecated-copy
-Wno-array-bounds
-Wno-cast-function-type
-Wno-maybe-uninitialized
-Wno-error=stringop-overread
-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 1.74 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}
${CMAKE_MODULE_PATH}
)
if(MITK_USE_DCMTK)
if(${_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()
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 ${MITK_EXTERNAL_PROJECT_PREFIX})
find_package(DCMQI REQUIRED)
endif()
if(MITK_USE_OpenIGTLink)
link_directories(${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_Qt6)
if(MITK_USE_BLUEBERRY)
option(BLUEBERRY_USE_QT_HELP "Enable support for integrating plugin documentation into Qt Help" ${DOXYGEN_FOUND})
mark_as_advanced(BLUEBERRY_USE_QT_HELP)
# Sanity checks for in-application BlueBerry plug-in help generation
if(BLUEBERRY_USE_QT_HELP)
set(_force_blueberry_use_qt_help_to_off 0)
if(NOT DOXYGEN_FOUND)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen was not found.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(DOXYGEN_FOUND AND DOXYGEN_VERSION VERSION_LESS 1.8.7)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen version 1.8.7 or newer not found.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT QT_HELPGENERATOR_EXECUTABLE)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because QT_HELPGENERATOR_EXECUTABLE is empty.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(NOT MITK_USE_Qt6)
message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because MITK_USE_Qt6 is OFF.")
set(_force_blueberry_use_qt_help_to_off 1)
endif()
if(_force_blueberry_use_qt_help_to_off)
set(BLUEBERRY_USE_QT_HELP OFF CACHE BOOL "Enable support for integrating plugin documentation into Qt Help" FORCE)
endif()
endif()
if(BLUEBERRY_QT_HELP_REQUIRED AND NOT BLUEBERRY_USE_QT_HELP)
message(FATAL_ERROR "BLUEBERRY_USE_QT_HELP is required to be set to ON")
endif()
endif()
endif()
#-----------------------------------------------------------------------------
# Testing
#-----------------------------------------------------------------------------
if(BUILD_TESTING)
# Configuration for the CMake-generated test driver
set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include <stdexcept>")
set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN "
try
{")
set(CMAKE_TESTDRIVER_AFTER_TESTMAIN "
}
catch (const std::exception& e)
{
fprintf(stderr, \"%s\\n\", e.what());
return EXIT_FAILURE;
}
catch (...)
{
printf(\"Exception caught in the test driver\\n\");
return EXIT_FAILURE;
}")
set(MITK_TEST_OUTPUT_DIR "${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
#-----------------------------------------------------------------------------
set(MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS)
set(MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS)
foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS})
set(MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS "${MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS} \"${MITK_EXTENSION_DIR}\"")
set(MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS "${MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS} \"${MITK_EXTENSION_DIR}\"")
endforeach()
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/Doxygen/2-UserManual/MITKPluginManualsList.dox b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
index 215faaecb1..615bef9dad 100644
--- a/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
+++ b/Documentation/Doxygen/2-UserManual/MITKPluginManualsList.dox
@@ -1,73 +1,70 @@
/**
\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.
<ul>
<li> \subpage org_mitk_views_basicimageprocessing </li>
<li> \subpage org_mitk_views_datamanager </li>
<li> \subpage org_mitk_editors_dicombrowser </li>
<li> \subpage org_mitk_views_dicominspector </li>
<li> \subpage org_mitk_views_imagecropper </li>
<li> \subpage org_mitk_views_imagenavigator </li>
<li> \subpage org_mitk_views_pixelvalue </li>
<li> \subpage org_blueberry_views_logview </li>
<li> \subpage org_mitk_views_matchpoint_algorithm_browser </li>
<li> \subpage org_mitk_views_matchpoint_algorithm_control </li>
<li> \subpage org_mitk_views_matchpoint_evaluator </li>
<li> \subpage org_mitk_views_matchpoint_framereg </li>
<li> \subpage org_mitk_views_matchpoint_manipulator </li>
<li> \subpage org_mitk_views_matchpoint_mapper </li>
<li> \subpage org_mitk_views_matchpoint_visualizer </li>
<li> \subpage org_mitk_gui_qt_measurementtoolbox
<ul>
<li> \subpage org_mitk_views_measurement </li>
<li> \subpage org_mitk_views_imagestatistics </li>
</ul>
</li>
<li> \subpage org_mitk_views_moviemaker </li>
<li> \subpage org_mitk_views_pointsetinteraction </li>
<li> \subpage org_mitk_views_python </li>
<li> \subpage org_mitk_views_remeshing </li>
<li> \subpage org_mitk_views_screenshotmaker </li>
<li> Segmentation
<ul>
<li> \subpage org_mitk_views_segmentation </li>
<li> \subpage org_mitk_views_segmentationutilities </li>
<li> \subpage org_mitk_views_segmentationtasklist </li>
</ul>
</li>
<li> \subpage org_mitk_editors_stdmultiwidget </li>
<li> \subpage org_mitk_editors_mxnmultiwidget </li>
- <li> \subpage org_mitk_views_deformableclippingplane </li>
<li> \subpage org_mitk_views_viewnavigator </li>
<li> \subpage org_mitk_views_volumevisualization </li>
<li> \subpage org_mitk_views_properties </li>
<li> \subpage org_mitk_gui_qt_flowapplication </li>
<li> \subpage org_mitk_gui_qt_flow_segmentation </li>
<li> \subpage org_mitk_gui_qt_aicpregistration </li>
<li> \subpage org_mitk_gui_qt_cest </li>
<li> \subpage org_mitk_views_pharmacokinetics_concentration_mri </li>
<li> \subpage org_mitk_views_pharmacokinetics_mri </li>
<li> \subpage org_mitk_views_pharmacokinetics_pet </li>
<li> \subpage org_mitk_gui_qt_examples </li>
- <li> \subpage org_mitk_gui_qt_geometrytools </li>
<li> \subpage org_mitk_gui_qt_igtexample </li>
<li> \subpage org_mitk_gui_qt_igttracking </li>
<li> \subpage org_mitk_views_igttrackingsemiautomaticmeasurement </li>
<li> \subpage org_mitk_views_fit_demo </li>
<li> \subpage org_mitk_views_fit_genericfitting </li>
<li> \subpage org_mitk_views_fit_inspector </li>
<li> \subpage org_mitkexamplesopencv </li>
<li> \subpage org_mitk_gui_qt_overlaymanager </li>
<li> \subpage org_mitk_gui_qt_preprocessing_resampling </li>
<li> \subpage org_mitk_views_pharmacokinetics_curvedescriptor </li>
<li> \subpage org_mitk_views_pharmacokinetics_simulation </li>
- <li> \subpage org_surfacematerialeditor </li>
<li> \subpage org_toftutorial </li>
<li> \subpage org_blueberry_ui_qt_objectinspector </li>
<li> \subpage org_mitk_gui_qt_ultrasound </li>
<li> \subpage org_mitk_gui_qt_xnat </li>
</ul>
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox b/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox
index ca06401761..670861fcdc 100644
--- a/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/MITKModuleManualsList.dox
@@ -1,17 +1,16 @@
/**
\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 mitkPython_Overview
\li \subpage RESTModule
\li \subpage GeneratingDeviceModulesPage
\li \subpage USModulePage
*/
diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox
index b96e8c8e25..b688859b3c 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/ThirdPartyLibs.dox
@@ -1,111 +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 ACVD
https://www.creatis.insa-lyon.fr/~valette/public/project/acvd/
\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
https://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 JSON for Modern C++
https://github.com/nlohmann/json
\par lz4
https://github.com/lz4/lz4
\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 PCRE
https://www.pcre.org/
\par POCO
https://pocoproject.org/
\par Python
https://www.python.org/
\par Qt
https://www.qt.io/
\par Qwt
https://qwt.sourceforge.io/
\par SWIG
https://www.swig.org/
\par TinyXML-2
https://www.grinninglizard.com/tinyxml2/
\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 1891d949b6..3aa31fd1c3 100644
--- a/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox
+++ b/Documentation/Doxygen/3-DeveloperManual/Toolkit/ModuleManuals/MITKModuleManualsList.dox
@@ -1,35 +1,34 @@
/**
\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 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/Documentation/doxygen.conf.in b/Documentation/doxygen.conf.in
index 7c4fdc3eec..613c132a49 100644
--- a/Documentation/doxygen.conf.in
+++ b/Documentation/doxygen.conf.in
@@ -1,2841 +1,2840 @@
# Doxyfile 1.9.6
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project.
#
# All text after a double hash (##) is considered a comment and is placed in
# front of the TAG it is preceding.
#
# All text after a single hash (#) is considered a comment and will be ignored.
# The format is:
# TAG = value [value, ...]
# For lists, items can also be appended using:
# TAG += value [value, ...]
# Values that contain spaces should be placed between quotes (\" \").
#
# Note:
#
# Use doxygen to compare the used configuration file with the template
# configuration file:
# doxygen -x [configFile]
# Use doxygen to compare the used configuration file with the template
# configuration file without replacing the environment variables or CMake type
# replacement variables:
# doxygen -x_noenv [configFile]
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
# This tag specifies the encoding used for all characters in the configuration
# file that follow. The default is UTF-8 which is also the encoding used for all
# text before the first occurrence of this tag. Doxygen uses libiconv (or the
# iconv built into libc) for the transcoding. See
# https://www.gnu.org/software/libiconv/ for the list of possible encodings.
# The default value is: UTF-8.
DOXYFILE_ENCODING = UTF-8
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by
# double-quotes, unless you are using Doxywizard) that should identify the
# project for which the documentation is generated. This name is used in the
# title of most generated pages and in a few other places.
# The default value is: My Project.
PROJECT_NAME = "Medical Imaging Interaction Toolkit"
# The PROJECT_NUMBER tag can be used to enter a project or revision number. This
# could be handy for archiving the generated documentation or if some version
# control system is used.
PROJECT_NUMBER = @MITK_VERSION_STRING@
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
# quick idea about the purpose of the project. Keep the description short.
PROJECT_BRIEF = "Medical Imaging Interaction Toolkit"
# With the PROJECT_LOGO tag one can specify a logo or an icon that is included
# in the documentation. The maximum height of the logo should not exceed 55
# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
# the logo to the output directory.
PROJECT_LOGO =
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
# into which the generated documentation will be written. If a relative path is
# entered, it will be relative to the location where doxygen was started. If
# left blank the current directory will be used.
OUTPUT_DIRECTORY = @MITK_DOXYGEN_OUTPUT_DIR@
# If the CREATE_SUBDIRS tag is set to YES then doxygen will create up to 4096
# sub-directories (in 2 levels) under the output directory of each output format
# and will distribute the generated files over these directories. Enabling this
# option can be useful when feeding doxygen a huge amount of source files, where
# putting all generated files in the same directory would otherwise causes
# performance problems for the file system. Adapt CREATE_SUBDIRS_LEVEL to
# control the number of sub-directories.
# The default value is: NO.
CREATE_SUBDIRS = NO
# Controls the number of sub-directories that will be created when
# CREATE_SUBDIRS tag is set to YES. Level 0 represents 16 directories, and every
# level increment doubles the number of directories, resulting in 4096
# directories at level 8 which is the default and also the maximum value. The
# sub-directories are organized in 2 levels, the first level always has a fixed
# number of 16 directories.
# Minimum value: 0, maximum value: 8, default value: 8.
# This tag requires that the tag CREATE_SUBDIRS is set to YES.
CREATE_SUBDIRS_LEVEL = 8
# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
# characters to appear in the names of generated files. If set to NO, non-ASCII
# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode
# U+3044.
# The default value is: NO.
ALLOW_UNICODE_NAMES = NO
# The OUTPUT_LANGUAGE tag is used to specify the language in which all
# documentation generated by doxygen is written. Doxygen will use this
# information to generate all constant output in the proper language.
# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Bulgarian,
# Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, English
# (United States), Esperanto, Farsi (Persian), Finnish, French, German, Greek,
# Hindi, Hungarian, Indonesian, Italian, Japanese, Japanese-en (Japanese with
# English messages), Korean, Korean-en (Korean with English messages), Latvian,
# Lithuanian, Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese,
# Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish,
# Swedish, Turkish, Ukrainian and Vietnamese.
# The default value is: English.
OUTPUT_LANGUAGE = English
# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member
# descriptions after the members that are listed in the file and class
# documentation (similar to Javadoc). Set to NO to disable this.
# The default value is: YES.
BRIEF_MEMBER_DESC = YES
# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief
# description of a member or function before the detailed description
#
# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
# brief descriptions will be completely suppressed.
# The default value is: YES.
REPEAT_BRIEF = YES
# This tag implements a quasi-intelligent brief description abbreviator that is
# used to form the text in various listings. Each string in this list, if found
# as the leading text of the brief description, will be stripped from the text
# and the result, after processing the whole list, is used as the annotated
# text. Otherwise, the brief description is used as-is. If left blank, the
# following values are used ($name is automatically replaced with the name of
# the entity):The $name class, The $name widget, The $name file, is, provides,
# specifies, contains, represents, a, an and the.
ABBREVIATE_BRIEF =
# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
# doxygen will generate a detailed section even if there is only a brief
# description.
# The default value is: NO.
ALWAYS_DETAILED_SEC = NO
# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
# inherited members of a class in the documentation of that class as if those
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
# The default value is: NO.
INLINE_INHERITED_MEMB = NO
# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path
# before files name in the file list and in the header files. If set to NO the
# shortest path that makes the file name unique will be used
# The default value is: YES.
FULL_PATH_NAMES = NO
# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path.
# Stripping is only done if one of the specified strings matches the left-hand
# part of the path. The tag can be used to show relative paths in the file list.
# If left blank the directory from which doxygen is run is used as the path to
# strip.
#
# Note that you can specify absolute paths here, but also relative paths, which
# will be relative from the directory where doxygen is started.
# This tag requires that the tag FULL_PATH_NAMES is set to YES.
STRIP_FROM_PATH =
# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
# path mentioned in the documentation of a class, which tells the reader which
# header file to include in order to use a class. If left blank only the name of
# the header file containing the class definition is used. Otherwise one should
# specify the list of include paths that are normally passed to the compiler
# using the -I flag.
STRIP_FROM_INC_PATH =
# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
# less readable) file names. This can be useful is your file systems doesn't
# support long names like on DOS, Mac, or CD-ROM.
# The default value is: NO.
SHORT_NAMES = NO
# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the
# first line (until the first dot) of a Javadoc-style comment as the brief
# description. If set to NO, the Javadoc-style will behave just like regular Qt-
# style comments (thus requiring an explicit @brief command for a brief
# description.)
# The default value is: NO.
JAVADOC_AUTOBRIEF = NO
# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line
# such as
# /***************
# as being the beginning of a Javadoc-style comment "banner". If set to NO, the
# Javadoc-style will behave just like regular comments and it will not be
# interpreted by doxygen.
# The default value is: NO.
JAVADOC_BANNER = NO
# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first
# line (until the first dot) of a Qt-style comment as the brief description. If
# set to NO, the Qt-style will behave just like regular Qt-style comments (thus
# requiring an explicit \brief command for a brief description.)
# The default value is: NO.
QT_AUTOBRIEF = NO
# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a
# multi-line C++ special comment block (i.e. a block of //! or /// comments) as
# a brief description. This used to be the default behavior. The new default is
# to treat a multi-line C++ comment block as a detailed description. Set this
# tag to YES if you prefer the old behavior instead.
#
# Note that setting this tag to YES also means that rational rose comments are
# not recognized any more.
# The default value is: NO.
MULTILINE_CPP_IS_BRIEF = NO
# By default Python docstrings are displayed as preformatted text and doxygen's
# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the
# doxygen's special commands can be used and the contents of the docstring
# documentation blocks is shown as doxygen documentation.
# The default value is: YES.
PYTHON_DOCSTRING = YES
# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the
# documentation from any documented member that it re-implements.
# The default value is: YES.
INHERIT_DOCS = YES
# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new
# page for each member. If set to NO, the documentation of a member will be part
# of the file/class/namespace that contains it.
# The default value is: NO.
SEPARATE_MEMBER_PAGES = NO
# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen
# uses this value to replace tabs by spaces in code fragments.
# Minimum value: 1, maximum value: 16, default value: 4.
TAB_SIZE = 8
# This tag can be used to specify a number of aliases that act as commands in
# the documentation. An alias has the form:
# name=value
# For example adding
# "sideeffect=@par Side Effects:^^"
# will allow you to put the command \sideeffect (or @sideeffect) in the
# documentation, which will result in a user-defined paragraph with heading
# "Side Effects:". Note that you cannot put \n's in the value part of an alias
# to insert newlines (in the resulting output). You can put ^^ in the value part
# of an alias to insert a newline as if a physical newline was in the original
# file. When you need a literal { or } or , in the value part of an alias you
# have to escape them by means of a backslash (\), this can lead to conflicts
# with the commands \{ and \} for these it is advised to use the version @{ and
# @} or use a double escape (\\{ and \\})
ALIASES = "FIXME=\par Fix Me's:\n" \
"BlueBerry=\if BLUEBERRY" \
"endBlueBerry=\endif" \
"bundlemainpage{1}=\page \1" \
"embmainpage{1}=\page \1" \
"github{2}=<a href=\"https://github.com/MITK/MITK/blob/master/\1\">\2</a>" \
"deprecatedSince{1}=\xrefitem deprecatedSince\1 \"\" \"Functions deprecated as of \1\" \deprecated (as of \1)" \
"minimumCMakeVersion=@MITK_CMAKE_MINIMUM_REQUIRED_VERSION@" \
"minimumQt6Version=@MITK_QT6_MINIMUM_VERSION@" \
"imageMacro{3}=\image html \1 \2 \n \image latex \1 \2 width=\3cm" \
"developersguidemainpage{1}=\page \1" \
"usersguidemainpage{1}=\page \1" \
"nondependentPluginLink{3}= \ref \1 \"\3\""
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
# only. Doxygen will then generate output that is more tailored for C. For
# instance, some of the names that are used will be different. The list of all
# members will be omitted, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_FOR_C = NO
# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or
# Python sources only. Doxygen will then generate output that is more tailored
# for that language. For instance, namespaces will be presented as packages,
# qualified scopes will look different, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_JAVA = NO
# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
# sources. Doxygen will then generate output that is tailored for Fortran.
# The default value is: NO.
OPTIMIZE_FOR_FORTRAN = NO
# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
# sources. Doxygen will then generate output that is tailored for VHDL.
# The default value is: NO.
OPTIMIZE_OUTPUT_VHDL = NO
# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice
# sources only. Doxygen will then generate output that is more tailored for that
# language. For instance, namespaces will be presented as modules, types will be
# separated into more groups, etc.
# The default value is: NO.
OPTIMIZE_OUTPUT_SLICE = NO
# Doxygen selects the parser to use depending on the extension of the files it
# parses. With this tag you can assign which parser to use for a given
# extension. Doxygen has a built-in mapping, but you can override or extend it
# using this tag. The format is ext=language, where ext is a file extension, and
# language is one of the parsers supported by doxygen: IDL, Java, JavaScript,
# Csharp (C#), C, C++, Lex, D, PHP, md (Markdown), Objective-C, Python, Slice,
# VHDL, Fortran (fixed format Fortran: FortranFixed, free formatted Fortran:
# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser
# tries to guess whether the code is fixed or free formatted code, this is the
# default for Fortran type files). For instance to make doxygen treat .inc files
# as Fortran files (default is PHP), and .f files as C (default is Fortran),
# use: inc=Fortran f=C.
#
# Note: For files without extension you can use no_extension as a placeholder.
#
# Note that for custom extensions you also need to set FILE_PATTERNS otherwise
# the files are not read by doxygen. When specifying no_extension you should add
# * to the FILE_PATTERNS.
#
# Note see also the list of default file extension mappings.
EXTENSION_MAPPING = cmake=c++
# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments
# according to the Markdown format, which allows for more readable
# documentation. See https://daringfireball.net/projects/markdown/ for details.
# The output of markdown processing is further processed by doxygen, so you can
# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in
# case of backward compatibilities issues.
# The default value is: YES.
MARKDOWN_SUPPORT = YES
# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up
# to that level are automatically included in the table of contents, even if
# they do not have an id attribute.
# Note: This feature currently applies only to Markdown headings.
# Minimum value: 0, maximum value: 99, default value: 5.
# This tag requires that the tag MARKDOWN_SUPPORT is set to YES.
TOC_INCLUDE_HEADINGS = 5
# When enabled doxygen tries to link words that correspond to documented
# classes, or namespaces to their corresponding documentation. Such a link can
# be prevented in individual cases by putting a % sign in front of the word or
# globally by setting AUTOLINK_SUPPORT to NO.
# The default value is: YES.
AUTOLINK_SUPPORT = YES
# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
# to include (a tag file for) the STL sources as input, then you should set this
# tag to YES in order to let doxygen match functions declarations and
# definitions whose arguments contain STL classes (e.g. func(std::string);
# versus func(std::string) {}). This also make the inheritance and collaboration
# diagrams that involve STL classes more complete and accurate.
# The default value is: NO.
BUILTIN_STL_SUPPORT = YES
# If you use Microsoft's C++/CLI language, you should set this option to YES to
# enable parsing support.
# The default value is: NO.
CPP_CLI_SUPPORT = NO
# Set the SIP_SUPPORT tag to YES if your project consists of sip (see:
# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen
# will parse them like normal C++ but will assume all classes use public instead
# of private inheritance when no explicit protection keyword is present.
# The default value is: NO.
SIP_SUPPORT = NO
# For Microsoft's IDL there are propget and propput attributes to indicate
# getter and setter methods for a property. Setting this option to YES will make
# doxygen to replace the get and set methods by a property in the documentation.
# This will only work if the methods are indeed getting or setting a simple
# type. If this is not the case, or you want to show the methods anyway, you
# should set this option to NO.
# The default value is: YES.
IDL_PROPERTY_SUPPORT = YES
# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
# tag is set to YES then doxygen will reuse the documentation of the first
# member in the group (if any) for the other members of the group. By default
# all members of a group must be documented explicitly.
# The default value is: NO.
DISTRIBUTE_GROUP_DOC = YES
# If one adds a struct or class to a group and this option is enabled, then also
# any nested class or struct is added to the same group. By default this option
# is disabled and one has to add nested compounds explicitly via \ingroup.
# The default value is: NO.
GROUP_NESTED_COMPOUNDS = NO
# Set the SUBGROUPING tag to YES to allow class member groups of the same type
# (for instance a group of public functions) to be put as a subgroup of that
# type (e.g. under the Public Functions section). Set it to NO to prevent
# subgrouping. Alternatively, this can be done per class using the
# \nosubgrouping command.
# The default value is: YES.
SUBGROUPING = YES
# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions
# are shown inside the group in which they are included (e.g. using \ingroup)
# instead of on a separate page (for HTML and Man pages) or section (for LaTeX
# and RTF).
#
# Note that this feature does not work in combination with
# SEPARATE_MEMBER_PAGES.
# The default value is: NO.
INLINE_GROUPED_CLASSES = NO
# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
# with only public data fields or simple typedef fields will be shown inline in
# the documentation of the scope in which they are defined (i.e. file,
# namespace, or group documentation), provided this scope is documented. If set
# to NO, structs, classes, and unions are shown on a separate page (for HTML and
# Man pages) or section (for LaTeX and RTF).
# The default value is: NO.
INLINE_SIMPLE_STRUCTS = NO
# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
# enum is documented as struct, union, or enum with the name of the typedef. So
# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
# with name TypeT. When disabled the typedef will appear as a member of a file,
# namespace, or class. And the struct will be named TypeS. This can typically be
# useful for C code in case the coding convention dictates that all compound
# types are typedef'ed and only the typedef is referenced, never the tag name.
# The default value is: NO.
TYPEDEF_HIDES_STRUCT = NO
# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
# cache is used to resolve symbols given their name and scope. Since this can be
# an expensive process and often the same symbol appears multiple times in the
# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small
# doxygen will become slower. If the cache is too large, memory is wasted. The
# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range
# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536
# symbols. At the end of a run doxygen will report the cache usage and suggest
# the optimal cache size from a speed point of view.
# Minimum value: 0, maximum value: 9, default value: 0.
LOOKUP_CACHE_SIZE = 0
# The NUM_PROC_THREADS specifies the number of threads doxygen is allowed to use
# during processing. When set to 0 doxygen will based this on the number of
# cores available in the system. You can set it explicitly to a value larger
# than 0 to get more control over the balance between CPU load and processing
# speed. At this moment only the input processing can be done using multiple
# threads. Since this is still an experimental feature the default is set to 1,
# which effectively disables parallel processing. Please report any issues you
# encounter. Generating dot graphs in parallel is controlled by the
# DOT_NUM_THREADS setting.
# Minimum value: 0, maximum value: 32, default value: 1.
NUM_PROC_THREADS = 1
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in
# documentation are documented, even if no documentation was available. Private
# class members and static file members will be hidden unless the
# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES.
# Note: This will also disable the warnings about undocumented members that are
# normally produced when WARNINGS is set to YES.
# The default value is: NO.
EXTRACT_ALL = YES
# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will
# be included in the documentation.
# The default value is: NO.
EXTRACT_PRIVATE = NO
# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual
# methods of a class will be included in the documentation.
# The default value is: NO.
EXTRACT_PRIV_VIRTUAL = NO
# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal
# scope will be included in the documentation.
# The default value is: NO.
EXTRACT_PACKAGE = NO
# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be
# included in the documentation.
# The default value is: NO.
EXTRACT_STATIC = YES
# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined
# locally in source files will be included in the documentation. If set to NO,
# only classes defined in header files are included. Does not have any effect
# for Java sources.
# The default value is: YES.
EXTRACT_LOCAL_CLASSES = @MITK_DOXYGEN_INTERNAL_DOCS@
# This flag is only useful for Objective-C code. If set to YES, local methods,
# which are defined in the implementation section but not in the interface are
# included in the documentation. If set to NO, only methods in the interface are
# included.
# The default value is: NO.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called
# 'anonymous_namespace{file}', where file will be replaced with the base name of
# the file that contains the anonymous namespace. By default anonymous namespace
# are hidden.
# The default value is: NO.
EXTRACT_ANON_NSPACES = NO
# If this flag is set to YES, the name of an unnamed parameter in a declaration
# will be determined by the corresponding definition. By default unnamed
# parameters remain unnamed in the output.
# The default value is: YES.
RESOLVE_UNNAMED_PARAMS = YES
# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all
# undocumented members inside documented classes or files. If set to NO these
# members will be included in the various overviews, but no documentation
# section is generated. This option has no effect if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_MEMBERS = NO
# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy. If set
# to NO, these classes will be included in the various overviews. This option
# will also hide undocumented C++ concepts if enabled. This option has no effect
# if EXTRACT_ALL is enabled.
# The default value is: NO.
HIDE_UNDOC_CLASSES = NO
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend
# declarations. If set to NO, these declarations will be included in the
# documentation.
# The default value is: NO.
HIDE_FRIEND_COMPOUNDS = @MITK_DOXYGEN_HIDE_FRIEND_COMPOUNDS@
# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any
# documentation blocks found inside the body of a function. If set to NO, these
# blocks will be appended to the function's detailed documentation block.
# The default value is: NO.
HIDE_IN_BODY_DOCS = NO
# The INTERNAL_DOCS tag determines if documentation that is typed after a
# \internal command is included. If the tag is set to NO then the documentation
# will be excluded. Set it to YES to include the internal documentation.
# The default value is: NO.
INTERNAL_DOCS = @MITK_DOXYGEN_INTERNAL_DOCS@
# With the correct setting of option CASE_SENSE_NAMES doxygen will better be
# able to match the capabilities of the underlying filesystem. In case the
# filesystem is case sensitive (i.e. it supports files in the same directory
# whose names only differ in casing), the option must be set to YES to properly
# deal with such files in case they appear in the input. For filesystems that
# are not case sensitive the option should be set to NO to properly deal with
# output files written for symbols that only differ in casing, such as for two
# classes, one named CLASS and the other named Class, and to also support
# references to files without having to specify the exact matching casing. On
# Windows (including Cygwin) and MacOS, users should typically set this option
# to NO, whereas on Linux or other Unix flavors it should typically be set to
# YES.
# Possible values are: SYSTEM, NO and YES.
# The default value is: SYSTEM.
CASE_SENSE_NAMES = YES
# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with
# their full class and namespace scopes in the documentation. If set to YES, the
# scope will be hidden.
# The default value is: NO.
HIDE_SCOPE_NAMES = NO
# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will
# append additional text to a page's title, such as Class Reference. If set to
# YES the compound reference will be hidden.
# The default value is: NO.
HIDE_COMPOUND_REFERENCE= NO
# If the SHOW_HEADERFILE tag is set to YES then the documentation for a class
# will show which file needs to be included to use the class.
# The default value is: YES.
SHOW_HEADERFILE = YES
# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of
# the files that are included by a file in the documentation of that file.
# The default value is: YES.
SHOW_INCLUDE_FILES = YES
# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each
# grouped member an include statement to the documentation, telling the reader
# which file to include in order to use the member.
# The default value is: NO.
SHOW_GROUPED_MEMB_INC = NO
# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include
# files with double quotes in the documentation rather than with sharp brackets.
# The default value is: NO.
FORCE_LOCAL_INCLUDES = NO
# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the
# documentation for inline members.
# The default value is: YES.
INLINE_INFO = YES
# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the
# (detailed) documentation of file and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order.
# The default value is: YES.
SORT_MEMBER_DOCS = YES
# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief
# descriptions of file, namespace and class members alphabetically by member
# name. If set to NO, the members will appear in declaration order. Note that
# this will also influence the order of the classes in the class list.
# The default value is: NO.
SORT_BRIEF_DOCS = NO
# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the
# (brief and detailed) documentation of class members so that constructors and
# destructors are listed first. If set to NO the constructors will appear in the
# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS.
# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief
# member documentation.
# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting
# detailed member documentation.
# The default value is: NO.
SORT_MEMBERS_CTORS_1ST = NO
# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy
# of group names into alphabetical order. If set to NO the group names will
# appear in their defined order.
# The default value is: NO.
SORT_GROUP_NAMES = NO
# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by
# fully-qualified names, including namespaces. If set to NO, the class list will
# be sorted only by class name, not including the namespace part.
# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
# Note: This option applies only to the class list, not to the alphabetical
# list.
# The default value is: NO.
SORT_BY_SCOPE_NAME = YES
# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper
# type resolution of all parameters of a function it will reject a match between
# the prototype and the implementation of a member function even if there is
# only one candidate or it is obvious which candidate to choose by doing a
# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still
# accept a match between prototype and implementation in such cases.
# The default value is: NO.
STRICT_PROTO_MATCHING = NO
# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo
# list. This list is created by putting \todo commands in the documentation.
# The default value is: YES.
GENERATE_TODOLIST = @MITK_DOXYGEN_GENERATE_TODOLIST@
# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test
# list. This list is created by putting \test commands in the documentation.
# The default value is: YES.
GENERATE_TESTLIST = YES
# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug
# list. This list is created by putting \bug commands in the documentation.
# The default value is: YES.
GENERATE_BUGLIST = @MITK_DOXYGEN_GENERATE_BUGLIST@
# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO)
# the deprecated list. This list is created by putting \deprecated commands in
# the documentation.
# The default value is: YES.
GENERATE_DEPRECATEDLIST= @MITK_DOXYGEN_GENERATE_DEPRECATEDLIST@
# The ENABLED_SECTIONS tag can be used to enable conditional documentation
# sections, marked by \if <section_label> ... \endif and \cond <section_label>
# ... \endcond blocks.
ENABLED_SECTIONS = @MITK_DOXYGEN_ENABLED_SECTIONS@
# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the
# initial value of a variable or macro / define can have for it to appear in the
# documentation. If the initializer consists of more lines than specified here
# it will be hidden. Use a value of 0 to hide initializers completely. The
# appearance of the value of individual variables and macros / defines can be
# controlled using \showinitializer or \hideinitializer command in the
# documentation regardless of this setting.
# Minimum value: 0, maximum value: 10000, default value: 30.
MAX_INITIALIZER_LINES = 0
# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at
# the bottom of the documentation of classes and structs. If set to YES, the
# list will mention the files that were used to generate the documentation.
# The default value is: YES.
SHOW_USED_FILES = YES
# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This
# will remove the Files entry from the Quick Index and from the Folder Tree View
# (if specified).
# The default value is: YES.
SHOW_FILES = YES
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces
# page. This will remove the Namespaces entry from the Quick Index and from the
# Folder Tree View (if specified).
# The default value is: YES.
SHOW_NAMESPACES = YES
# The FILE_VERSION_FILTER tag can be used to specify a program or script that
# doxygen should invoke to get the current version for each file (typically from
# the version control system). Doxygen will invoke the program by executing (via
# popen()) the command command input-file, where command is the value of the
# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided
# by doxygen. Whatever the program writes to standard output is used as the file
# version. For an example see the documentation.
FILE_VERSION_FILTER =
# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
# by doxygen. The layout file controls the global structure of the generated
# output files in an output format independent way. To create the layout file
# that represents doxygen's defaults, run doxygen with the -l option. You can
# optionally specify a file name after the option, if omitted DoxygenLayout.xml
# will be used as the name of the layout file. See also section "Changing the
# layout of pages" for information.
#
# Note that if you run doxygen from a directory containing a file called
# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE
# tag is left empty.
LAYOUT_FILE = @MITK_SOURCE_DIR@/Documentation/MITKDoxygenLayout.xml
# The CITE_BIB_FILES tag can be used to specify one or more bib files containing
# the reference definitions. This must be a list of .bib files. The .bib
# extension is automatically appended if omitted. This requires the bibtex tool
# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info.
# For LaTeX the style of the bibliography can be controlled using
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.
CITE_BIB_FILES =
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
#---------------------------------------------------------------------------
# The QUIET tag can be used to turn on/off the messages that are generated to
# standard output by doxygen. If QUIET is set to YES this implies that the
# messages are off.
# The default value is: NO.
QUIET = YES
# The WARNINGS tag can be used to turn on/off the warning messages that are
# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES
# this implies that the warnings are on.
#
# Tip: Turn warnings on while writing the documentation.
# The default value is: YES.
WARNINGS = YES
# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate
# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: YES.
WARN_IF_UNDOCUMENTED = YES
# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for
# potential errors in the documentation, such as documenting some parameters in
# a documented function twice, or documenting parameters that don't exist or
# using markup commands wrongly.
# The default value is: YES.
WARN_IF_DOC_ERROR = YES
# If WARN_IF_INCOMPLETE_DOC is set to YES, doxygen will warn about incomplete
# function parameter documentation. If set to NO, doxygen will accept that some
# parameters have no documentation without warning.
# The default value is: YES.
WARN_IF_INCOMPLETE_DOC = YES
# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that
# are documented, but have no documentation for their parameters or return
# value. If set to NO, doxygen will only warn about wrong parameter
# documentation, but not about the absence of documentation. If EXTRACT_ALL is
# set to YES then this flag will automatically be disabled. See also
# WARN_IF_INCOMPLETE_DOC
# The default value is: NO.
WARN_NO_PARAMDOC = NO
# If WARN_IF_UNDOC_ENUM_VAL option is set to YES, doxygen will warn about
# undocumented enumeration values. If set to NO, doxygen will accept
# undocumented enumeration values. If EXTRACT_ALL is set to YES then this flag
# will automatically be disabled.
# The default value is: NO.
WARN_IF_UNDOC_ENUM_VAL = NO
# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when
# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS
# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but
# at the end of the doxygen process doxygen will return with a non-zero status.
# Possible values are: NO, YES and FAIL_ON_WARNINGS.
# The default value is: NO.
WARN_AS_ERROR = NO
# The WARN_FORMAT tag determines the format of the warning messages that doxygen
# can produce. The string should contain the $file, $line, and $text tags, which
# will be replaced by the file and line number from which the warning originated
# and the warning text. Optionally the format may contain $version, which will
# be replaced by the version of the file (if it could be obtained via
# FILE_VERSION_FILTER)
# See also: WARN_LINE_FORMAT
# The default value is: $file:$line: $text.
WARN_FORMAT = "$file:$line: $text"
# In the $text part of the WARN_FORMAT command it is possible that a reference
# to a more specific place is given. To make it easier to jump to this place
# (outside of doxygen) the user can define a custom "cut" / "paste" string.
# Example:
# WARN_LINE_FORMAT = "'vi $file +$line'"
# See also: WARN_FORMAT
# The default value is: at line $line of file $file.
WARN_LINE_FORMAT = "at line $line of file $file"
# The WARN_LOGFILE tag can be used to specify a file to which warning and error
# messages should be written. If left blank the output is written to standard
# error (stderr). In case the file specified cannot be opened for writing the
# warning and error messages are written to standard error. When as file - is
# specified the warning and error messages are written to standard output
# (stdout).
WARN_LOGFILE =
#---------------------------------------------------------------------------
# Configuration options related to the input files
#---------------------------------------------------------------------------
# The INPUT tag is used to specify the files and/or directories that contain
# documented source files. You may enter file names like myfile.cpp or
# directories like /usr/src/myproject. Separate the files or directories with
# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
# Note: If this tag is empty the current directory is searched.
INPUT = "@MITK_SOURCE_DIR@" \
"@MITK_BINARY_DIR@" \
@MITK_DOXYGEN_ADDITIONAL_INPUT_DIRS@
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
# libiconv (or the iconv built into libc) for the transcoding. See the libiconv
# documentation (see:
# https://www.gnu.org/software/libiconv/) for the list of possible encodings.
# See also: INPUT_FILE_ENCODING
# The default value is: UTF-8.
INPUT_ENCODING = UTF-8
# This tag can be used to specify the character encoding of the source files
# that doxygen parses The INPUT_FILE_ENCODING tag can be used to specify
# character encoding on a per file pattern basis. Doxygen will compare the file
# name with each pattern and apply the encoding instead of the default
# INPUT_ENCODING) if there is a match. The character encodings are a list of the
# form: pattern=encoding (like *.php=ISO-8859-1). See cfg_input_encoding
# "INPUT_ENCODING" for further information on supported encodings.
INPUT_FILE_ENCODING =
# If the value of the INPUT tag contains directories, you can use the
# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and
# *.h) to filter out the source-files in the directories.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# read by doxygen.
#
# Note the list of default checked file patterns might differ from the list of
# default file extension mappings.
#
# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp,
# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h,
# *.hh, *.hxx, *.hpp, *.h++, *.l, *.cs, *.d, *.php, *.php4, *.php5, *.phtml,
# *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C
# comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd,
# *.vhdl, *.ucf, *.qsf and *.ice.
FILE_PATTERNS = *.h \
*.dox \
*.md
# The RECURSIVE tag can be used to specify whether or not subdirectories should
# be searched for input files as well.
# The default value is: NO.
RECURSIVE = YES
# The EXCLUDE tag can be used to specify files and/or directories that should be
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
#
# Note that relative paths are relative to the directory from which doxygen is
# run.
EXCLUDE = "@MITK_SOURCE_DIR@/Utilities/qtsingleapplication/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/doc/snippets/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/doc/doxygen/standalone/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/test/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/examples/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/src/util/jsoncpp.cpp" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/third_party" \
"@MITK_SOURCE_DIR@/CMake/PackageDepends" \
"@MITK_SOURCE_DIR@/CMakeExternals" \
"@MITK_SOURCE_DIR@/Licenses" \
"@MITK_BINARY_DIR@/Documentation/Doxygen" \
"@MITK_BINARY_DIR@/bin/" \
"@MITK_BINARY_DIR@/PT/" \
"@MITK_BINARY_DIR@/GP/" \
"@MITK_BINARY_DIR@/_CPack_Packages/" \
@MITK_DOXYGEN_ADDITIONAL_EXCLUDE_DIRS@
# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
# directories that are symbolic links (a Unix file system feature) are excluded
# from the input.
# The default value is: NO.
EXCLUDE_SYMLINKS = NO
# If the value of the INPUT tag contains directories, you can use the
# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
# certain files from those directories.
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories for example use the pattern */test/*
EXCLUDE_PATTERNS = README* \
moc_* \
ui_* \
qrc_* \
wrap_* \
Register* \
*/files.cmake \
*/.git/* \
*_p.h \
*Private.* \
*/Internal/* \
*/internal/* \
*/Snippets/* \
*/snippets/* \
*/testing/* \
*/Testing/* \
*/test/* \
*/resource/* \
"@MITK_BINARY_DIR@/*.cmake" \
@MITK_DOXYGEN_EXCLUDE_PATTERNS@
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
# output. The symbol name can be a fully qualified name, a word, or if the
# wildcard * is used, a substring. Examples: ANamespace, AClass,
# ANamespace::AClass, ANamespace::*Test
#
# Note that the wildcards are matched against the file with absolute path, so to
# exclude all test directories use the pattern */test/*
EXCLUDE_SYMBOLS =
# The EXAMPLE_PATH tag can be used to specify one or more files or directories
# that contain example code fragments that are included (see the \include
# command).
EXAMPLE_PATH = "@MITK_SOURCE_DIR@/Examples/" \
"@MITK_SOURCE_DIR@/Examples/Tutorial/" \
"@MITK_SOURCE_DIR@/Examples/Plugins/" \
"@MITK_SOURCE_DIR@/Examples/QtFreeRender/" \
"@MITK_SOURCE_DIR@/Modules/Core/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/doc/snippets/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/core/examples/" \
"@MITK_SOURCE_DIR@/Modules/CppMicroServices/" \
- "@MITK_SOURCE_DIR@/Modules/OpenCL/Documentation/doxygen/snippets/" \
"@MITK_SOURCE_DIR@/Modules/IGT/Tutorial/" \
"@MITK_SOURCE_DIR@/Plugins/org.mitk.gui.common/src/" \
"@MITK_SOURCE_DIR@/Plugins/org.mitk.gui.qt.igtexamples/" \
"@MITK_SOURCE_DIR@/Plugins/org.mitk.gui.qt.igttracking/"
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
# *.h) to filter out the source-files in the directories. If left blank all
# files are included.
EXAMPLE_PATTERNS =
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude commands
# irrespective of the value of the RECURSIVE tag.
# The default value is: NO.
EXAMPLE_RECURSIVE = YES
# The IMAGE_PATH tag can be used to specify one or more files or directories
# that contain images that are to be included in the documentation (see the
# \image command).
IMAGE_PATH = "@MITK_SOURCE_DIR@/Documentation/Doxygen/" \
"@MITK_SOURCE_DIR@" \
@MITK_DOXYGEN_ADDITIONAL_IMAGE_PATHS@
# The INPUT_FILTER tag can be used to specify a program that doxygen should
# invoke to filter for each input file. Doxygen will invoke the filter program
# by executing (via popen()) the command:
#
# <filter> <input-file>
#
# where <filter> is the value of the INPUT_FILTER tag, and <input-file> is the
# name of an input file. Doxygen will then use the output that the filter
# program writes to standard output. If FILTER_PATTERNS is specified, this tag
# will be ignored.
#
# Note that the filter must not add or remove lines; it is applied before the
# code is scanned, but not when the output code is generated. If lines are added
# or removed, the anchors will not be placed correctly.
#
# Note that doxygen will use the data processed and written to standard output
# for further processing, therefore nothing else, like debug statements or used
# commands (so in case of a Windows batch file always use @echo OFF), should be
# written to standard output.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
INPUT_FILTER =
# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
# basis. Doxygen will compare the file name with each pattern and apply the
# filter if there is a match. The filters are a list of the form: pattern=filter
# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how
# filters are used. If the FILTER_PATTERNS tag is empty or if none of the
# patterns match the file name, INPUT_FILTER is applied.
#
# Note that for custom extensions or not directly supported extensions you also
# need to set EXTENSION_MAPPING for the extension otherwise the files are not
# properly processed by doxygen.
FILTER_PATTERNS = *.cmake=@CMakeDoxygenFilter_EXECUTABLE@
# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
# INPUT_FILTER) will also be used to filter the input files that are used for
# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES).
# The default value is: NO.
FILTER_SOURCE_FILES = NO
# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and
# it is also possible to disable source filtering for a specific pattern using
# *.ext= (so without naming a filter).
# This tag requires that the tag FILTER_SOURCE_FILES is set to YES.
FILTER_SOURCE_PATTERNS =
# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that
# is part of the input, its contents will be placed on the main page
# (index.html). This can be useful if you have a project on for instance GitHub
# and want to reuse the introduction page also for the doxygen output.
USE_MDFILE_AS_MAINPAGE =
# The Fortran standard specifies that for fixed formatted Fortran code all
# characters from position 72 are to be considered as comment. A common
# extension is to allow longer lines before the automatic comment starts. The
# setting FORTRAN_COMMENT_AFTER will also make it possible that longer lines can
# be processed before the automatic comment starts.
# Minimum value: 7, maximum value: 10000, default value: 72.
FORTRAN_COMMENT_AFTER = 72
#---------------------------------------------------------------------------
# Configuration options related to source browsing
#---------------------------------------------------------------------------
# If the SOURCE_BROWSER tag is set to YES then a list of source files will be
# generated. Documented entities will be cross-referenced with these sources.
#
# Note: To get rid of all source code in the generated output, make sure that
# also VERBATIM_HEADERS is set to NO.
# The default value is: NO.
SOURCE_BROWSER = YES
# Setting the INLINE_SOURCES tag to YES will include the body of functions,
# classes and enums directly into the documentation.
# The default value is: NO.
INLINE_SOURCES = NO
# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any
# special comment blocks from generated source code fragments. Normal C, C++ and
# Fortran comments will always remain visible.
# The default value is: YES.
STRIP_CODE_COMMENTS = YES
# If the REFERENCED_BY_RELATION tag is set to YES then for each documented
# entity all documented functions referencing it will be listed.
# The default value is: NO.
REFERENCED_BY_RELATION = YES
# If the REFERENCES_RELATION tag is set to YES then for each documented function
# all documented entities called/used by that function will be listed.
# The default value is: NO.
REFERENCES_RELATION = YES
# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
# to YES then the hyperlinks from functions in REFERENCES_RELATION and
# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will
# link to the documentation.
# The default value is: YES.
REFERENCES_LINK_SOURCE = YES
# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the
# source code will show a tooltip with additional information such as prototype,
# brief description and links to the definition and documentation. Since this
# will make the HTML file larger and loading of large files a bit slower, you
# can opt to disable this feature.
# The default value is: YES.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
SOURCE_TOOLTIPS = YES
# If the USE_HTAGS tag is set to YES then the references to source code will
# point to the HTML generated by the htags(1) tool instead of doxygen built-in
# source browser. The htags tool is part of GNU's global source tagging system
# (see https://www.gnu.org/software/global/global.html). You will need version
# 4.8.6 or higher.
#
# To use it do the following:
# - Install the latest version of global
# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file
# - Make sure the INPUT points to the root of the source tree
# - Run doxygen as normal
#
# Doxygen will invoke htags (and that will in turn invoke gtags), so these
# tools must be available from the command line (i.e. in the search path).
#
# The result: instead of the source browser generated by doxygen, the links to
# source code will now point to the output of htags.
# The default value is: NO.
# This tag requires that the tag SOURCE_BROWSER is set to YES.
USE_HTAGS = NO
# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a
# verbatim copy of the header file for each class for which an include is
# specified. Set to NO to disable this.
# See also: Section \class.
# The default value is: YES.
VERBATIM_HEADERS = YES
# If the CLANG_ASSISTED_PARSING tag is set to YES then doxygen will use the
# clang parser (see:
# http://clang.llvm.org/) for more accurate parsing at the cost of reduced
# performance. This can be particularly helpful with template rich C++ code for
# which doxygen's built-in parser lacks the necessary type information.
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse_libclang=ON option for CMake.
# The default value is: NO.
CLANG_ASSISTED_PARSING = NO
# If the CLANG_ASSISTED_PARSING tag is set to YES and the CLANG_ADD_INC_PATHS
# tag is set to YES then doxygen will add the directory of each input to the
# include path.
# The default value is: YES.
# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
CLANG_ADD_INC_PATHS = YES
# If clang assisted parsing is enabled you can provide the compiler with command
# line options that you would normally use when invoking the compiler. Note that
# the include paths will already be set by doxygen for the files and directories
# specified with INPUT and INCLUDE_PATH.
# This tag requires that the tag CLANG_ASSISTED_PARSING is set to YES.
CLANG_OPTIONS =
# If clang assisted parsing is enabled you can provide the clang parser with the
# path to the directory containing a file called compile_commands.json. This
# file is the compilation database (see:
# http://clang.llvm.org/docs/HowToSetupToolingForLLVM.html) containing the
# options used when the source files were built. This is equivalent to
# specifying the -p option to a clang tool, such as clang-check. These options
# will then be passed to the parser. Any options specified with CLANG_OPTIONS
# will be added as well.
# Note: The availability of this option depends on whether or not doxygen was
# generated with the -Duse_libclang=ON option for CMake.
CLANG_DATABASE_PATH =
#---------------------------------------------------------------------------
# Configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all
# compounds will be generated. Enable this if the project contains a lot of
# classes, structs, unions or interfaces.
# The default value is: YES.
ALPHABETICAL_INDEX = YES
# The IGNORE_PREFIX tag can be used to specify a prefix (or a list of prefixes)
# that should be ignored while generating the index headers. The IGNORE_PREFIX
# tag works for classes, function and member names. The entity will be placed in
# the alphabetical list under the first letter of the entity name that remains
# after removing the prefix.
# This tag requires that the tag ALPHABETICAL_INDEX is set to YES.
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the HTML output
#---------------------------------------------------------------------------
# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output
# The default value is: YES.
GENERATE_HTML = YES
# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_OUTPUT = html
# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
# generated HTML page (for example: .htm, .php, .asp).
# The default value is: .html.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FILE_EXTENSION = .html
# The HTML_HEADER tag can be used to specify a user-defined HTML header file for
# each generated HTML page. If the tag is left blank doxygen will generate a
# standard header.
#
# To get valid HTML the header file that includes any scripts and style sheets
# that doxygen needs, which is dependent on the configuration options used (e.g.
# the setting GENERATE_TREEVIEW). It is highly recommended to start with a
# default header using
# doxygen -w html new_header.html new_footer.html new_stylesheet.css
# YourConfigFile
# and then modify the file new_header.html. See also section "Doxygen usage"
# for information on how to generate the default header that doxygen normally
# uses.
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. For a description
# of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_HEADER =
# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
# generated HTML page. If the tag is left blank doxygen will generate a standard
# footer. See HTML_HEADER for more information on how to generate a default
# footer and what special commands can be used inside the footer. See also
# section "Doxygen usage" for information on how to generate the default footer
# that doxygen normally uses.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FOOTER =
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
# sheet that is used by each HTML page. It can be used to fine-tune the look of
# the HTML output. If left blank doxygen will generate a default style sheet.
# See also section "Doxygen usage" for information on how to generate the style
# sheet that doxygen normally uses.
# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as
# it is more robust and this tag (HTML_STYLESHEET) will in the future become
# obsolete.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_STYLESHEET =
# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# cascading style sheets that are included after the standard style sheets
# created by doxygen. Using this option one can overrule certain style aspects.
# This is preferred over using HTML_STYLESHEET since it does not replace the
# standard style sheet and is therefore more robust against future updates.
# Doxygen will copy the style sheet files to the output directory.
# Note: The order of the extra style sheet files is of importance (e.g. the last
# style sheet in the list overrules the setting of the previous ones in the
# list).
# Note: Since the styling of scrollbars can currently not be overruled in
# Webkit/Chromium, the styling will be left out of the default doxygen.css if
# one or more extra stylesheets have been specified. So if scrollbar
# customization is desired it has to be added explicitly. For an example see the
# documentation.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_STYLESHEET = @MITK_DOXYGEN_STYLESHEET@
# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the HTML output directory. Note
# that these files will be copied to the base HTML output directory. Use the
# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
# files. In the HTML_STYLESHEET file, use the file name only. Also note that the
# files will be copied as-is; there are no commands or markers available.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_EXTRA_FILES = "@MITK_SOURCE_DIR@/Documentation/Doxygen/mitkLogo.jpg"
# The HTML_COLORSTYLE tag can be used to specify if the generated HTML output
# should be rendered with a dark or light theme.
# Possible values are: LIGHT always generate light mode output, DARK always
# generate dark mode output, AUTO_LIGHT automatically set the mode according to
# the user preference, use light mode if no preference is set (the default),
# AUTO_DARK automatically set the mode according to the user preference, use
# dark mode if no preference is set and TOGGLE allow to user to switch between
# light and dark mode via a button.
# The default value is: AUTO_LIGHT.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE = AUTO_LIGHT
# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
# will adjust the colors in the style sheet and background images according to
# this color. Hue is specified as an angle on a color-wheel, see
# https://en.wikipedia.org/wiki/Hue for more information. For instance the value
# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300
# purple, and 360 is red again.
# Minimum value: 0, maximum value: 359, default value: 220.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_HUE = 220
# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors
# in the HTML output. For a value of 0 the output will use gray-scales only. A
# value of 255 will produce the most vivid colors.
# Minimum value: 0, maximum value: 255, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_SAT = 100
# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the
# luminance component of the colors in the HTML output. Values below 100
# gradually make the output lighter, whereas values above 100 make the output
# darker. The value divided by 100 is the actual gamma applied, so 80 represents
# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not
# change the gamma.
# Minimum value: 40, maximum value: 240, default value: 80.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_COLORSTYLE_GAMMA = 80
# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
# page will contain the date and time when the page was generated. Setting this
# to YES can help to show when doxygen was last run and thus if the
# documentation is up to date.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_TIMESTAMP = YES
# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML
# documentation will contain a main index with vertical navigation menus that
# are dynamically created via JavaScript. If disabled, the navigation index will
# consists of multiple levels of tabs that are statically embedded in every HTML
# page. Disable this option to support browsers that do not have JavaScript,
# like the Qt help browser.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_MENUS = YES
# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
# documentation will contain sections that can be hidden and shown after the
# page has loaded.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_DYNAMIC_SECTIONS = @MITK_DOXYGEN_HTML_DYNAMIC_SECTIONS@
# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries
# shown in the various tree structured indices initially; the user can expand
# and collapse entries dynamically later on. Doxygen will expand the tree to
# such a level that at most the specified number of entries are visible (unless
# a fully collapsed tree already exceeds this amount). So setting the number of
# entries 1 will produce a full collapsed tree by default. 0 is a special value
# representing an infinite number of entries and will result in a full expanded
# tree by default.
# Minimum value: 0, maximum value: 9999, default value: 100.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_INDEX_NUM_ENTRIES = 100
# If the GENERATE_DOCSET tag is set to YES, additional index files will be
# generated that can be used as input for Apple's Xcode 3 integrated development
# environment (see:
# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To
# create a documentation set, doxygen will generate a Makefile in the HTML
# output directory. Running make will produce the docset in that directory and
# running make install will install the docset in
# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at
# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy
# genXcode/_index.html for more information.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_DOCSET = NO
# This tag determines the name of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# The default value is: Doxygen generated docs.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDNAME = "Doxygen generated docs"
# This tag determines the URL of the docset feed. A documentation feed provides
# an umbrella under which multiple documentation sets from a single provider
# (such as a company or product suite) can be grouped.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_FEEDURL =
# This tag specifies a string that should uniquely identify the documentation
# set bundle. This should be a reverse domain-name style string, e.g.
# com.mycompany.MyDocSet. Doxygen will append .docset to the name.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_BUNDLE_ID = org.doxygen.Project
# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify
# the documentation publisher. This should be a reverse domain-name style
# string, e.g. com.mycompany.MyDocSet.documentation.
# The default value is: org.doxygen.Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_ID = org.doxygen.Publisher
# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher.
# The default value is: Publisher.
# This tag requires that the tag GENERATE_DOCSET is set to YES.
DOCSET_PUBLISHER_NAME = Publisher
# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three
# additional HTML index files: index.hhp, index.hhc, and index.hhk. The
# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop
# on Windows. In the beginning of 2021 Microsoft took the original page, with
# a.o. the download links, offline the HTML help workshop was already many years
# in maintenance mode). You can download the HTML help workshop from the web
# archives at Installation executable (see:
# http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo
# ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe).
#
# The HTML Help Workshop contains a compiler that can convert all HTML output
# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML
# files are now used as the Windows 98 help format, and will replace the old
# Windows help format (.hlp) on all Windows platforms in the future. Compressed
# HTML files also contain an index, a table of contents, and you can search for
# words in the documentation. The HTML workshop also contains a viewer for
# compressed HTML files.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_HTMLHELP = NO
# The CHM_FILE tag can be used to specify the file name of the resulting .chm
# file. You can add a path in front of the file if the result should not be
# written to the html output directory.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_FILE =
# The HHC_LOCATION tag can be used to specify the location (absolute path
# including file name) of the HTML help compiler (hhc.exe). If non-empty,
# doxygen will try to run the HTML help compiler on the generated index.hhp.
# The file has to be specified with full path.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
HHC_LOCATION =
# The GENERATE_CHI flag controls if a separate .chi index file is generated
# (YES) or that it should be included in the main .chm file (NO).
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
GENERATE_CHI = NO
# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc)
# and project file content.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
CHM_INDEX_ENCODING =
# The BINARY_TOC flag controls whether a binary table of contents is generated
# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it
# enables the Previous and Next buttons.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
BINARY_TOC = NO
# The TOC_EXPAND flag can be set to YES to add extra items for group members to
# the table of contents of the HTML help documentation and to the tree view.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTMLHELP is set to YES.
TOC_EXPAND = NO
# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that
# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help
# (.qch) of the generated HTML documentation.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_QHP = @MITK_DOXYGEN_GENERATE_QHP@
# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify
# the file name of the resulting .qch file. The path specified is relative to
# the HTML output folder.
# This tag requires that the tag GENERATE_QHP is set to YES.
QCH_FILE = @MITK_DOXYGEN_QCH_FILE@
# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help
# Project output. For more information please see Qt Help Project / Namespace
# (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace).
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_NAMESPACE = org.mitk
# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt
# Help Project output. For more information please see Qt Help Project / Virtual
# Folders (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders).
# The default value is: doc.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_VIRTUAL_FOLDER = MITK
# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom
# filter to add. For more information please see Qt Help Project / Custom
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_NAME =
# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the
# custom filter to add. For more information please see Qt Help Project / Custom
# Filters (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_CUST_FILTER_ATTRS =
# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
# project's filter section matches. Qt Help Project / Filter Attributes (see:
# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes).
# This tag requires that the tag GENERATE_QHP is set to YES.
QHP_SECT_FILTER_ATTRS =
# The QHG_LOCATION tag can be used to specify the location (absolute path
# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to
# run qhelpgenerator on the generated .qhp file.
# This tag requires that the tag GENERATE_QHP is set to YES.
QHG_LOCATION = @QT_HELPGENERATOR_EXECUTABLE@
# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be
# generated, together with the HTML files, they form an Eclipse help plugin. To
# install this plugin and make it available under the help contents menu in
# Eclipse, the contents of the directory containing the HTML and XML files needs
# to be copied into the plugins directory of eclipse. The name of the directory
# within the plugins directory should be the same as the ECLIPSE_DOC_ID value.
# After copying Eclipse needs to be restarted before the help appears.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_ECLIPSEHELP = NO
# A unique identifier for the Eclipse help plugin. When installing the plugin
# the directory name containing the HTML and XML files should also have this
# name. Each documentation set should have its own identifier.
# The default value is: org.doxygen.Project.
# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES.
ECLIPSE_DOC_ID = org.doxygen.Project
# If you want full control over the layout of the generated HTML pages it might
# be necessary to disable the index and replace it with your own. The
# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top
# of each HTML page. A value of NO enables the index and the value YES disables
# it. Since the tabs in the index contain the same information as the navigation
# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
DISABLE_INDEX = NO
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
# value is set to YES, a side panel will be generated containing a tree-like
# index structure (just like the one that is generated for HTML Help). For this
# to work a browser that supports JavaScript, DHTML, CSS and frames is required
# (i.e. any modern browser). Windows users are probably better off using the
# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can
# further fine tune the look of the index (see "Fine-tuning the output"). As an
# example, the default style sheet generated by doxygen has an example that
# shows how to put an image at the root of the tree instead of the PROJECT_NAME.
# Since the tree basically has the same information as the tab index, you could
# consider setting DISABLE_INDEX to YES when enabling this option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
GENERATE_TREEVIEW = YES
# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the
# FULL_SIDEBAR option determines if the side bar is limited to only the treeview
# area (value NO) or if it should extend to the full height of the window (value
# YES). Setting this to YES gives a layout similar to
# https://docs.readthedocs.io with more room for contents, but less room for the
# project logo, title, and description. If either GENERATE_TREEVIEW or
# DISABLE_INDEX is set to NO, this option has no effect.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
FULL_SIDEBAR = NO
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
#
# Note that a value of 0 will completely suppress the enum values from appearing
# in the overview section.
# Minimum value: 0, maximum value: 20, default value: 4.
# This tag requires that the tag GENERATE_HTML is set to YES.
ENUM_VALUES_PER_LINE = 4
# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used
# to set the initial width (in pixels) of the frame in which the tree is shown.
# Minimum value: 0, maximum value: 1500, default value: 250.
# This tag requires that the tag GENERATE_HTML is set to YES.
TREEVIEW_WIDTH = 300
# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to
# external symbols imported via tag files in a separate window.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
EXT_LINKS_IN_WINDOW = NO
# If the OBFUSCATE_EMAILS tag is set to YES, doxygen will obfuscate email
# addresses.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
OBFUSCATE_EMAILS = YES
# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg
# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see
# https://inkscape.org) to generate formulas as SVG images instead of PNGs for
# the HTML output. These images will generally look nicer at scaled resolutions.
# Possible values are: png (the default) and svg (looks nicer but requires the
# pdf2svg or inkscape tool).
# The default value is: png.
# This tag requires that the tag GENERATE_HTML is set to YES.
HTML_FORMULA_FORMAT = png
# Use this tag to change the font size of LaTeX formulas included as images in
# the HTML documentation. When you change the font size after a successful
# doxygen run you need to manually remove any form_*.png images from the HTML
# output directory to force them to be regenerated.
# Minimum value: 8, maximum value: 50, default value: 10.
# This tag requires that the tag GENERATE_HTML is set to YES.
FORMULA_FONTSIZE = 10
# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands
# to create new LaTeX commands to be used in formulas as building blocks. See
# the section "Including formulas" for details.
FORMULA_MACROFILE =
# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see
# https://www.mathjax.org) which uses client side JavaScript for the rendering
# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX
# installed or if you want to formulas look prettier in the HTML output. When
# enabled you may also need to install MathJax separately and configure the path
# to it using the MATHJAX_RELPATH option.
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
USE_MATHJAX = YES
# With MATHJAX_VERSION it is possible to specify the MathJax version to be used.
# Note that the different versions of MathJax have different requirements with
# regards to the different settings, so it is possible that also other MathJax
# settings have to be changed when switching between the different MathJax
# versions.
# Possible values are: MathJax_2 and MathJax_3.
# The default value is: MathJax_2.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_VERSION = MathJax_2
# When MathJax is enabled you can set the default output format to be used for
# the MathJax output. For more details about the output format see MathJax
# version 2 (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3
# (see:
# http://docs.mathjax.org/en/latest/web/components/output.html).
# Possible values are: HTML-CSS (which is slower, but has the best
# compatibility. This is the name for Mathjax version 2, for MathJax version 3
# this will be translated into chtml), NativeMML (i.e. MathML. Only supported
# for NathJax 2. For MathJax version 3 chtml will be used instead.), chtml (This
# is the name for Mathjax version 3, for MathJax version 2 this will be
# translated into HTML-CSS) and SVG.
# The default value is: HTML-CSS.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_FORMAT = HTML-CSS
# When MathJax is enabled you need to specify the location relative to the HTML
# output directory using the MATHJAX_RELPATH option. The destination directory
# should contain the MathJax.js script. For instance, if the mathjax directory
# is located at the same level as the HTML output directory, then
# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax
# Content Delivery Network so you can quickly see the result without installing
# MathJax. However, it is strongly recommended to install a local copy of
# MathJax from https://www.mathjax.org before deployment. The default value is:
# - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2
# - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_RELPATH = http://www.mathjax.org/mathjax
# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
# extension names that should be enabled during MathJax rendering. For example
# for MathJax version 2 (see
# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions):
# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols
# For example for MathJax version 3 (see
# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html):
# MATHJAX_EXTENSIONS = ams
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_EXTENSIONS =
# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces
# of code that will be used on startup of the MathJax code. See the MathJax site
# (see:
# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an
# example see the documentation.
# This tag requires that the tag USE_MATHJAX is set to YES.
MATHJAX_CODEFILE =
# When the SEARCHENGINE tag is enabled doxygen will generate a search box for
# the HTML output. The underlying search engine uses javascript and DHTML and
# should work on any modern browser. Note that when using HTML help
# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET)
# there is already a search function so this one should typically be disabled.
# For large projects the javascript based search engine can be slow, then
# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to
# search using the keyboard; to jump to the search box use <access key> + S
# (what the <access key> is depends on the OS and browser, but it is typically
# <CTRL>, <ALT>/<option>, or both). Inside the search box use the <cursor down
# key> to jump into the search results window, the results can be navigated
# using the <cursor keys>. Press <Enter> to select an item or <escape> to cancel
# the search. The filter options can be selected when the cursor is inside the
# search box by pressing <Shift>+<cursor down>. Also here use the <cursor keys>
# to select a filter and <Enter> or <escape> to activate or cancel the filter
# option.
# The default value is: YES.
# This tag requires that the tag GENERATE_HTML is set to YES.
SEARCHENGINE = YES
# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
# implemented using a web server instead of a web client using JavaScript. There
# are two flavors of web server based searching depending on the EXTERNAL_SEARCH
# setting. When disabled, doxygen will generate a PHP script for searching and
# an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing
# and searching needs to be provided by external tools. See the section
# "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
SERVER_BASED_SEARCH = NO
# When EXTERNAL_SEARCH tag is enabled doxygen will no longer generate the PHP
# script for searching. Instead the search results are written to an XML file
# which needs to be processed by an external indexer. Doxygen will invoke an
# external search engine pointed to by the SEARCHENGINE_URL option to obtain the
# search results.
#
# Doxygen ships with an example indexer (doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see:
# https://xapian.org/).
#
# See the section "External Indexing and Searching" for details.
# The default value is: NO.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH = NO
# The SEARCHENGINE_URL should point to a search engine hosted by a web server
# which will return the search results when EXTERNAL_SEARCH is enabled.
#
# Doxygen ships with an example indexer (doxyindexer) and search engine
# (doxysearch.cgi) which are based on the open source search engine library
# Xapian (see:
# https://xapian.org/). See the section "External Indexing and Searching" for
# details.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHENGINE_URL =
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the unindexed
# search data is written to a file for indexing by an external tool. With the
# SEARCHDATA_FILE tag the name of this file can be specified.
# The default file is: searchdata.xml.
# This tag requires that the tag SEARCHENGINE is set to YES.
SEARCHDATA_FILE = searchdata.xml
# When SERVER_BASED_SEARCH and EXTERNAL_SEARCH are both enabled the
# EXTERNAL_SEARCH_ID tag can be used as an identifier for the project. This is
# useful in combination with EXTRA_SEARCH_MAPPINGS to search through multiple
# projects and redirect the results back to the right project.
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTERNAL_SEARCH_ID =
# The EXTRA_SEARCH_MAPPINGS tag can be used to enable searching through doxygen
# projects other than the one defined by this configuration file, but that are
# all added to the same external search index. Each project needs to have a
# unique id set via EXTERNAL_SEARCH_ID. The search mapping then maps the id of
# to a relative location where the documentation can be found. The format is:
# EXTRA_SEARCH_MAPPINGS = tagname1=loc1 tagname2=loc2 ...
# This tag requires that the tag SEARCHENGINE is set to YES.
EXTRA_SEARCH_MAPPINGS =
#---------------------------------------------------------------------------
# Configuration options related to the LaTeX output
#---------------------------------------------------------------------------
# If the GENERATE_LATEX tag is set to YES, doxygen will generate LaTeX output.
# The default value is: YES.
GENERATE_LATEX = NO
# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: latex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_OUTPUT = latex
# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
# invoked.
#
# Note that when not enabling USE_PDFLATEX the default is latex when enabling
# USE_PDFLATEX the default is pdflatex and when in the later case latex is
# chosen this is overwritten by pdflatex. For specific output languages the
# default can have been set differently, this depends on the implementation of
# the output language.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_CMD_NAME = latex
# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate
# index for LaTeX.
# Note: This tag is used in the Makefile / make.bat.
# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file
# (.tex).
# The default file is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
MAKEINDEX_CMD_NAME = makeindex
# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to
# generate index for LaTeX. In case there is no backslash (\) as first character
# it will be automatically added in the LaTeX code.
# Note: This tag is used in the generated output file (.tex).
# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat.
# The default value is: makeindex.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_MAKEINDEX_CMD = makeindex
# If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
COMPACT_LATEX = NO
# The PAPER_TYPE tag can be used to set the paper type that is used by the
# printer.
# Possible values are: a4 (210 x 297 mm), letter (8.5 x 11 inches), legal (8.5 x
# 14 inches) and executive (7.25 x 10.5 inches).
# The default value is: a4.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PAPER_TYPE = a4
# The EXTRA_PACKAGES tag can be used to specify one or more LaTeX package names
# that should be included in the LaTeX output. The package can be specified just
# by its name or with the correct syntax as to be used with the LaTeX
# \usepackage command. To get the times font for instance you can specify :
# EXTRA_PACKAGES=times or EXTRA_PACKAGES={times}
# To use the option intlimits with the amsmath package you can specify:
# EXTRA_PACKAGES=[intlimits]{amsmath}
# If left blank no extra packages will be included.
# This tag requires that the tag GENERATE_LATEX is set to YES.
EXTRA_PACKAGES = amssymb
# The LATEX_HEADER tag can be used to specify a user-defined LaTeX header for
# the generated LaTeX document. The header should contain everything until the
# first chapter. If it is left blank doxygen will generate a standard header. It
# is highly recommended to start with a default header using
# doxygen -w latex new_header.tex new_footer.tex new_stylesheet.sty
# and then modify the file new_header.tex. See also section "Doxygen usage" for
# information on how to generate the default header that doxygen normally uses.
#
# Note: Only use a user-defined header if you know what you are doing!
# Note: The header is subject to change so you typically have to regenerate the
# default header when upgrading to a newer version of doxygen. The following
# commands have a special meaning inside the header (and footer): For a
# description of the possible markers and block names see the documentation.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HEADER =
# The LATEX_FOOTER tag can be used to specify a user-defined LaTeX footer for
# the generated LaTeX document. The footer should contain everything after the
# last chapter. If it is left blank doxygen will generate a standard footer. See
# LATEX_HEADER for more information on how to generate a default footer and what
# special commands can be used inside the footer. See also section "Doxygen
# usage" for information on how to generate the default footer that doxygen
# normally uses. Note: Only use a user-defined footer if you know what you are
# doing!
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_FOOTER =
# The LATEX_EXTRA_STYLESHEET tag can be used to specify additional user-defined
# LaTeX style sheets that are included after the standard style sheets created
# by doxygen. Using this option one can overrule certain style aspects. Doxygen
# will copy the style sheet files to the output directory.
# Note: The order of the extra style sheet files is of importance (e.g. the last
# style sheet in the list overrules the setting of the previous ones in the
# list).
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_STYLESHEET =
# The LATEX_EXTRA_FILES tag can be used to specify one or more extra images or
# other source files which should be copied to the LATEX_OUTPUT output
# directory. Note that the files will be copied as-is; there are no commands or
# markers available.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EXTRA_FILES =
# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated is
# prepared for conversion to PDF (using ps2pdf or pdflatex). The PDF file will
# contain links (just like the HTML output) instead of page references. This
# makes the output suitable for online browsing using a PDF viewer.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
PDF_HYPERLINKS = NO
# If the USE_PDFLATEX tag is set to YES, doxygen will use the engine as
# specified with LATEX_CMD_NAME to generate the PDF file directly from the LaTeX
# files. Set this option to YES, to get a higher quality PDF documentation.
#
# See also section LATEX_CMD_NAME for selecting the engine.
# The default value is: YES.
# This tag requires that the tag GENERATE_LATEX is set to YES.
USE_PDFLATEX = NO
# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \batchmode
# command to the generated LaTeX files. This will instruct LaTeX to keep running
# if errors occur, instead of asking the user for help.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BATCHMODE = NO
# If the LATEX_HIDE_INDICES tag is set to YES then doxygen will not include the
# index chapters (such as File Index, Compound Index, etc.) in the output.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_HIDE_INDICES = NO
# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
# bibliography, e.g. plainnat, or ieeetr. See
# https://en.wikipedia.org/wiki/BibTeX and \cite for more info.
# The default value is: plain.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_BIB_STYLE = plain
# If the LATEX_TIMESTAMP tag is set to YES then the footer of each generated
# page will contain the date and time when the page was generated. Setting this
# to NO can help when comparing the output of multiple runs.
# The default value is: NO.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_TIMESTAMP = NO
# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute)
# path from which the emoji images will be read. If a relative path is entered,
# it will be relative to the LATEX_OUTPUT directory. If left blank the
# LATEX_OUTPUT directory will be used.
# This tag requires that the tag GENERATE_LATEX is set to YES.
LATEX_EMOJI_DIRECTORY =
#---------------------------------------------------------------------------
# Configuration options related to the RTF output
#---------------------------------------------------------------------------
# If the GENERATE_RTF tag is set to YES, doxygen will generate RTF output. The
# RTF output is optimized for Word 97 and may not look too pretty with other RTF
# readers/editors.
# The default value is: NO.
GENERATE_RTF = NO
# The RTF_OUTPUT tag is used to specify where the RTF docs will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: rtf.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_OUTPUT = rtf
# If the COMPACT_RTF tag is set to YES, doxygen generates more compact RTF
# documents. This may be useful for small projects and may help to save some
# trees in general.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
COMPACT_RTF = NO
# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated will
# contain hyperlink fields. The RTF file will contain links (just like the HTML
# output) instead of page references. This makes the output suitable for online
# browsing using Word or some other Word compatible readers that support those
# fields.
#
# Note: WordPad (write) and others do not support links.
# The default value is: NO.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_HYPERLINKS = NO
# Load stylesheet definitions from file. Syntax is similar to doxygen's
# configuration file, i.e. a series of assignments. You only have to provide
# replacements, missing definitions are set to their default value.
#
# See also section "Doxygen usage" for information on how to generate the
# default style sheet that doxygen normally uses.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_STYLESHEET_FILE =
# Set optional variables used in the generation of an RTF document. Syntax is
# similar to doxygen's configuration file. A template extensions file can be
# generated using doxygen -e rtf extensionFile.
# This tag requires that the tag GENERATE_RTF is set to YES.
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# Configuration options related to the man page output
#---------------------------------------------------------------------------
# If the GENERATE_MAN tag is set to YES, doxygen will generate man pages for
# classes and files.
# The default value is: NO.
GENERATE_MAN = NO
# The MAN_OUTPUT tag is used to specify where the man pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it. A directory man3 will be created inside the directory specified by
# MAN_OUTPUT.
# The default directory is: man.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_OUTPUT = man
# The MAN_EXTENSION tag determines the extension that is added to the generated
# man pages. In case the manual section does not start with a number, the number
# 3 is prepended. The dot (.) at the beginning of the MAN_EXTENSION tag is
# optional.
# The default value is: .3.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_EXTENSION = .3
# The MAN_SUBDIR tag determines the name of the directory created within
# MAN_OUTPUT in which the man pages are placed. If defaults to man followed by
# MAN_EXTENSION with the initial . removed.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_SUBDIR =
# If the MAN_LINKS tag is set to YES and doxygen generates man output, then it
# will generate one additional man file for each entity documented in the real
# man page(s). These additional files only source the real man page, but without
# them the man command would be unable to find the correct page.
# The default value is: NO.
# This tag requires that the tag GENERATE_MAN is set to YES.
MAN_LINKS = NO
#---------------------------------------------------------------------------
# Configuration options related to the XML output
#---------------------------------------------------------------------------
# If the GENERATE_XML tag is set to YES, doxygen will generate an XML file that
# captures the structure of the code including all documentation.
# The default value is: NO.
GENERATE_XML = NO
# The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
# it.
# The default directory is: xml.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_OUTPUT = xml
# If the XML_PROGRAMLISTING tag is set to YES, doxygen will dump the program
# listings (including syntax highlighting and cross-referencing information) to
# the XML output. Note that enabling this will significantly increase the size
# of the XML output.
# The default value is: YES.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_PROGRAMLISTING = YES
# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include
# namespace members in file scope as well, matching the HTML output.
# The default value is: NO.
# This tag requires that the tag GENERATE_XML is set to YES.
XML_NS_MEMB_FILE_SCOPE = NO
#---------------------------------------------------------------------------
# Configuration options related to the DOCBOOK output
#---------------------------------------------------------------------------
# If the GENERATE_DOCBOOK tag is set to YES, doxygen will generate Docbook files
# that can be used to generate PDF.
# The default value is: NO.
GENERATE_DOCBOOK = NO
# The DOCBOOK_OUTPUT tag is used to specify where the Docbook pages will be put.
# If a relative path is entered the value of OUTPUT_DIRECTORY will be put in
# front of it.
# The default directory is: docbook.
# This tag requires that the tag GENERATE_DOCBOOK is set to YES.
DOCBOOK_OUTPUT = docbook
#---------------------------------------------------------------------------
# Configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
# If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an
# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures
# the structure of the code including all documentation. Note that this feature
# is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# Configuration options related to the Perl module output
#---------------------------------------------------------------------------
# If the GENERATE_PERLMOD tag is set to YES, doxygen will generate a Perl module
# file that captures the structure of the code including all documentation.
#
# Note that this feature is still experimental and incomplete at the moment.
# The default value is: NO.
GENERATE_PERLMOD = NO
# If the PERLMOD_LATEX tag is set to YES, doxygen will generate the necessary
# Makefile rules, Perl scripts and LaTeX code to be able to generate PDF and DVI
# output from the Perl module output.
# The default value is: NO.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_LATEX = NO
# If the PERLMOD_PRETTY tag is set to YES, the Perl module output will be nicely
# formatted so it can be parsed by a human reader. This is useful if you want to
# understand what is going on. On the other hand, if this tag is set to NO, the
# size of the Perl module output will be much smaller and Perl will parse it
# just the same.
# The default value is: YES.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_PRETTY = YES
# The names of the make variables in the generated doxyrules.make file are
# prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX. This is useful
# so different doxyrules.make files included by the same Makefile don't
# overwrite each other's variables.
# This tag requires that the tag GENERATE_PERLMOD is set to YES.
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
# If the ENABLE_PREPROCESSING tag is set to YES, doxygen will evaluate all
# C-preprocessor directives found in the sources and include files.
# The default value is: YES.
ENABLE_PREPROCESSING = YES
# If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
# in the source code. If set to NO, only conditional compilation will be
# performed. Macro expansion can be done in a controlled way by setting
# EXPAND_ONLY_PREDEF to YES.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
MACRO_EXPANSION = YES
# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
# the macro expansion is limited to the macros specified with the PREDEFINED and
# EXPAND_AS_DEFINED tags.
# The default value is: NO.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_ONLY_PREDEF = NO
# If the SEARCH_INCLUDES tag is set to YES, the include files in the
# INCLUDE_PATH will be searched if a #include is found.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SEARCH_INCLUDES = YES
# The INCLUDE_PATH tag can be used to specify one or more directories that
# contain include files that are not input files but should be processed by the
# preprocessor. Note that the INCLUDE_PATH is not recursive, so the setting of
# RECURSIVE has no effect here.
# This tag requires that the tag SEARCH_INCLUDES is set to YES.
INCLUDE_PATH =
# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
# patterns (like *.h and *.hpp) to filter out the header-files in the
# directories. If left blank, the patterns specified with FILE_PATTERNS will be
# used.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
INCLUDE_FILE_PATTERNS =
# The PREDEFINED tag can be used to specify one or more macro names that are
# defined before the preprocessor is started (similar to the -D option of e.g.
# gcc). The argument of the tag is a list of macros of the form: name or
# name=definition (no spaces). If the definition and the "=" are omitted, "=1"
# is assumed. To prevent a macro definition from being undefined via #undef or
# recursively expanded use the := operator instead of the = operator.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
PREDEFINED = itkNotUsed(x)= \
"itkSetMacro(name,type)=virtual void Set##name (type _arg);" \
"itkGetMacro(name,type)=virtual type Get##name ();" \
"itkGetConstMacro(name,type)=virtual type Get##name () const;" \
"itkSetStringMacro(name)=virtual void Set##name (const char* _arg);" \
"itkGetStringMacro(name)=virtual const char* Get##name () const;" \
"itkSetClampMacro(name,type,min,max)=virtual void Set##name (type _arg);" \
"itkSetObjectMacro(name,type)=virtual void Set##name (type* _arg);" \
"itkGetObjectMacro(name,type)=virtual type* Get##name ();" \
"itkSetConstObjectMacro(name,type)=virtual void Set##name ( const type* _arg);" \
"itkGetConstObjectMacro(name,type)=virtual const type* Get##name ();" \
"itkGetConstReferenceMacro(name,type)=virtual const type& Get##name ();" \
"itkGetConstReferenceObjectMacro(name,type)=virtual const type::Pointer& Get##name () const;" \
"itkBooleanMacro(name)=virtual void name##On (); virtual void name##Off ();" \
"itkSetVector2Macro(name,type)=virtual void Set##name (type _arg1, type _arg2) virtual void Set##name (type _arg[2]);" \
"itkGetVector2Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2) const; virtual void Get##name (type _arg[2]) const;" \
"itkSetVector3Macro(name,type)=virtual void Set##name (type _arg1, type _arg2, type _arg3) virtual void Set##name (type _arg[3]);" \
"itkGetVector3Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3) const; virtual void Get##name (type _arg[3]) const;" \
"itkSetVector4Macro(name,type)=virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4) virtual void Set##name (type _arg[4]);" \
"itkGetVector4Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4) const; virtual void Get##name (type _arg[4]) const;" \
"itkSetVector6Macro(name,type)=virtual void Set##name (type _arg1, type _arg2, type _arg3, type _arg4, type _arg5, type _arg6) virtual void Set##name (type _arg[6]);" \
"itkGetVector6Macro(name,type)=virtual type* Get##name () const; virtual void Get##name (type& _arg1, type& _arg2, type& _arg3, type& _arg4, type& _arg5, type& _arg6) const; virtual void Get##name (type _arg[6]) const;" \
"itkSetVectorMacro(name,type,count)=virtual void Set##name(type data[]);" \
"itkGetVectorMacro(name,type,count)=virtual type* Get##name () const;" \
"itkNewMacro(type)=static Pointer New();" \
"itkFactorylessNewMacro(type)=static Pointer New();" \
"itkCloneMacro(type)=Pointer Clone() const;" \
"itkTypeMacro(thisClass,superclass)=virtual const char *GetClassName() const;" \
"itkConceptMacro(name,concept)=enum { name = 0 };" \
"ITK_NUMERIC_LIMITS=std::numeric_limits" \
"ITK_TYPENAME=typename" \
"FEM_ABSTRACT_CLASS(thisClass,parentClass)=public: /** Standard Self typedef.*/ typedef thisClass Self; /** Standard Superclass typedef. */ typedef parentClass Superclass; /** Pointer or SmartPointer to an object. */ typedef Self* Pointer; /** Const pointer or SmartPointer to an object. */ typedef const Self* ConstPointer; private:" \
"FEM_CLASS(thisClass,parentClass)=FEM_ABSTRACT_CLASS(thisClass,parentClass) public: /** Create a new object from the existing one */ virtual Baseclass::Pointer Clone() const; /** Class ID for FEM object factory */ static const int CLID; /** Virtual function to access the class ID */ virtual int ClassID() const { return CLID; /** Object creation in an itk compatible way */ static Self::Pointer New() { return new Self(); } private:" \
FREEVERSION \
ERROR_CHECKING \
HAS_TIFF \
HAS_JPEG \
HAS_NETLIB \
HAS_PNG \
HAS_ZLIB \
HAS_GLUT \
HAS_QT \
VCL_USE_NATIVE_STL=1 \
VCL_USE_NATIVE_COMPLEX=1 \
VCL_HAS_BOOL=1 \
VXL_BIG_ENDIAN=1 \
VXL_LITTLE_ENDIAN=0 \
VNL_DLL_DATA= \
"US_PREPEND_NAMESPACE(x)=us::x" \
"US_BEGIN_NAMESPACE= namespace us {" \
"US_END_NAMESPACE=}" \
"US_BASECLASS_NAME=itk::LightObject" \
US_EXPORT= \
"DEPRECATED(func)=func" \
"mitkSegmentationTaskValueMacro(type, name)=bool Has##name() const; type Get##name() const; void Set##name(const type& value);" \
"mitkSegmentationTaskListValueMacro(type, name)=bool Has##name(size_t index) const; type Get##name(size_t index) const; void SetDefault##name(const type& value);" \
@US_PLATFORM@
# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
# tag can be used to specify a list of macro names that should be expanded. The
# macro definition that is found in the sources will be used. Use the PREDEFINED
# tag if you want to use a different macro definition that overrules the
# definition found in the source code.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
EXPAND_AS_DEFINED =
# If the SKIP_FUNCTION_MACROS tag is set to YES then doxygen's preprocessor will
# remove all references to function-like macros that are alone on a line, have
# an all uppercase name, and do not end with a semicolon. Such function macros
# are typically used for boiler-plate code, and will confuse the parser if not
# removed.
# The default value is: YES.
# This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration options related to external references
#---------------------------------------------------------------------------
# The TAGFILES tag can be used to specify one or more tag files. For each tag
# file the location of the external documentation should be added. The format of
# a tag file without this location is as follows:
# TAGFILES = file1 file2 ...
# Adding location for the tag files is done as follows:
# TAGFILES = file1=loc1 "file2 = loc2" ...
# where loc1 and loc2 can be relative or absolute paths or URLs. See the
# section "Linking to external documentation" for more information about the use
# of tag files.
# Note: Each tag file must have a unique name (where the name does NOT include
# the path). If a tag file is not located in the directory in which doxygen is
# run, you must also specify the path to the tagfile here.
TAGFILES =
# When a file name is specified after GENERATE_TAGFILE, doxygen will create a
# tag file that is based on the input files it reads. See section "Linking to
# external documentation" for more information about the usage of tag files.
GENERATE_TAGFILE = @MITK_DOXYGEN_TAGFILE_NAME@
# If the ALLEXTERNALS tag is set to YES, all external class will be listed in
# the class index. If set to NO, only the inherited external classes will be
# listed.
# The default value is: NO.
ALLEXTERNALS = NO
# If the EXTERNAL_GROUPS tag is set to YES, all external groups will be listed
# in the modules index. If set to NO, only the current project's groups will be
# listed.
# The default value is: YES.
EXTERNAL_GROUPS = NO
# If the EXTERNAL_PAGES tag is set to YES, all external pages will be listed in
# the related pages index. If set to NO, only the current project's pages will
# be listed.
# The default value is: YES.
EXTERNAL_PAGES = YES
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
# You can include diagrams made with dia in doxygen documentation. Doxygen will
# then run dia to produce the diagram and insert it in the documentation. The
# DIA_PATH tag allows you to specify the directory where the dia binary resides.
# If left empty dia is assumed to be found in the default search path.
DIA_PATH =
# If set to YES the inheritance and collaboration graphs will hide inheritance
# and usage relations if the target is undocumented or is not a class.
# The default value is: YES.
HIDE_UNDOC_RELATIONS = YES
# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
# available from the path. This tool is part of Graphviz (see:
# http://www.graphviz.org/), a graph visualization toolkit from AT&T and Lucent
# Bell Labs. The other options in this section have no effect if this option is
# set to NO
# The default value is: NO.
HAVE_DOT = @HAVE_DOT@
# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
# to run in parallel. When set to 0 doxygen will base this on the number of
# processors available in the system. You can set it explicitly to a value
# larger than 0 to get control over the balance between CPU load and processing
# speed.
# Minimum value: 0, maximum value: 32, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NUM_THREADS = @MITK_DOXYGEN_DOT_NUM_THREADS@
# DOT_COMMON_ATTR is common attributes for nodes, edges and labels of
# subgraphs. When you want a differently looking font in the dot files that
# doxygen generates you can specify fontname, fontcolor and fontsize attributes.
# For details please see <a href=https://graphviz.org/doc/info/attrs.html>Node,
# Edge and Graph Attributes specification</a> You need to make sure dot is able
# to find the font, which can be done by putting it in a standard location or by
# setting the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
# directory containing the font. Default graphviz fontsize is 14.
# The default value is: fontname=Helvetica,fontsize=10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_COMMON_ATTR = "fontname=Helvetica,fontsize=10"
# DOT_EDGE_ATTR is concatenated with DOT_COMMON_ATTR. For elegant style you can
# add 'arrowhead=open, arrowtail=open, arrowsize=0.5'. <a
# href=https://graphviz.org/doc/info/arrows.html>Complete documentation about
# arrows shapes.</a>
# The default value is: labelfontname=Helvetica,labelfontsize=10.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_EDGE_ATTR = "labelfontname=Helvetica,labelfontsize=10"
# DOT_NODE_ATTR is concatenated with DOT_COMMON_ATTR. For view without boxes
# around nodes set 'shape=plain' or 'shape=plaintext' <a
# href=https://www.graphviz.org/doc/info/shapes.html>Shapes specification</a>
# The default value is: shape=box,height=0.2,width=0.4.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_NODE_ATTR = "shape=box,height=0.2,width=0.4"
# You can set the path where dot can find font specified with fontname in
# DOT_COMMON_ATTR and others dot attributes.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_FONTPATH =
# If the CLASS_GRAPH tag is set to YES (or GRAPH) then doxygen will generate a
# graph for each documented class showing the direct and indirect inheritance
# relations. In case HAVE_DOT is set as well dot will be used to draw the graph,
# otherwise the built-in generator will be used. If the CLASS_GRAPH tag is set
# to TEXT the direct and indirect inheritance relations will be shown as texts /
# links.
# Possible values are: NO, YES, TEXT and GRAPH.
# The default value is: YES.
CLASS_GRAPH = YES
# If the COLLABORATION_GRAPH tag is set to YES then doxygen will generate a
# graph for each documented class showing the direct and indirect implementation
# dependencies (inheritance, containment, and class references variables) of the
# class with other documented classes.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
COLLABORATION_GRAPH = YES
# If the GROUP_GRAPHS tag is set to YES then doxygen will generate a graph for
# groups, showing the direct groups dependencies. See also the chapter Grouping
# in the manual.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
GROUP_GRAPHS = YES
# If the UML_LOOK tag is set to YES, doxygen will generate inheritance and
# collaboration diagrams in a style similar to the OMG's Unified Modeling
# Language.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
UML_LOOK = @MITK_DOXYGEN_UML_LOOK@
# If the UML_LOOK tag is enabled, the fields and methods are shown inside the
# class node. If there are many fields or methods and many nodes the graph may
# become too big to be useful. The UML_LIMIT_NUM_FIELDS threshold limits the
# number of items for each type to make the size more manageable. Set this to 0
# for no limit. Note that the threshold may be exceeded by 50% before the limit
# is enforced. So when you set the threshold to 10, up to 15 fields may appear,
# but if the number exceeds 15, the total amount of fields shown is limited to
# 10.
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# This tag requires that the tag UML_LOOK is set to YES.
UML_LIMIT_NUM_FIELDS = 10
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# methods without types and arguments in the UML graphs. If the DOT_UML_DETAILS
# tag is set to YES, doxygen will add type and arguments for attributes and
# methods in the UML graphs. If the DOT_UML_DETAILS tag is set to NONE, doxygen
# will not generate fields with class member information in the UML graphs. The
# class diagrams will look similar to the default class diagrams but using UML
# notation for the relationships.
# Possible values are: NO, YES and NONE.
# The default value is: NO.
# This tag requires that the tag UML_LOOK is set to YES.
DOT_UML_DETAILS = NO
# The DOT_WRAP_THRESHOLD tag can be used to set the maximum number of characters
# to display on a single line. If the actual line length exceeds this threshold
# significantly it will wrapped across multiple lines. Some heuristics are apply
# to avoid ugly line breaks.
# Minimum value: 0, maximum value: 1000, default value: 17.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_WRAP_THRESHOLD = 17
# If the TEMPLATE_RELATIONS tag is set to YES then the inheritance and
# collaboration graphs will show the relations between templates and their
# instances.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
TEMPLATE_RELATIONS = YES
# If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to
# YES then doxygen will generate a graph for each documented file showing the
# direct and indirect include dependencies of the file with other documented
# files.
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# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDE_GRAPH = NO
# If the INCLUDED_BY_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are
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# This tag requires that the tag HAVE_DOT is set to YES.
INCLUDED_BY_GRAPH = NO
# If the CALL_GRAPH tag is set to YES then doxygen will generate a call
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# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable call graphs for selected
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CALL_GRAPH = NO
# If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller
# dependency graph for every global function or class method.
#
# Note that enabling this option will significantly increase the time of a run.
# So in most cases it will be better to enable caller graphs for selected
# functions only using the \callergraph command. Disabling a caller graph can be
# accomplished by means of the command \hidecallergraph.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
CALLER_GRAPH = NO
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# hierarchy of all classes instead of a textual one.
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# If the DIRECTORY_GRAPH tag is set to YES then doxygen will show the
# dependencies a directory has on other directories in a graphical way. The
# dependency relations are determined by the #include relations between the
# files in the directories.
# The default value is: YES.
# This tag requires that the tag HAVE_DOT is set to YES.
DIRECTORY_GRAPH = YES
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# of child directories generated in directory dependency graphs by dot.
# Minimum value: 1, maximum value: 25, default value: 1.
# This tag requires that the tag DIRECTORY_GRAPH is set to YES.
DIR_GRAPH_MAX_DEPTH = 1
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# generated by dot. For an explanation of the image formats see the section
# output formats in the documentation of the dot tool (Graphviz (see:
# http://www.graphviz.org/)).
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# to make the SVG files visible in IE 9+ (other browsers do not have this
# requirement).
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DOT_IMAGE_FORMAT = png
# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
# enable generation of interactive SVG images that allow zooming and panning.
#
# Note that this requires a modern browser other than Internet Explorer. Tested
# and working are Firefox, Chrome, Safari, and Opera.
# Note: For IE 9+ you need to set HTML_FILE_EXTENSION to xhtml in order to make
# the SVG files visible. Older versions of IE do not have SVG support.
# The default value is: NO.
# This tag requires that the tag HAVE_DOT is set to YES.
INTERACTIVE_SVG = NO
# The DOT_PATH tag can be used to specify the path where the dot tool can be
# found. If left blank, it is assumed the dot tool can be found in the path.
# This tag requires that the tag HAVE_DOT is set to YES.
DOT_PATH = @DOXYGEN_DOT_PATH@
# The DOTFILE_DIRS tag can be used to specify one or more directories that
# contain dot files that are included in the documentation (see the \dotfile
# command).
# This tag requires that the tag HAVE_DOT is set to YES.
DOTFILE_DIRS =
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# contain msc files that are included in the documentation (see the \mscfile
# command).
MSCFILE_DIRS =
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# contain dia files that are included in the documentation (see the \diafile
# command).
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# When using plantuml, the PLANTUML_JAR_PATH tag should be used to specify the
# path where java can find the plantuml.jar file or to the filename of jar file
# to be used. If left blank, it is assumed PlantUML is not used or called during
# a preprocessing step. Doxygen will generate a warning when it encounters a
# \startuml command in this case and will not generate output for the diagram.
PLANTUML_JAR_PATH =
# When using plantuml, the PLANTUML_CFG_FILE tag can be used to specify a
# configuration file for plantuml.
PLANTUML_CFG_FILE =
# When using plantuml, the specified paths are searched for files specified by
# the !include statement in a plantuml block.
PLANTUML_INCLUDE_PATH =
# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of nodes
# that will be shown in the graph. If the number of nodes in a graph becomes
# larger than this value, doxygen will truncate the graph, which is visualized
# by representing a node as a red box. Note that doxygen if the number of direct
# children of the root node in a graph is already larger than
# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note that
# the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
# Minimum value: 0, maximum value: 10000, default value: 50.
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# generated by dot. A depth value of 3 means that only nodes reachable from the
# root by following a path via at most 3 edges will be shown. Nodes that lay
# further from the root node will be omitted. Note that setting this option to 1
# or 2 may greatly reduce the computation time needed for large code bases. Also
# note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
# Minimum value: 0, maximum value: 1000, default value: 0.
# This tag requires that the tag HAVE_DOT is set to YES.
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# Set the DOT_MULTI_TARGETS tag to YES to allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10) support
# this, this feature is disabled by default.
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# explaining the meaning of the various boxes and arrows in the dot generated
# graphs.
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# graphical representation for inheritance and collaboration diagrams is used.
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diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake
index b027952284..c2f46614f9 100644
--- a/Modules/ModuleList.cmake
+++ b/Modules/ModuleList.cmake
@@ -1,78 +1,74 @@
# The entries in the mitk_modules list must be
# ordered according to their dependencies.
set(MITK_MODULES
Log
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
US
USUI
DICOMUI
Remeshing
Python
QtPython
Persistence
OpenIGTLinkUI
IGTUI
RT
RTUI
IOExt
XNAT
- TubeGraph
BoundingShape
RenderWindowManagerUI
- SemanticRelations
- SemanticRelationsUI
CEST
BasicImageProcessing
ModelFit
ModelFitUI
Pharmacokinetics
PharmacokineticsUI
DICOMPM
REST
RESTService
DICOMweb
ROI
)
diff --git a/Modules/OpenCL/CMakeLists.txt b/Modules/OpenCL/CMakeLists.txt
deleted file mode 100644
index c782ddf6d0..0000000000
--- a/Modules/OpenCL/CMakeLists.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-if(MITK_USE_OpenCL)
-
- # create the module
- MITK_CREATE_MODULE(
- DEPENDS MitkCore
- PACKAGE_DEPENDS
- PUBLIC OpenCL
- )
-
- add_subdirectory(Testing)
-endif(MITK_USE_OpenCL)
diff --git a/Modules/OpenCL/Documentation/doxygen/MitkOpenCL.dox b/Modules/OpenCL/Documentation/doxygen/MitkOpenCL.dox
deleted file mode 100644
index bbe20e21d7..0000000000
--- a/Modules/OpenCL/Documentation/doxygen/MitkOpenCL.dox
+++ /dev/null
@@ -1,48 +0,0 @@
-
-/**
-
-\page MitkOpenCL_Example Examples
-
-This is a list of available examples:
-- \subpage MitkOpenCL_BinaryThresholdFilter
-
-*/
-
-
-/**
-
-\page MitkOpenCL_Overview OpenCL Module
-
-The MITK OpenCL Module provides a basic class structure to allow usage of OpenCL-accelerated parallel computing.
-
-<h1> Build Instructions </h1>
-
-The MITK OpenCL module needs an OpenCL Device ( most likely a graphics card, but works also on some CPUs ) and the corresponding driver. Furthermore the OpenCL library and the headers are needed. A list of supported hardware is provided by <a href="https://www.khronos.org/conformance/adopters/conformant-products/opencl"> Khronos.org </a>. For the driver and the libraries please look at the support pages of the hardware manufacturer. Quick Links to the most likely of them:
-- <a href="https://developer.nvidia.com/opencl"> NVIDIA OpenCL Page </a>
-- <a href="https://software.intel.com/content/www/us/en/develop/tools/opencl-sdk.html"> Intel OpenCL SDK </a>
-
-To activate the module, you have to activate the CMake option
-
-\verbatim
-MITK_USE_OpenCL
-\endverbatim
-
-The build system tries to find the OpenCL library and the include path automatically. If this attempt failes, you will be prompted to manually specify following variables:
-
-\verbatim
-OPENCL_INCLUDE_DIRS
-OPENCL_LIBRARIES
-\endverbatim
-
-
-
-<h1> Detailed description </h1>
-
-For own implementations, the OpenCL Module allows for building up a filtering pipeline in MITK Style ( see more in \ref PipelineingConceptPage ). The OpenCL filter can be simply connected also to an existing MITK image filtering pipeline since the mitk::OclImageToImageFilter provide a SetInput and GetOutput methods expecting an mitk::Image and returning it respectively.
-
-<h1> Examples </h1>
-
-Here is a list of \subpage MitkOpenCL_Example "examples":
- - \ref MitkOpenCL_BinaryThresholdFilter
-
- */
diff --git a/Modules/OpenCL/Documentation/doxygen/examples/MitkOpenCL_BinaryThresholdFilter.md b/Modules/OpenCL/Documentation/doxygen/examples/MitkOpenCL_BinaryThresholdFilter.md
deleted file mode 100644
index c79cb673e6..0000000000
--- a/Modules/OpenCL/Documentation/doxygen/examples/MitkOpenCL_BinaryThresholdFilter.md
+++ /dev/null
@@ -1,41 +0,0 @@
-Implementing Own OpenCL-based Image Filter {#MitkOpenCL_BinaryThresholdFilter}
-==========================================
-
-This example demonstrates how to implement an image-to-image filter with some computations done on
-an OpenCL device ( most likely a GPU ). This particular example presents a simple threshold filter
-which uses an upper and lower threshold to map the pixel to the specified inside and outside value.
-
-Since the filter we want to implement is an image-to-image filter, we will inherit from the
-mitk::OclImageToImageFilter class.
-
-In the constructor, we set the source file of the filter, in this case is the file located in the default
-directory placed in the module itself. We also se the unique filter id string which serves as an identifier
-for storing and getting the associated program through the OclResourceService.
-
-\snippet mitkOcl-binarythrfilter/main.cpp Create
-
-\snippet mitkOcl-binarythrfilter/main.cpp Initialize
-
-For preparing the execution we call the InitExec method
-provided by the superclass. We also catch exceptions singalising some initialization errors
-
-\snippet mitkOcl-binarythrfilter/main.cpp ExecutePrepare
-
-In this example, the header of the OpenCL-Kernel to be executed is the following
-
-\snippet mitkOcl-binarythrfilter/gpucode.cl GPUHeader
-
-The InitExec methods takes care of initializing the input and output images and their OpenCL counterparts.
-In addition both parameters are passed to the filter and the input data is copied (if necessary).
-If the first initialization part was successfull, we continue by passing in the values for the filter
-specific parameters:
-
-\snippet mitkOcl-binarythrfilter/main.cpp SetKernelArguments
-
-If this passes, we tell the superclass to execute our compiled kernel. The second argument specifies the dimensionality
-of the OpenCL NDRange ( the parallel execution grid ). In this example we use the 3D-Grid:
-
-\snippet mitkOcl-binarythrfilter/main.cpp Execute
-
-Through the last line we signalize that the OpenCL-side data of the output image is modified. This is essential for getting
-the result data when calling GetOutput() afterwards.
diff --git a/Modules/OpenCL/Documentation/doxygen/snippets/mitkOcl-binarythrfilter/gpucode.cl b/Modules/OpenCL/Documentation/doxygen/snippets/mitkOcl-binarythrfilter/gpucode.cl
deleted file mode 100644
index 6c0348be42..0000000000
--- a/Modules/OpenCL/Documentation/doxygen/snippets/mitkOcl-binarythrfilter/gpucode.cl
+++ /dev/null
@@ -1,18 +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.
-
-============================================================================*/
-//! [GPUHeader]
-__kernel void ckBinaryThreshold(
- __read_only image3d_t dSource, // input image
- __global uchar* dDest, // output buffer
- int lowerT, int upperT, int outsideVal, int insideVal // parameters
-)
-//! [GPUHeader]
diff --git a/Modules/OpenCL/Documentation/doxygen/snippets/mitkOcl-binarythrfilter/main.cpp b/Modules/OpenCL/Documentation/doxygen/snippets/mitkOcl-binarythrfilter/main.cpp
deleted file mode 100644
index a7fddfbb16..0000000000
--- a/Modules/OpenCL/Documentation/doxygen/snippets/mitkOcl-binarythrfilter/main.cpp
+++ /dev/null
@@ -1,99 +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 "mitkOclBinaryThresholdImageFilter.h"
-
-mitk::OclBinaryThresholdImageFilter::OclBinaryThresholdImageFilter()
-: m_ckBinaryThreshold( nullptr )
-{
-//! [Create]
- std::string path = "BinaryThresholdFilter.cl";
- this->SetSourceFile( path.c_str() );
- this->m_FilterID = "BinaryThreshold";
-//! [Create]
- this->m_lowerThr = 10;
- this->m_upperThr = 200;
-
- this->m_insideVal = 100;
- this->m_outsideVal = 0;
-}
-
-mitk::OclBinaryThresholdImageFilter::~OclBinaryThresholdImageFilter()
-{
- if ( this->m_ckBinaryThreshold )
- {
- clReleaseKernel( m_ckBinaryThreshold );
- }
-}
-
-void mitk::OclBinaryThresholdImageFilter::Update()
-{
- //Check if context & program available
- if (!this->Initialize())
- {
- // clean-up also the resources
- OpenCLActivator::GetResourceServiceRef()->InvalidateStorage();
- mitkThrow() <<"Filter is not initialized. Cannot update.";
- }
- else{
- // Execute
- this->Execute();
- }
-}
-
-void mitk::OclBinaryThresholdImageFilter::Execute()
-{
- cl_int clErr = 0;
-//! [ExecutePrepare]
- try
- {
- this->InitExec( this->m_ckBinaryThreshold );
- }
- catch( const mitk::Exception& e)
- {
- MITK_ERROR << "Catched exception while initializing filter: " << e.what();
- return;
- }
-//! [ExecutePrepare]
-
- // set kernel arguments
-//! [SetKernelArguments]
- clErr = clSetKernelArg( this->m_ckBinaryThreshold, 2, sizeof(cl_int), &(this->m_lowerThr) );
- clErr |= clSetKernelArg( this->m_ckBinaryThreshold, 3, sizeof(cl_int), &(this->m_upperThr) );
- clErr |= clSetKernelArg( this->m_ckBinaryThreshold, 4, sizeof(cl_int), &(this->m_outsideVal) );
- clErr |= clSetKernelArg( this->m_ckBinaryThreshold, 5, sizeof(cl_int), &(this->m_insideVal) );
- CHECK_OCL_ERR( clErr );
-//! [SetKernelArguments]
-
- // execute the filter on a 3D NDRange
- //! [Execute]
- this->ExecuteKernel( m_ckBinaryThreshold, 3);
-
- // signalize the GPU-side data changed
- m_output->Modified( GPU_DATA );
- //! [Execute]
-
-}
-
-bool mitk::OclBinaryThresholdImageFilter::Initialize()
-{
- bool buildErr = true;
- cl_int clErr = 0;
-//! [Initialize]
- if ( OclFilter::Initialize() )
- {
- this->m_ckBinaryThreshold = clCreateKernel( this->m_clProgram, "ckBinaryThreshold", &clErr);
- buildErr |= CHECK_OCL_ERR( clErr );
- }
-//! [Initialize]
- return (Superclass::IsInitialized() && buildErr );
-}
diff --git a/Modules/OpenCL/Resources/BinaryThresholdFilter.cl b/Modules/OpenCL/Resources/BinaryThresholdFilter.cl
deleted file mode 100644
index 51c3a8978d..0000000000
--- a/Modules/OpenCL/Resources/BinaryThresholdFilter.cl
+++ /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.
-
-============================================================================*/
-
-__kernel void ckBinaryThreshold(
- __read_only image3d_t dSource, // input image
- __global uchar* dDest, // output buffer
- int lowerT, int upperT, int outsideVal, int insideVal // 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);
-
- // get image width and weight
- const unsigned int uiWidth = get_image_width( dSource );
- const unsigned int uiHeight = get_image_height( dSource );
- const unsigned int uiDepth = get_image_depth( dSource );
-
- // create an image sampler
- const sampler_t defaultSampler = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST ;
-
- // terminate non-valid threads
- if ( globalPosX < uiWidth && globalPosY < uiHeight && globalPosZ < uiDepth )
- {
- int result = outsideVal;
-
- // get input value
- int4 pixelValue = read_imagei( dSource, defaultSampler, (int4) (globalPosX, globalPosY, globalPosZ, 0 ));
-
- if( (pixelValue.x >= lowerT) && (pixelValue.x <= upperT ) )
- {
- result = insideVal;
- }
-
- // store the result
- dDest[ globalPosZ * uiWidth * uiHeight + globalPosY * uiWidth + globalPosX ] = result;
- }
-
-}
diff --git a/Modules/OpenCL/Testing/CMakeLists.txt b/Modules/OpenCL/Testing/CMakeLists.txt
deleted file mode 100644
index 153cd81e2e..0000000000
--- a/Modules/OpenCL/Testing/CMakeLists.txt
+++ /dev/null
@@ -1 +0,0 @@
-MITK_CREATE_MODULE_TESTS()
diff --git a/Modules/OpenCL/Testing/files.cmake b/Modules/OpenCL/Testing/files.cmake
deleted file mode 100644
index 10dff632d7..0000000000
--- a/Modules/OpenCL/Testing/files.cmake
+++ /dev/null
@@ -1,6 +0,0 @@
-set(MODULE_TESTS
- mitkOclResourceServiceTest.cpp
- mitkOclImageTest.cpp
- mitkOclBinaryThresholdImageFilterTest.cpp
- mitkOclReferenceCountTest.cpp
-)
diff --git a/Modules/OpenCL/Testing/mitkOclBinaryThresholdImageFilterTest.cpp b/Modules/OpenCL/Testing/mitkOclBinaryThresholdImageFilterTest.cpp
deleted file mode 100644
index 413bcb7810..0000000000
--- a/Modules/OpenCL/Testing/mitkOclBinaryThresholdImageFilterTest.cpp
+++ /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.
-
-============================================================================*/
-
-#include <mitkImage.h>
-#include <mitkTestingMacros.h>
-#include <mitkTestFixture.h>
-
-#include <mitkImageGenerator.h>
-#include <mitkImageCast.h>
-
-#include <mitkOclBinaryThresholdImageFilter.h>
-#include <mitkException.h>
-
-//ITK Filter as reference computation
-#include <itkBinaryThresholdImageFilter.h>
-
-class mitkOclBinaryThresholdImageFilterTestSuite : public mitk::TestFixture
-{
-
- CPPUNIT_TEST_SUITE(mitkOclBinaryThresholdImageFilterTestSuite);
- MITK_TEST(SetInput_2DImage_ThrowsException);
- MITK_TEST(GenerateData_3DImage_CompareToReference);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- /** Members used inside the different (sub-)tests. All members are initialized via setUp().
- */
- mitk::OclBinaryThresholdImageFilter::Pointer m_oclBinaryFilter;
-
- mitk::Image::Pointer m_Random2DImage;
- mitk::Image::Pointer m_Random3DImage;
- mitk::Image::Pointer m_ReferenceImage;
-
-public:
-
- /**
- * @brief Setup a recorder including a device. Here, we use a player, because in an automatic test
- * hardware is not useful.
- */
- void setUp()
- {
- //Random input images
- m_Random3DImage = mitk::ImageGenerator::GenerateRandomImage<unsigned char>(119, 204, 52, 1, // dimension
- 1.0f, 1.0f, 1.0f, // spacing
- 255, 0); // max, min
-
- m_Random2DImage = mitk::ImageGenerator::GenerateRandomImage<unsigned char>(119, 204, 0, 0, // dimension
- 1.0f, 1.0f, 1.0f, // spacing
- 255, 0); // max, min
- m_oclBinaryFilter = mitk::OclBinaryThresholdImageFilter::New();
- }
-
- void tearDown()
- {
- m_oclBinaryFilter = nullptr;
- }
-
- void SetInput_2DImage_ThrowsException()
- {
- CPPUNIT_ASSERT_THROW( m_oclBinaryFilter->SetInput( m_Random2DImage ), mitk::Exception );
- }
-
- void GenerateData_3DImage_CompareToReference()
- {
- int upperThr = 255;
- int lowerThr = 60;
-
- int outsideVal = 0;
- int insideVal = 100;
-
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
- resources->GetContext(); //todo why do i need to call this before GetMaximumImageSize()?
- if(resources->GetMaximumImageSize(2, CL_MEM_OBJECT_IMAGE3D) == 0)
- {
- //GPU device does not support 3D images. Skip this test.
- MITK_INFO << "Skipping test.";
- return;
- }
-
- try{
-
- m_oclBinaryFilter->SetInput( m_Random3DImage );
- m_oclBinaryFilter->SetUpperThreshold( upperThr );
- m_oclBinaryFilter->SetLowerThreshold( lowerThr );
- m_oclBinaryFilter->SetOutsideValue( outsideVal );
- m_oclBinaryFilter->SetInsideValue( insideVal );
- m_oclBinaryFilter->Update();
-
- mitk::Image::Pointer outputImage = mitk::Image::New();
- outputImage = m_oclBinaryFilter->GetOutput();
-
- // reference computation
- //This is not optimal here, but since we use a random image
- //we cannot know the reference image at this point.
- typedef itk::Image< unsigned char, 3> ImageType;
- typedef itk::BinaryThresholdImageFilter< ImageType, ImageType > ThresholdFilterType;
-
- ImageType::Pointer itkInputImage = ImageType::New();
- CastToItkImage( m_Random3DImage, itkInputImage );
-
- ThresholdFilterType::Pointer refThrFilter = ThresholdFilterType::New();
- refThrFilter->SetInput( itkInputImage );
- refThrFilter->SetLowerThreshold( lowerThr );
- refThrFilter->SetUpperThreshold( upperThr );
- refThrFilter->SetOutsideValue( outsideVal );
- refThrFilter->SetInsideValue( insideVal );
- refThrFilter->Update();
- mitk::Image::Pointer referenceImage = mitk::Image::New();
- mitk::CastToMitkImage(refThrFilter->GetOutput(), referenceImage);
-
- MITK_ASSERT_EQUAL( referenceImage, outputImage,
- "OclBinaryThresholdFilter should be equal to regular itkBinaryThresholdImageFilter.");
- }
- catch(mitk::Exception &e)
- {
- std::string errorMessage = "Caught unexpected exception ";
- errorMessage.append(e.what());
- CPPUNIT_FAIL(errorMessage.c_str());
- }
-
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkOclBinaryThresholdImageFilter)
diff --git a/Modules/OpenCL/Testing/mitkOclImageTest.cpp b/Modules/OpenCL/Testing/mitkOclImageTest.cpp
deleted file mode 100644
index c1312627af..0000000000
--- a/Modules/OpenCL/Testing/mitkOclImageTest.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 <mitkTestingMacros.h>
-#include <mitkImageGenerator.h>
-#include <mitkOclImage.h>
-
-using namespace mitk;
-
-/**
- This function is testing the mitk::OclImage class.
- */
-int mitkOclImageTest( int /*argc*/, char* /*argv*/[] )
-{
- MITK_TEST_BEGIN("mitkOclImageTest");
-
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- MITK_TEST_CONDITION_REQUIRED( ref != 0, "Got valid ServiceReference" );
-
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
- MITK_TEST_CONDITION_REQUIRED( resources != nullptr, "OpenCL Resource service available." );
-
- cl_context gpuContext = resources->GetContext();
- MITK_TEST_CONDITION_REQUIRED( gpuContext != nullptr, "Got not-null OpenCL context.");
-
- cl_device_id gpuDevice = resources->GetCurrentDevice();
- MITK_TEST_CONDITION_REQUIRED( gpuDevice != nullptr, "Got not-null OpenCL device.");
-
- //create a random image
- mitk::Image::Pointer reference;
- //check if 3D images are supported by the device and initialize image accordingly
- if( resources->GetMaximumImageSize(2, CL_MEM_OBJECT_IMAGE3D) == 0 ) //2D required
- {
- //Create a random reference image
- reference = mitk::ImageGenerator::GenerateRandomImage<unsigned char>(119, 204, 0, 0, // dimension
- 1.0f, 1.0f, 1.0f, // spacing
- 255, 0); // max, min
- }
- else //3D ok
- {
- //Create a random reference image
- reference = mitk::ImageGenerator::GenerateRandomImage<unsigned char>(119, 204, 52, 1, // dimension
- 1.0f, 1.0f, 1.0f, // spacing
- 255, 0); // max, min
- }
- MITK_TEST_CONDITION_REQUIRED( reference.IsNotNull(), "Reference mitk::Image object instantiated.");
-
- mitk::OclImage::Pointer oclTestImage = mitk::OclImage::New();
- oclTestImage->InitializeByMitkImage(reference);
- MITK_TEST_CONDITION_REQUIRED(oclTestImage.IsNotNull(), "oclImage object instantiated.");
-
- // test if oclImage correct initialized
- MITK_TEST_CONDITION( oclTestImage->GetMITKImage() == reference, "oclImage has the correct reference mitk::Image");
- MITK_TEST_CONDITION( (unsigned int)oclTestImage->GetDimension() == reference->GetDimension(), "Same dimensionality.");
-
- cl_int clErr = 0;
- cl_command_queue cmdQueue = clCreateCommandQueue( gpuContext, gpuDevice,
- 0 ,&clErr);
- MITK_TEST_CONDITION_REQUIRED( clErr == CL_SUCCESS, "A command queue was created.");
-
- // Allocate and copy image data to GPU
- try
- {
- oclTestImage->TransferDataToGPU(cmdQueue);
- MITK_TEST_CONDITION( oclTestImage->IsModified(0), "Modified flag for GPU correctly set.");
-
- // check if the created GPU object is valid
- cl_mem gpuImage = oclTestImage->GetGPUImage(cmdQueue);
- MITK_TEST_CONDITION_REQUIRED( gpuImage != nullptr, "oclImage returned a valid GPU memory pointer");
- size_t returned = 0;
- cl_image_format imgFmt;
- clErr = clGetImageInfo( gpuImage, CL_IMAGE_FORMAT, sizeof(cl_image_format),
- (void*) &imgFmt, &returned );
- MITK_TEST_CONDITION( clErr == CL_SUCCESS, "oclImage has created a valid GPU image");
-
- // test for dimensions
- size_t imagesize = 0;
- clErr = clGetImageInfo( gpuImage, CL_IMAGE_WIDTH, sizeof(size_t),
- (void*) &imagesize, &returned );
- MITK_TEST_CONDITION( imagesize == static_cast<size_t>(oclTestImage->GetDimension(0)), "Image width corresponds" );
-
- clErr = clGetImageInfo( gpuImage, CL_IMAGE_HEIGHT, sizeof(size_t),
- (void*) &imagesize, &returned );
- MITK_TEST_CONDITION( imagesize == static_cast<size_t>(oclTestImage->GetDimension(1)), "Image height corresponds" );
-
- clErr = clGetImageInfo( gpuImage, CL_IMAGE_DEPTH, sizeof(size_t),
- (void*) &imagesize, &returned );
- MITK_TEST_CONDITION( imagesize == static_cast<size_t>(oclTestImage->GetDimension(2)), "Image depth corresponds" );
-
- // clean up
- clReleaseCommandQueue( cmdQueue );
- }
- catch(mitk::ImageTypeIsNotSupportedByGPU& e)
- {
- MITK_ERROR << "Caught exception: " << e.what();
- //Image type is not supported -> skip test.
- }
-
- MITK_TEST_END();
-}
diff --git a/Modules/OpenCL/Testing/mitkOclReferenceCountTest.cpp b/Modules/OpenCL/Testing/mitkOclReferenceCountTest.cpp
deleted file mode 100644
index 171a06c9c4..0000000000
--- a/Modules/OpenCL/Testing/mitkOclReferenceCountTest.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 <mitkTestingMacros.h>
-#include <mitkImageGenerator.h>
-#include <mitkOclBinaryThresholdImageFilter.h>
-
-using namespace mitk;
-
-/**
- This function is testing the OclFilter class and the
- OpenCL resource service. To prevent segmentation faults
- a mutexed reference counter is implemented in the resource service.
- It tracks the number of opencl program references for the corresponding filter
- and delete only the opencl programm if the reference count reaches 0.
- Every new instance of a filter increases the reference count by 1.
- This test runs successfull if the 2 filters are initialized, run
- and deleted without any crash.
- */
-int mitkOclReferenceCountTest( int /*argc*/, char* /*argv*/[] )
-{
- MITK_TEST_BEGIN("mitkOclReferenceCountTest");
-
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
- resources->GetContext(); //todo why do i need to call this before GetMaximumImageSize()?
- if(resources->GetMaximumImageSize(2, CL_MEM_OBJECT_IMAGE3D) == 0)
- {
- //GPU device does not support 3D images. Skip this test.
- MITK_INFO << "Skipping test.";
- return 0;
- }
-
- mitk::Image::Pointer inputImage = mitk::ImageGenerator::GenerateRandomImage<unsigned char>(119, 204, 52, 1, // dimension
- 1.0f, 1.0f, 1.0f, // spacing
- 255, 0); // max, min
- int upperThr = 255;
- int lowerThr = 60;
- int outsideVal = 0;
- int insideVal = 100;
-
- mitk::OclBinaryThresholdImageFilter::Pointer oclFilter1 = mitk::OclBinaryThresholdImageFilter::New();
- oclFilter1->SetInput( inputImage );
- oclFilter1->SetUpperThreshold( upperThr );
- oclFilter1->SetLowerThreshold( lowerThr );
- oclFilter1->SetOutsideValue( outsideVal );
- oclFilter1->SetInsideValue( insideVal );
- oclFilter1->Update();
-
- mitk::Image::Pointer outputImage1 = mitk::Image::New();
- outputImage1 = oclFilter1->GetOutput();
-
- mitk::OclBinaryThresholdImageFilter::Pointer oclFilter2 = mitk::OclBinaryThresholdImageFilter::New();
-
- oclFilter2->SetInput( inputImage );
- oclFilter2->SetUpperThreshold( upperThr );
- oclFilter2->SetLowerThreshold( lowerThr );
- oclFilter2->SetOutsideValue( outsideVal );
- oclFilter2->SetInsideValue( insideVal );
- oclFilter2->Update();
-
- mitk::Image::Pointer outputImage2 = mitk::Image::New();
- outputImage2 = oclFilter2->GetOutput();
-
- // delete filters
- oclFilter1 = nullptr;
- oclFilter2 = nullptr;
-
- // this is only visible if the delete did not cause a segmentation fault
- // it is always true and successfull if the program reaches this state
- MITK_TEST_CONDITION_REQUIRED( true, "2 Filters deleted without a crash -> success ");
-
- MITK_TEST_END();
-}
diff --git a/Modules/OpenCL/Testing/mitkOclResourceServiceTest.cpp b/Modules/OpenCL/Testing/mitkOclResourceServiceTest.cpp
deleted file mode 100644
index 7521f13015..0000000000
--- a/Modules/OpenCL/Testing/mitkOclResourceServiceTest.cpp
+++ /dev/null
@@ -1,103 +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 <mitkTestingMacros.h>
-#include <mitkOclUtils.h>
-#include <mitkOclResourceService.h>
-#include <mitkException.h>
-
-#include <usModuleContext.h>
-#include <usGetModuleContext.h>
-
-using namespace mitk;
-
-/**
- This function is testing the class mitk::OclResourceService.
- */
-int mitkOclResourceServiceTest( int /*argc*/, char* /*argv*/[] )
-{
- MITK_TEST_BEGIN("mitkOclResourceServiceTest");
-
- us::ServiceReference<OclResourceService> ref = us::GetModuleContext()->GetServiceReference<OclResourceService>();
- MITK_TEST_CONDITION_REQUIRED( ref != nullptr, "Resource service available." );
-
- OclResourceService* resources = us::GetModuleContext()->GetService<OclResourceService>(ref);
- MITK_TEST_CONDITION_REQUIRED( resources != nullptr, "Resource service available." );
-
- cl_context first = resources->GetContext();
- MITK_TEST_CONDITION_REQUIRED(first != nullptr, "Got not-null OpenCL context.");
-
- OclResourceService* resources_2 = us::GetModuleContext()->GetService<OclResourceService>(ref);
- MITK_TEST_CONDITION_REQUIRED( resources == resources_2, "Same resource reference the second time." );
-
- cl_context second = resources_2->GetContext();
- MITK_TEST_CONDITION_REQUIRED( first == second, "Both return same context");
-
- // further tests requires for valid context
- if( first )
- {
- cl_image_format testFmt;
- testFmt.image_channel_data_type = CL_FLOAT;
- testFmt.image_channel_order = CL_RGBA;
-
- MITK_TEST_CONDITION( resources->GetIsFormatSupported( &testFmt ), "Checking if format CL_FLOAT / CL_RGBA supported." );
- }
-
- // create test program
- const std::string testProgramSource =
- "__kernel void testKernel( __global uchar* buffer ){ \
- const unsigned int globalPosX = get_global_id(0); \
- buffer[globalPosX] = buffer[globalPosX] + 1;}";
-
- cl_int err = 0;
- size_t progSize = testProgramSource.length();
- const char* progSource = testProgramSource.c_str();
- cl_program testProgram = clCreateProgramWithSource( first, 1, &progSource, &progSize, &err );
-
- MITK_TEST_CONDITION_REQUIRED( err == CL_SUCCESS, "Test program loaded succesfully.");
-
- err = clBuildProgram(testProgram, 0, nullptr, nullptr, nullptr, nullptr);
- MITK_TEST_CONDITION_REQUIRED( err == CL_SUCCESS, "Test program built succesfully.");
-
- resources->InsertProgram( testProgram, "test_program", true);
- MITK_TEST_CONDITION( resources->GetProgram("test_program") == testProgram, "Program correctly stored by ResourceService");
-
- // the manger throws exception when accessing non-existant programs
- MITK_TEST_FOR_EXCEPTION( mitk::Exception, resources->GetProgram("blah"); );
-
- // another test source, this one does not compile
- const std::string testProgramSource_notCompiling =
- "__kernel void testKernel( __global uchar* buffer ){ \
- const unsigned intt globalPosX = get_global_id(0); }";
-
- progSize = testProgramSource_notCompiling.length();
- const char* progSource2 = testProgramSource_notCompiling.c_str();
- cl_program notComp_testProgram = clCreateProgramWithSource( first, 1, &progSource2, &progSize, &err );
-
- // the error in the source code has no influence on loading the program
- MITK_TEST_CONDITION_REQUIRED( err == CL_SUCCESS, "Test program 2 loaded succesfully.");
-
- err = clBuildProgram(notComp_testProgram, 0, nullptr, nullptr, nullptr, nullptr);
- MITK_TEST_CONDITION_REQUIRED( err == CL_BUILD_PROGRAM_FAILURE, "Test program 2 failed to build.");
- std::cout << " --> The (expected) OpenCL Build Error occured : ";// << GetOclErrorString(err);
-
- resources->InsertProgram( notComp_testProgram, "test_program_failed", true);
- MITK_TEST_CONDITION( resources->GetProgram("test_program_failed") == notComp_testProgram, "Program correctly stored by ResourceService");
-
- // calling the InvalidateStorage() will result in removing the _failed test program inserted above
- resources->InvalidateStorage();
-
- // the second test program should no more exist in the storage, hence we await an exception
- MITK_TEST_FOR_EXCEPTION( mitk::Exception, resources->GetProgram("test_program_failed"); );
-
- MITK_TEST_END();
-}
diff --git a/Modules/OpenCL/files.cmake b/Modules/OpenCL/files.cmake
deleted file mode 100644
index c1f158a404..0000000000
--- a/Modules/OpenCL/files.cmake
+++ /dev/null
@@ -1,26 +0,0 @@
-set(CPP_FILES
-# helper classes
- mitkOclUtils.cpp
- mitkOclResourceServiceImpl_Private.cpp
- mitkOclImageFormats.cpp
-
-# module activator
- mitkOpenCLActivator.cpp
-
-# base data and filter objects
- mitkOclBaseData.cpp
- mitkOclImage.cpp
- mitkOclDataSet.cpp
- mitkOclFilter.cpp
- mitkOclImageFilter.cpp
- mitkOclDataSetFilter.cpp
- mitkOclImageToImageFilter.cpp
- mitkOclDataSetToDataSetFilter.cpp
-
-# own filter implementations
- mitkOclBinaryThresholdImageFilter.cpp
-)
-
-set(RESOURCE_FILES
- BinaryThresholdFilter.cl
-)
diff --git a/Modules/OpenCL/mitkOclBaseData.cpp b/Modules/OpenCL/mitkOclBaseData.cpp
deleted file mode 100644
index cb55ab283a..0000000000
--- a/Modules/OpenCL/mitkOclBaseData.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 "mitkOclBaseData.h"
-
-mitk::OclBaseData::OclBaseData()
-: m_BufferSize ( 0 ), m_GPUBuffer( nullptr ), m_CPUBuffer( nullptr )
-{
-}
-
-mitk::OclBaseData::~OclBaseData()
-{
- if (m_GPUBuffer) clReleaseMemObject( m_GPUBuffer );
- if (m_CPUBuffer) free( m_CPUBuffer );
-}
-
-cl_mem mitk::OclBaseData::GetGPUBuffer()
-{
- return this->m_GPUBuffer;
-}
diff --git a/Modules/OpenCL/mitkOclBaseData.h b/Modules/OpenCL/mitkOclBaseData.h
deleted file mode 100644
index 49e5f1c40f..0000000000
--- a/Modules/OpenCL/mitkOclBaseData.h
+++ /dev/null
@@ -1,74 +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 mitkOclBaseData_h
-#define mitkOclBaseData_h
-
-#include "MitkOpenCLExports.h"
-#include "mitkOclUtils.h"
-
-#include "mitkOpenCL.h"
-
-#include <mitkCommon.h>
-#include <itkObjectFactory.h>
-#include <itkObject.h>
-
-namespace mitk
-{
-
- class MITKOPENCL_EXPORT OclBaseData : public itk::Object
- {
- public:
- mitkClassMacroItkParent(OclBaseData, itk::Object);
-
- /*! \brief Copies the RAM-stored data to GPU-MEM.
- * This method has to be implemented for each data type.
- */
- virtual int TransferDataToGPU(cl_command_queue) = 0;
-
- /*! \brief Copies the in GPU-MEM stored data to RAM
- * This method has to be implemented for each data type.
- */
- virtual void* TransferDataToCPU(cl_command_queue) = 0;
-
- /** \brief Set the modified flag for one of the GPU buffer */
- void GPUModified();
-
- /** \brief Set the modified flag for one of the CPU buffer */
- void CPUModified();
-
-
- /** \brief Get the pointer to the buffer on the device (GPU) */
- virtual cl_mem GetGPUBuffer();
-
- protected:
- /** \brief Default constructor. */
- OclBaseData();
-
- /** \brief Default destructor. */
- virtual ~OclBaseData();
-
- private:
-
- /** \brief Size of the data buffer. CPU size equals GPU size. */
- size_t m_BufferSize;
-
- /** \brief Pointer to the buffer on the device (GPU) */
- cl_mem m_GPUBuffer;
-
- /** \brief Pointer to the buffer on the host (CPU) */
- void* m_CPUBuffer;
- };
-
-}
-
-#endif
diff --git a/Modules/OpenCL/mitkOclBinaryThresholdImageFilter.cpp b/Modules/OpenCL/mitkOclBinaryThresholdImageFilter.cpp
deleted file mode 100644
index 1f750ef5c4..0000000000
--- a/Modules/OpenCL/mitkOclBinaryThresholdImageFilter.cpp
+++ /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.
-
-============================================================================*/
-
-#include "mitkOclBinaryThresholdImageFilter.h"
-#include "usServiceReference.h"
-
-mitk::OclBinaryThresholdImageFilter::OclBinaryThresholdImageFilter()
-: m_ckBinaryThreshold( nullptr )
-{
- this->AddSourceFile("BinaryThresholdFilter.cl");
- this->m_FilterID = "BinaryThreshold";
-
- this->m_LowerThreshold = 10;
- this->m_UpperThreshold = 200;
-
- this->m_InsideValue = 100;
- this->m_OutsideValue = 0;
-}
-
-mitk::OclBinaryThresholdImageFilter::~OclBinaryThresholdImageFilter()
-{
- if ( this->m_ckBinaryThreshold )
- {
- clReleaseKernel( m_ckBinaryThreshold );
- }
-}
-
-void mitk::OclBinaryThresholdImageFilter::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::OclBinaryThresholdImageFilter::Execute()
-{
- cl_int clErr = 0;
-
- try
- {
- this->InitExec( this->m_ckBinaryThreshold );
- }
- catch( const mitk::Exception& e)
- {
- MITK_ERROR << "Catched exception while initializing filter: " << e.what();
- return;
- }
-
- // set kernel arguments
- clErr = clSetKernelArg( this->m_ckBinaryThreshold, 2, sizeof(cl_int), &(this->m_LowerThreshold) );
- clErr |= clSetKernelArg( this->m_ckBinaryThreshold, 3, sizeof(cl_int), &(this->m_UpperThreshold) );
- clErr |= clSetKernelArg( this->m_ckBinaryThreshold, 4, sizeof(cl_int), &(this->m_OutsideValue) );
- clErr |= clSetKernelArg( this->m_ckBinaryThreshold, 5, sizeof(cl_int), &(this->m_InsideValue) );
- CHECK_OCL_ERR( clErr );
-
- // execute the filter on a 3D NDRange
- this->ExecuteKernel( m_ckBinaryThreshold, 3);
-
- // signalize the GPU-side data changed
- m_Output->Modified( GPU_DATA );
-}
-
-us::Module *mitk::OclBinaryThresholdImageFilter::GetModule()
-{
- return us::GetModuleContext()->GetModule();
-}
-
-bool mitk::OclBinaryThresholdImageFilter::Initialize()
-{
- bool buildErr = true;
- cl_int clErr = 0;
-
- if ( OclFilter::Initialize() )
- {
- this->m_ckBinaryThreshold = clCreateKernel( this->m_ClProgram, "ckBinaryThreshold", &clErr);
- buildErr |= CHECK_OCL_ERR( clErr );
- }
-
- return (OclFilter::IsInitialized() && buildErr );
-}
-
-void mitk::OclBinaryThresholdImageFilter::SetInput(mitk::Image::Pointer image)
-{
- if(image->GetDimension() != 3)
- {
- mitkThrowException(mitk::Exception) << "Input for " << this->GetNameOfClass() <<
- " is not 3D. The filter only supports 3D. Please change your input.";
- }
- OclImageToImageFilter::SetInput(image);
-}
diff --git a/Modules/OpenCL/mitkOclBinaryThresholdImageFilter.h b/Modules/OpenCL/mitkOclBinaryThresholdImageFilter.h
deleted file mode 100644
index 0488e3fb6f..0000000000
--- a/Modules/OpenCL/mitkOclBinaryThresholdImageFilter.h
+++ /dev/null
@@ -1,121 +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 mitkOclBinaryThresholdImageFilter_h
-#define mitkOclBinaryThresholdImageFilter_h
-
-#include "mitkOclImageToImageFilter.h"
-#include <itkObject.h>
-
-namespace mitk
-{
-class OclImageToImageFilter;
-
-/** Documentation
- *
- * \brief The OclBinaryThresholdImageFilter computes a binary segmentation based on given
- threshold values.
-
- *
- * The filter requires two threshold values ( the upper and the lower threshold ) and two image values ( inside and outside ). The resulting voxel of the segmentation image is assigned the inside value 1 if the image value is between the given thresholds and the outside value otherwise.
- */
-class MITKOPENCL_EXPORT OclBinaryThresholdImageFilter : public OclImageToImageFilter, public itk::Object
-{
-
-public:
- mitkClassMacroItkParent(OclBinaryThresholdImageFilter, itk::Object);
- itkNewMacro(Self);
-
- /**
- * @brief SetInput Set the input image. Only 3D images are supported for now.
- * @param image a 3D image.
- * @throw mitk::Exception if the dimesion is not 3.
- */
- void SetInput(Image::Pointer image);
-
- /** Update the filter */
- void Update();
-
- /** Set the lower threshold
- @param lowerThreshold Threshold value
- */
- void SetLowerThreshold( int lowerThreshold )
- {
- this->m_LowerThreshold = lowerThreshold;
- }
-
- /** Set the upper threshold
- @param upperThreshold Threshold value
- */
- void SetUpperThreshold( int upperThreshold )
- {
- this->m_UpperThreshold = upperThreshold;
- }
-
- /** Set the outside value
-
- @param outsideValue The outside value
- */
- void SetOutsideValue( int outsideValue )
- {
- this->m_OutsideValue = outsideValue;
- }
-
- /** Set the inside value
- @param insideValue The inside value
- */
- void SetInsideValue( int insideValue )
- {
- this->m_InsideValue = insideValue;
- }
-
-protected:
-
- /** Constructor */
- OclBinaryThresholdImageFilter();
-
- /** Destructor */
- virtual ~OclBinaryThresholdImageFilter();
-
- /** Initialize the filter */
- bool Initialize();
-
- void Execute();
-
- mitk::PixelType GetOutputType()
- {
- return mitk::MakeScalarPixelType<unsigned char>();
- }
-
- int GetBytesPerElem()
- {
- return sizeof(unsigned char);
- }
-
- virtual us::Module* GetModule();
-
-private:
- /** The OpenCL kernel for the filter */
- cl_kernel m_ckBinaryThreshold;
-
- int m_LowerThreshold;
-
- int m_UpperThreshold;
-
- int m_InsideValue;
-
- int m_OutsideValue;
-};
-}
-
-
-#endif
diff --git a/Modules/OpenCL/mitkOclDataSet.cpp b/Modules/OpenCL/mitkOclDataSet.cpp
deleted file mode 100644
index 5337a5981d..0000000000
--- a/Modules/OpenCL/mitkOclDataSet.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 "mitkOclDataSet.h"
-#include "mitkCommon.h"
-#include "mitkLog.h"
-
-#include "mitkOclUtils.h"
-
-#include <fstream>
-
-//#define SHOW_MEM_INFO
-
-mitk::OclDataSet::OclDataSet() : m_gpuBuffer(nullptr), m_context(nullptr), m_bufferSize(0), m_gpuModified(false), m_cpuModified(false),
- m_Data(nullptr), m_BpE(1)
-{
-}
-
-mitk::OclDataSet::~OclDataSet()
-{
- MITK_DEBUG << "OclDataSet Destructor";
-
- //release GMEM Image buffer
- if (m_gpuBuffer) clReleaseMemObject(m_gpuBuffer);
-}
-
-
-cl_mem mitk::OclDataSet::CreateGPUBuffer()
-{
- MITK_DEBUG << "InitializeGPUBuffer call with: BPE=" << m_BpE;
-
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- m_context = resources->GetContext();
-
- int clErr;
- if (m_gpuBuffer) clReleaseMemObject(m_gpuBuffer);
-
- m_gpuBuffer = clCreateBuffer(m_context, CL_MEM_READ_WRITE, m_bufferSize * (size_t)m_BpE, nullptr, &clErr);
-
- #ifdef SHOW_MEM_INFO
- MITK_INFO << "Created GPU Buffer Object of size: " << (size_t)m_BpE * m_bufferSize << " Bytes";
- #endif
-
- CHECK_OCL_ERR(clErr);
-
- if (clErr != CL_SUCCESS)
- mitkThrow() << "openCL Error when creating Buffer";
-
- return m_gpuBuffer;
-}
-
-bool mitk::OclDataSet::IsModified(int _type)
-{
- if (_type) return m_cpuModified;
- else return m_gpuModified;
-}
-
-void mitk::OclDataSet::Modified(int _type)
-{
- // defines... GPU: 0, CPU: 1
- m_cpuModified = _type;
- m_gpuModified = !_type;
-}
-
-int mitk::OclDataSet::TransferDataToGPU(cl_command_queue gpuComQueue)
-{
- cl_int clErr = 0;
-
- // check whether an image present
- if (m_Data == nullptr){
- MITK_ERROR("ocl.DataSet") << "(mitk) No data present!\n";
- return -1;
- }
-
- // there is a need for copy only if RAM-Data newer then GMEM data
- if (m_cpuModified)
- {
- //check the buffer
- if(m_gpuBuffer == nullptr)
- {
- CreateGPUBuffer();
- }
-
- if (m_gpuBuffer != nullptr)
- {
- clErr = clEnqueueWriteBuffer(gpuComQueue, m_gpuBuffer, CL_TRUE, 0, m_bufferSize * (size_t)m_BpE, m_Data, 0, NULL, NULL);
- MITK_DEBUG << "Wrote Data to GPU Buffer Object.";
-
- CHECK_OCL_ERR(clErr);
- m_gpuModified = true;
-
- if (clErr != CL_SUCCESS)
- mitkThrow() << "openCL Error when writing Buffer";
- }
- else
- {
- MITK_ERROR << "No GPU buffer present!";
- }
- }
-
- return clErr;
-}
-
-cl_mem mitk::OclDataSet::GetGPUBuffer()
-{
- // query image object info only if already initialized
- if( this->m_gpuBuffer )
- {
- #ifdef SHOW_MEM_INFO
- cl_int clErr = 0;
- // clGetMemObjectInfo()
- cl_mem_object_type memInfo;
- clErr = clGetMemObjectInfo(this->m_gpuBuffer, CL_MEM_TYPE, sizeof(cl_mem_object_type), &memInfo, nullptr );
- CHECK_OCL_ERR(clErr);
- MITK_DEBUG << "Querying info for object, recieving: " << memInfo;
- #endif
- }
-
- return m_gpuBuffer;
-}
-
-void* mitk::OclDataSet::TransferDataToCPU(cl_command_queue gpuComQueue)
-{
- cl_int clErr = 0;
-
- // if image created on GPU, needs to create mitk::Image
- if( m_gpuBuffer == nullptr ){
- MITK_ERROR("ocl.DataSet") << "(mitk) No buffer present!\n";
- return nullptr;
- }
-
- // check buffersize
- char* data = new char[m_bufferSize * (size_t)m_BpE];
-
- // debug info
- #ifdef SHOW_MEM_INFO
- oclPrintMemObjectInfo( m_gpuBuffer );
- #endif
-
- clErr = clEnqueueReadBuffer( gpuComQueue, m_gpuBuffer, CL_TRUE, 0, m_bufferSize * (size_t)m_BpE, data ,0, nullptr, nullptr);
- CHECK_OCL_ERR(clErr);
-
- if(clErr != CL_SUCCESS)
- mitkThrow() << "openCL Error when reading Output Buffer";
-
- clFlush( gpuComQueue );
- // the cpu data is same as gpu
- this->m_gpuModified = false;
-
- return (void*) data;
-}
-
-void mitk::OclDataSet::SetBufferSize(size_t size)
-{
- m_bufferSize = size;
-}
-
-void mitk::OclDataSet::SetBpE(unsigned short BpE)
-{
- m_BpE = BpE;
-}
diff --git a/Modules/OpenCL/mitkOclDataSet.h b/Modules/OpenCL/mitkOclDataSet.h
deleted file mode 100644
index 8239efdbe3..0000000000
--- a/Modules/OpenCL/mitkOclDataSet.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkOclDataSet_h
-#define mitkOclDataSet_h
-
-#define GPU_DATA 0
-#define CPU_DATA 1
-
-#include <mitkImage.h>
-#include "MitkOpenCLExports.h"
-
-#include "mitkOclBaseData.h"
-#include "mitkOpenCLActivator.h"
-
-#include <mitkException.h>
-
-namespace mitk {
-
-/*!
- * \brief Class implementing processing of arbitrary data sets for GPU Image Processing
- *
- * The class holds a pointer to the data stored in RAM and performs an
- * on-demand-copy to the graphics memory. It is the basic data structure for all
- * mitk::oclDataSetToDataSetFilter classes
- */
-class MITKOPENCL_EXPORT OclDataSet : public OclBaseData
-{
-public:
- mitkClassMacro(OclDataSet, OclBaseData);
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- /*! \brief Copies the RAM-stored data to GMEM */
- virtual int TransferDataToGPU(cl_command_queue);
-
- /*! \brief Copies the in GMEM stored data to RAM */
- virtual void* TransferDataToCPU(cl_command_queue);
-
- /*! \brief Returns the pointer to the referenced data */
- void* GetData()
- {
- return m_Data;
- }
-
- /** Returns the pointer to the GPU buffer */
- cl_mem GetGPUBuffer();
-
- /** Create the GPU buffer for image
- *
- */
- cl_mem CreateGPUBuffer();
-
- /** \brief Returns the status of the image buffer
- *
- * @param _type The flag to specify the buffer type ( GPU / CPU )
- */
- bool IsModified(int _type);
-
- using OclBaseData::Modified;
-
- /** \brief Set the modified flag for one of the buffers
- *
- * @param _type The flag to specify the buffer type ( GPU / CPU )
- */
- void Modified(int _type);
-
- /** \brief Initialze the OclDataSet with data. */
- void SetData(void* data)
- {
- this->m_cpuModified = true;
- this->m_gpuModified = false;
- m_Data = data;
- }
-
- /*! \brief returns the amount of elements in the DataSet */
- size_t GetBufferSize() const
- {
- return this->m_bufferSize;
- }
-
- short GetBytesPerElement() const
- {
- return this->m_BpE;
- }
-
- /** @brief Set the amount of elements in buffer*/
- void SetBufferSize(size_t size);
-
- /** @brief Set the DataSet memory Size per Element in Bytes*/
- void SetBpE(unsigned short BpE);
-
-protected:
- /*! \brief Constructor */
- OclDataSet();
-
- /** @brief Destructor */
- virtual ~OclDataSet();
-
- /*! GMEM Image buffer */
- cl_mem m_gpuBuffer;
-
- /*! GPU Context the Buffer was created in, needed for access */
- cl_context m_context;
-
-private:
- /*! GMEM Buffer Size in elements*/
- size_t m_bufferSize;
-
- bool m_gpuModified;
- bool m_cpuModified;
-
- /*! Reference to the data */
- void* m_Data;
-
- /*! Bytes per Element in Buffer*/
- unsigned short m_BpE;
-};
-
-}
-#endif
diff --git a/Modules/OpenCL/mitkOclDataSetFilter.cpp b/Modules/OpenCL/mitkOclDataSetFilter.cpp
deleted file mode 100644
index bc4ab4edfc..0000000000
--- a/Modules/OpenCL/mitkOclDataSetFilter.cpp
+++ /dev/null
@@ -1,51 +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 "mitkOclDataSetFilter.h"
-#include "mitkOclFilter.h"
-#include "mitkOclDataSet.h"
-#include "mitkImageReadAccessor.h"
-
-mitk::OclDataSetFilter::OclDataSetFilter()
-{
-}
-
-mitk::OclDataSetFilter::~OclDataSetFilter()
-{
-}
-
-void mitk::OclDataSetFilter::SetInput(mitk::OclDataSet::Pointer DataSet)
-{
- m_Input = DataSet;
-}
-
-void mitk::OclDataSetFilter::SetInput(void* DataSet, unsigned int size, unsigned int BpE)
-{
- m_Input = mitk::OclDataSet::New();
- m_Input->SetData(DataSet);
- m_Input->SetBufferSize(size);
- m_Input->SetBpE(BpE);
- m_CurrentSize = BpE;
-}
-
-void mitk::OclDataSetFilter::SetInput(mitk::Image::Pointer image)
-{
- m_Input = mitk::OclDataSet::New();
- mitk::ImageReadAccessor reader(image);
-
- m_Input->SetData(const_cast<void*>(reader.GetData()));
- m_CurrentSize = (unsigned int)(image->GetPixelType().GetBitsPerComponent() / 8);
- unsigned int elements = image->GetDimension(0) * image->GetDimension(1) * image->GetDimension(2);
-
- m_Input->SetBufferSize(elements);
- m_Input->SetBpE(m_CurrentSize);
-}
diff --git a/Modules/OpenCL/mitkOclDataSetFilter.h b/Modules/OpenCL/mitkOclDataSetFilter.h
deleted file mode 100644
index 9ac247fab0..0000000000
--- a/Modules/OpenCL/mitkOclDataSetFilter.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 mitkOclDataSetFilter_h
-#define mitkOclDataSetFilter_h
-
-#include "mitkOclFilter.h"
-#include "mitkOclDataSet.h"
-
-#define FILTER_UCHAR 0
-#define FILTER_SHORT 1
-
-namespace mitk
-{
-class OclFilter;
-class OclDataSetFilter;
-
- /**
- * \brief The OclDataSetFilter is the topmost class for all filter which take DataSets as input.
- *
- * The input DataSet can be intialized via an oclDataSet or a pointer to the data
- * This makes it possible to create a filter pipeline of GPU-based filters
- * and to bind this part into the CPU (ITK) filter pipeline.
- */
-class MITKOPENCL_EXPORT OclDataSetFilter: public OclFilter
-{
-public:
- /**
- * @brief SetInput SetInput Set the input DataSet (as mitk::OclDataSet).
- * @param DataSet The DataSet in mitk::OclDataSet.
- */
- void SetInput(mitk::OclDataSet::Pointer DataSet);
-
- /**
- * @brief SetInput Set the input DataSet (as a pointer to the data).
- * @param DataSet The DataSet in mitk::OclDataSet.
- * @param size
- * @param BpE
- */
- void SetInput(void* DataSet, unsigned int size, unsigned int BpE);
-
- /**
- * @brief SetInput Set the input DataSet (as mitk::Image).
- * @param image The DataSet in mitk::OclDataSet.
- */
- void SetInput(mitk::Image::Pointer image);
-
-protected:
- OclDataSetFilter();
-
- virtual ~OclDataSetFilter();
-
- /** The input DataSet */
- mitk::OclDataSet::Pointer m_Input;
- unsigned int m_CurrentSize;
-};
-}
-#endif
diff --git a/Modules/OpenCL/mitkOclDataSetToDataSetFilter.cpp b/Modules/OpenCL/mitkOclDataSetToDataSetFilter.cpp
deleted file mode 100644
index 99fffdb4b8..0000000000
--- a/Modules/OpenCL/mitkOclDataSetToDataSetFilter.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.
-
-============================================================================*/
-
-#include "mitkOclDataSetToDataSetFilter.h"
-#include "mitkOclDataSet.h"
-
-#include "mitkException.h"
-
-mitk::OclDataSetToDataSetFilter::OclDataSetToDataSetFilter()
-{
- m_Output = mitk::OclDataSet::New();
-}
-
-mitk::OclDataSetToDataSetFilter::~OclDataSetToDataSetFilter()
-{
-}
-
-mitk::OclDataSet::Pointer mitk::OclDataSetToDataSetFilter::GetGPUOutput()
-{
- return this->m_Output;
-}
-
-void* mitk::OclDataSetToDataSetFilter::GetOutput()
-{
- void* pData = m_Output->TransferDataToCPU(m_CommandQue);
- return pData;
-}
-
-int mitk::OclDataSetToDataSetFilter::GetBytesPerElem()
-{
- return this->m_CurrentSizeOutput;
-}
-
-bool mitk::OclDataSetToDataSetFilter::InitExec(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE)
-{
- cl_int clErr = 0;
-
- if (m_Input.IsNull())
- mitkThrow() << "Input DataSet is null.";
-
- // get DataSet size once
- const unsigned int uiDataSetWidth = dimensions[0];
- const unsigned int uiDataSetHeight = dimensions[1];
- const unsigned int uiDataSetDepth = dimensions[2];
-
- // compute work sizes
- this->SetWorkingSize(8, uiDataSetWidth, 8, uiDataSetHeight, 8, uiDataSetDepth);
-
- cl_mem clBuffIn = m_Input->GetGPUBuffer();
- cl_mem clBuffOut = m_Output->GetGPUBuffer();
-
- if (!clBuffIn)
- {
- if (m_Input->TransferDataToGPU(m_CommandQue) != CL_SUCCESS)
- {
- mitkThrow() << "Could not create / initialize gpu DataSet.";
- }
-
- clBuffIn = m_Input->GetGPUBuffer();
- }
-
- // output DataSet not initialized or output buffer size changed
- if (!clBuffOut || (size_t)m_Output->GetBufferSize() != outputDataSize)
- {
- MITK_DEBUG << "Create GPU DataSet call " << uiDataSetWidth << "x" << uiDataSetHeight << "x" << uiDataSetDepth;
- MITK_INFO << "Create GPU Buffer of size " << outputDataSize * outputBpE / 1024.f / 1024.f << "MB";
- m_Output->SetBpE(outputBpE);
- m_Output->SetBufferSize(outputDataSize);
- clBuffOut = m_Output->CreateGPUBuffer();
- m_CurrentSizeOutput = outputBpE;
- }
-
- clErr = 0;
- clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffIn);
- clErr |= clSetKernelArg(ckKernel, 1, sizeof(cl_mem), &clBuffOut);
- CHECK_OCL_ERR(clErr);
-
- if (clErr != CL_SUCCESS)
- mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr);
-
- return(clErr == CL_SUCCESS);
-}
-
-bool mitk::OclDataSetToDataSetFilter::InitExecNoInput(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE)
-{
- cl_int clErr = 0;
-
- // get DataSet size once
- const unsigned int uiDataSetWidth = dimensions[0];
- const unsigned int uiDataSetHeight = dimensions[1];
- const unsigned int uiDataSetDepth = dimensions[2];
-
- // compute work sizes
- this->SetWorkingSize(8, uiDataSetWidth, 8, uiDataSetHeight, 8, uiDataSetDepth);
-
- cl_mem clBuffOut = m_Output->GetGPUBuffer();
-
- // output DataSet not initialized or output buffer size changed
- if (!clBuffOut || (size_t)m_Output->GetBufferSize() != outputDataSize)
- {
- MITK_DEBUG << "Create GPU DataSet call " << uiDataSetWidth << "x" << uiDataSetHeight << "x" << uiDataSetDepth;
- m_Output->SetBpE(outputBpE);
- m_Output->SetBufferSize(outputDataSize);
- clBuffOut = m_Output->CreateGPUBuffer();
- m_CurrentSizeOutput = outputBpE;
- }
-
- clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffOut);
- CHECK_OCL_ERR(clErr);
-
- if (clErr != CL_SUCCESS)
- mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr);
-
- return(clErr == CL_SUCCESS);
-}
diff --git a/Modules/OpenCL/mitkOclDataSetToDataSetFilter.h b/Modules/OpenCL/mitkOclDataSetToDataSetFilter.h
deleted file mode 100644
index d3f22d4c46..0000000000
--- a/Modules/OpenCL/mitkOclDataSetToDataSetFilter.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 mitkOclDataSetToDataSetFilter_h
-#define mitkOclDataSetToDataSetFilter_h
-
-#include "mitkOclDataSetFilter.h"
-
-namespace mitk
-{
-class OclDataSetFilter;
-class OclDataSetToDataSetFilter;
-
-/** @class OclDataSetToDataSetFilter
- * @brief The OclDataSetToDataSetFilter is the base class for all OpenCL DataSet filter generating DataSets.
- */
-class MITKOPENCL_EXPORT OclDataSetToDataSetFilter: public OclDataSetFilter
-{
-public:
- /*!
- * \brief Returns an pointer to the filtered data.
- */
- void* GetOutput();
-
- /*!
- * \brief Returns a pointer to the graphics memory.
- *
- * Use this method when executing two and more filters on the GPU for fast access.
- * This method does not copy the data to RAM. It returns only a pointer.
- */
- mitk::OclDataSet::Pointer GetGPUOutput();
-
-protected:
- /**
- * @brief OclDataSetToDataSetFilter Default constructor.
- */
- OclDataSetToDataSetFilter();
-
- /** @brief Destructor */
- virtual ~OclDataSetToDataSetFilter();
-
- /** Output DataSet */
- mitk::OclDataSet::Pointer m_Output;
-
- /** @brief (Virtual) method Update() to be implemented in derived classes. */
- virtual void Update() = 0;
-
- /**
- * @brief InitExec Initialize the execution
- * @param ckKernel The GPU kernel.
- * @param dimensions
- * @param outputDataSize
- * @param outputBpE
- * @throws mitk::Exception if something goes wrong.
- * @return True for success.
- */
- bool InitExec(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE);
-
- bool InitExecNoInput(cl_kernel ckKernel, unsigned int* dimensions, size_t outputDataSize, unsigned int outputBpE);
-
- /** @brief Get the memory size needed for each element */
- virtual int GetBytesPerElem();
-
- unsigned int m_CurrentSizeOutput;
-
-private:
- /** Block dimensions */
- unsigned int m_BlockDims[3];
-};
-}
-#endif
diff --git a/Modules/OpenCL/mitkOclFilter.cpp b/Modules/OpenCL/mitkOclFilter.cpp
deleted file mode 100644
index db9772822d..0000000000
--- a/Modules/OpenCL/mitkOclFilter.cpp
+++ /dev/null
@@ -1,351 +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.
-
-============================================================================*/
-
-//Ocl
-#include "mitkOclFilter.h"
-#include "mitkOclUtils.h"
-#include "mitkOpenCLActivator.h"
-
-
-//Mitk
-#include <mitkLog.h>
-#include <mitkConfig.h>
-
-//usService
-#include "usServiceReference.h"
-#include <usServiceRegistration.h>
-#include <usModuleContext.h>
-#include <usGetModuleContext.h>
-#include <usModule.h>
-#include <usModuleResource.h>
-#include <usModuleResourceStream.h>
-
-//standard library
-#include <thread>
-
-mitk::OclFilter::OclFilter()
- : m_ClCompilerFlags(""),
- m_ClProgram(nullptr),
- m_CommandQue(nullptr),
- m_FilterID("mitkOclFilter"),
- m_Preambel(" "),
- m_Initialized(false)
-{
-}
-
-mitk::OclFilter::OclFilter(const char* filename)
- : m_ClCompilerFlags(""),
- m_ClProgram(nullptr),
- m_CommandQue(nullptr),
- m_FilterID(filename),
- m_Preambel(" "),
- m_Initialized(false)
-{
- m_ClFiles.push_back(filename);
-}
-
-mitk::OclFilter::~OclFilter()
-{
- MITK_DEBUG << "OclFilter Destructor";
-
- // release program
- if (m_ClProgram)
- {
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- // remove program from storage
- resources->RemoveProgram(m_FilterID);
- }
-}
-
-bool mitk::OclFilter::ExecuteKernel( cl_kernel kernel, unsigned int workSizeDim )
-{
- cl_int clErr = 0;
-
- clErr = clEnqueueNDRangeKernel( this->m_CommandQue, kernel, workSizeDim,
- nullptr, this->m_GlobalWorkSize, m_LocalWorkSize, 0, nullptr, nullptr);
-
- CHECK_OCL_ERR( clErr );
-
- return ( clErr == CL_SUCCESS );
-}
-
-bool mitk::OclFilter::ExecuteKernelChunks( cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim )
-{
- size_t offset[3] ={0, 0, 0};
- cl_int clErr = 0;
-
- if(workSizeDim == 2)
- {
- for(offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0])
- {
- for(offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1])
- {
- clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim,
- offset, chunksDim, m_LocalWorkSize, 0, nullptr, nullptr);
- }
- }
- }
- else if(workSizeDim == 3)
- {
- for(offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0])
- {
- for(offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1])
- {
- for(offset[2] = 0; offset[2] < m_GlobalWorkSize[2]; offset[2] += chunksDim[2])
- {
- clErr |= clEnqueueNDRangeKernel( this->m_CommandQue, kernel, workSizeDim,
- offset, chunksDim, m_LocalWorkSize, 0, nullptr, nullptr);
- }
- }
- }
- }
-
- CHECK_OCL_ERR(clErr);
-
- return ( clErr == CL_SUCCESS );
-}
-
-bool mitk::OclFilter::ExecuteKernelChunksInBatches(cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim, size_t batchSize, int waitTimems)
-{
- size_t offset[3] = { 0, 0, 0 };
- cl_int clErr = 0;
-
- unsigned int currentChunk = 0;
- cl_event* waitFor = new cl_event[batchSize];
-
- if (workSizeDim == 2)
- {
- for (offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0])
- {
- for (offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1])
- {
- if (currentChunk % batchSize == 0 && currentChunk != 0)
- {
- clWaitForEvents(batchSize, &waitFor[0]);
- std::this_thread::sleep_for(std::chrono::milliseconds(waitTimems));
- clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim,
- offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[0]);
- }
- else
- {
- clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim,
- offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[currentChunk % batchSize]);
- }
- currentChunk++;
- }
- }
- }
- else if (workSizeDim == 3)
- {
- for (offset[0] = 0; offset[0] < m_GlobalWorkSize[0]; offset[0] += chunksDim[0])
- {
- for (offset[1] = 0; offset[1] < m_GlobalWorkSize[1]; offset[1] += chunksDim[1])
- {
- for (offset[2] = 0; offset[2] < m_GlobalWorkSize[2]; offset[2] += chunksDim[2])
- {
- if (currentChunk % batchSize == 0 && currentChunk != 0)
- {
- clWaitForEvents(batchSize, &waitFor[0]);
- std::this_thread::sleep_for(std::chrono::milliseconds(waitTimems));
- clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim,
- offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[0]);
- }
- else
- {
- clErr |= clEnqueueNDRangeKernel(this->m_CommandQue, kernel, workSizeDim,
- offset, chunksDim, m_LocalWorkSize, 0, nullptr, &waitFor[currentChunk % batchSize]);
- }
- currentChunk++;
- }
- }
- }
- }
- CHECK_OCL_ERR(clErr);
-
- return (clErr == CL_SUCCESS);
-}
-
-
-bool mitk::OclFilter::Initialize()
-{
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- m_CommandQue = resources->GetCommandQueue();
-
- cl_int clErr = 0;
- m_Initialized = CHECK_OCL_ERR(clErr);
-
- if ( m_ClFiles.empty())
- {
- MITK_ERROR<<"No OpenCL Source FILE specified";
- return false;
- }
-
- if (m_ClProgram == nullptr)
- {
- try
- {
- this->m_ClProgram = resources->GetProgram( this->m_FilterID );
- }
- catch(const mitk::Exception& e)
- {
- MITK_INFO << "Program not stored in resource manager, compiling. " << e;
- this->CompileSource();
- }
- }
-
- return m_Initialized;
-}
-
-void mitk::OclFilter::LoadSourceFiles(CStringList &sourceCode, ClSizeList &sourceCodeSize)
-{
- for( CStringList::iterator it = m_ClFiles.begin(); it != m_ClFiles.end(); ++it )
- {
- MITK_DEBUG << "Load file :" << *it;
- us::ModuleResource mdr = GetModule()->GetResource(*it);
-
- if( !mdr.IsValid() )
- MITK_WARN << "Could not load resource: " << mdr.GetName() << " is invalid!";
-
- us::ModuleResourceStream rss(mdr);
-
- // read resource file to a string
- std::istreambuf_iterator<char> eos;
- std::string source(std::istreambuf_iterator<char>(rss), eos);
-
- // add preambel and build up string to compile
- std::string src(m_Preambel);
- src.append("\n");
- src.append(source);
-
- // allocate new char buffer
- char* tmp = new char[src.size() + 1];
- strcpy(tmp,src.c_str());
-
- // add source to list
- sourceCode.push_back((const char*)tmp);
- sourceCodeSize.push_back(src.size());
- }
-}
-
-void mitk::OclFilter::CompileSource()
-{
- // helper variable
- int clErr = 0;
- CStringList sourceCode;
- ClSizeList sourceCodeSize;
-
- if (m_ClFiles.empty())
- {
- MITK_ERROR("ocl.filter") << "No shader source file was set";
- return;
- }
-
- //get a valid opencl context
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- cl_context gpuContext = resources->GetContext();
- // load the program source from file
- LoadSourceFiles(sourceCode, sourceCodeSize);
-
- if ( !sourceCode.empty() )
- {
- // create program from all files in the file list
- m_ClProgram = clCreateProgramWithSource(gpuContext, sourceCode.size(), &sourceCode[0], &sourceCodeSize[0], &clErr);
- CHECK_OCL_ERR(clErr);
-
- // build the source code
- MITK_DEBUG << "Building Program Source";
- std::string compilerOptions = "";
- compilerOptions.append(m_ClCompilerFlags);
-
- MITK_DEBUG("ocl.filter") << "cl compiler flags: " << compilerOptions.c_str();
-
- clErr = clBuildProgram(m_ClProgram, 0, nullptr, compilerOptions.c_str(), nullptr, nullptr);
- CHECK_OCL_ERR(clErr);
-
- // if OpenCL Source build failed
- if (clErr != CL_SUCCESS)
- {
- MITK_ERROR("ocl.filter") << "Failed to build source";
- oclLogBuildInfo(m_ClProgram, resources->GetCurrentDevice() );
- oclLogBinary(m_ClProgram, resources->GetCurrentDevice() );
- m_Initialized = false;
- }
-
- // store the succesfully build program into the program storage provided by the resource service
- resources->InsertProgram(m_ClProgram, m_FilterID, true);
-
- // free the char buffers with the source code
- for( CStringList::iterator it = sourceCode.begin(); it != sourceCode.end(); ++it )
- {
- delete[] *it;
- }
- }
- else
- {
- MITK_ERROR("ocl.filter") << "Could not load from source";
- m_Initialized = false;
- }
-}
-
-void mitk::OclFilter::SetWorkingSize(unsigned int locx, unsigned int dimx, unsigned int locy, unsigned int dimy, unsigned int locz, unsigned int dimz)
-{
- // set the local work size
- this->m_LocalWorkSize[0] = locx;
- this->m_LocalWorkSize[1] = locy;
- this->m_LocalWorkSize[2] = locz;
-
- this->m_GlobalWorkSize[0] = dimx;
- this->m_GlobalWorkSize[1] = dimy;
- this->m_GlobalWorkSize[2] = dimz;
-
- // estimate the global work size
- this->m_GlobalWorkSize[0] = iDivUp( dimx, this->m_LocalWorkSize[0]) * this->m_LocalWorkSize[0];
-
- if ( dimy > 1)
- this->m_GlobalWorkSize[1] = iDivUp( dimy, this->m_LocalWorkSize[1]) * this->m_LocalWorkSize[1];
- if( dimz > 1 )
- this->m_GlobalWorkSize[2] = iDivUp( dimz, this->m_LocalWorkSize[2]) * this->m_LocalWorkSize[2];
-}
-
-void mitk::OclFilter::SetSourcePreambel(const char* preambel)
-{
- this->m_Preambel = preambel;
-}
-
-void mitk::OclFilter::AddSourceFile(const char* filename)
-{
- m_ClFiles.push_back(filename);
-}
-
-void mitk::OclFilter::SetCompilerFlags(const char* flags)
-{
- m_ClCompilerFlags = flags;
-}
-
-
-bool mitk::OclFilter::IsInitialized()
-{
- return m_Initialized;
-}
-
-unsigned long mitk::OclFilter::GetDeviceMemory()
-{
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(GetModuleContext()->GetServiceReference<OclResourceService>());
- auto device = resources->GetCurrentDevice();
- return oclGetGlobalMemSize(device);
-}
diff --git a/Modules/OpenCL/mitkOclFilter.h b/Modules/OpenCL/mitkOclFilter.h
deleted file mode 100644
index 93b6ddf5c0..0000000000
--- a/Modules/OpenCL/mitkOclFilter.h
+++ /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.
-
-============================================================================*/
-
-
-#ifndef mitkOclFilter_h
-#define mitkOclFilter_h
-
-#include "mitkOclUtils.h"
-#include "mitkCommon.h"
-
-#include <vector>
-#include <usModule.h>
-
-#include <MitkOpenCLExports.h>
-
-namespace mitk
-{
-/**
- @class OclFilter
- @brief Superclass for all OpenCL based filter.
-
- This class takes care of loading and compiling the external GPU program code.
- */
-class MITKOPENCL_EXPORT OclFilter
-{
-public:
- /**
- * @brief Add a source file from the resource files to the
- * OpenCL shader file list. Multiple files can be added to the list.
- *
- * @param filename of the file in the resource system
- */
- void AddSourceFile(const char* filename);
-
- /**
- * @brief Set specific compilerflags to compile the CL source. Default is set to nullptr;
- * example: "-cl-fast-relaxed-math -cl-mad-enable -cl-strict-aliasing"
- *
- * @param flags to the modulefolder that contains the gpuSource
- */
- void SetCompilerFlags(const char* flags);
-
- /**
- * @brief Returns true if the initialization was successfull
- */
- virtual bool IsInitialized();
-
- /**
- * @brief Returns the amount of global memory of the used device in bytes
- */
- virtual unsigned long GetDeviceMemory();
-
- /** @brief Destructor */
- virtual ~OclFilter();
-
-protected:
-
- typedef std::vector<const char*> CStringList;
- typedef std::vector<size_t> ClSizeList;
-
- /** @brief Constructor */
- OclFilter();
-
- /** @brief Constructor ( overloaded ) */
- OclFilter(const char* filename);
-
- /** @brief String that contains the compiler flags */
- const char* m_ClCompilerFlags;
-
- /** @brief The compiled OpenCL program */
- cl_program m_ClProgram;
-
- /** @brief Command queue for the filter */
- cl_command_queue m_CommandQue;
-
- /** @brief Unique ID of the filter, needs to be specified in the constructor of the derived class */
- std::string m_FilterID;
-
- /*! @brief source preambel for e.g. \c \#define commands to be inserted into the OpenCL source */
- const char* m_Preambel;
-
- /** @brief List of sourcefiles that will be compiled for this filter.*/
- CStringList m_ClFiles;
-
- /** @brief status of the filter */
- bool m_Initialized;
-
- /** @brief The local work size fo the filter */
- size_t m_LocalWorkSize[3];
-
- /** @brief The global work size of the filter */
- size_t m_GlobalWorkSize[3];
-
- /** @brief Set the working size for the following OpenCL kernel call */
- void SetWorkingSize(unsigned int locx, unsigned int dimx,
- unsigned int locy = 1, unsigned int dimy = 1,
- unsigned int locz = 1, unsigned int dimz = 1);
-
- /** @brief Execute the given kernel on the OpenCL Index-Space defined by the local and global work sizes
- */
- bool ExecuteKernel( cl_kernel kernel, unsigned int workSizeDim );
-
- /** @brief Execute the given kernel on the OpenCL Index-Space defined by the local and global work sizes, but divide it into chunks of dimension chunksDim
- */
- bool ExecuteKernelChunks( cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim );
-
- /** @brief Execute the given kernel on the OpenCL Index-Space defined by the local and global work sizes, but divide it into chunks of dimension chunksDim and wait between
- * batches of batchSize chunks a time of waitTimems milliseconds
- */
- bool ExecuteKernelChunksInBatches(cl_kernel kernel, unsigned int workSizeDim, size_t* chunksDim, size_t batchSize, int waitTimems);
- /**
- * \brief Initialize all necessary parts of the filter
- *
- * The Initialize() method creates the command queue and the m_clProgram.
- * The program is either compiled from the given source or taken from the
- * OclResourceManager if the program was compiled already.
- */
- bool Initialize();
-
- /**
- * @brief Compile the program source
- */
- void CompileSource();
-
- /**
- * @brief Add some source code on the beginning of the loaded source
- *
- * In this way, some preprocessor flags for the CL compiler can at the beginning of the filter
- * @param preambel Source preambel for e.g. \c \#define commands to be inserted into the OpenCL source
- */
- void SetSourcePreambel(const char* preambel);
-
- /**
- * @brief Get the Module of the filter. Needs to be implemented by every subclass.
- * The filter will load the OpenCL sourcefiles from this module context.
- */
- virtual us::Module* GetModule() = 0;
-
- /**
- * @brief Helper functions that load sourcefiles from the module context in the Initialize function.
- * @param SourceCodeList holds the sourcecode for every file as string, the SourceCodeSizeList holst the
- * size of every file in bytes.
- * @param SourceCodeSizeList
- */
- void LoadSourceFiles(CStringList &SourceCodeList, ClSizeList &SourceCodeSizeList);
-};
-}
-#endif
diff --git a/Modules/OpenCL/mitkOclImage.cpp b/Modules/OpenCL/mitkOclImage.cpp
deleted file mode 100644
index 31aa963c8d..0000000000
--- a/Modules/OpenCL/mitkOclImage.cpp
+++ /dev/null
@@ -1,359 +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 "mitkOclImage.h"
-#include "mitkImageDataItem.h"
-#include "mitkCommon.h"
-#include "mitkLog.h"
-
-#include "mitkOclUtils.h"
-
-#include <mitkImageReadAccessor.h>
-#include <fstream>
-
-mitk::OclImage::OclImage() : m_gpuImage(nullptr), m_context(nullptr), m_bufferSize(0), m_gpuModified(false), m_cpuModified(false),
- m_Image(nullptr), m_dim(0), m_Dims(nullptr), m_BpE(1), m_formatSupported(false)
-{
-}
-
-mitk::OclImage::~OclImage()
-{
- MITK_INFO << "OclImage Destructor";
-
- //release GMEM Image buffer
- if (m_gpuImage) clReleaseMemObject(m_gpuImage);
-}
-
-
-cl_mem mitk::OclImage::CreateGPUImage(unsigned int _wi, unsigned int _he, unsigned int _de,
- unsigned int _bpp)
-{
- MITK_INFO << "CreateGPUImage call with: BPP=" << _bpp;
-
- this->m_Dims = new unsigned int[MAX_DIMS];
-
- m_Dims[0] = _wi;
- m_Dims[1] = _he;
- m_Dims[2] = _de;
-
- for (unsigned int i=3; i<MAX_DIMS; i++)
- m_Dims[i] = 1;
-
- m_bufferSize = _wi * _he * _de;
-
- m_BpE = _bpp;
-
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- cl_context gpuContext = resources->GetContext();
-
- int clErr;
- m_gpuImage = clCreateBuffer( gpuContext, CL_MEM_READ_WRITE, m_bufferSize * m_BpE, nullptr, &clErr);
-
- CHECK_OCL_ERR(clErr);
-
- return m_gpuImage;
-}
-
-void mitk::OclImage::InitializeByMitkImage(mitk::Image::Pointer _image)
-{
- this->m_Image = _image;
- this->m_cpuModified = true;
- this->m_gpuModified = false;
-
- this->m_gpuImage = nullptr;
-
- // compute the size of the GMEM buffer
- this->m_dim = this->m_Image->GetDimension();
- this->m_Dims = this->m_Image->GetDimensions();
- MITK_INFO << "Image: " << this->m_Dims[0] <<"x"<< this->m_Dims[1] <<"x"<< this->m_Dims[2];
-
- // get the dimensions
- this->m_bufferSize = 1;
- for (unsigned int i=0; i<this->m_dim; i++)
- {
- this->m_bufferSize *= this->m_Dims[i];
- }
-
- // multiply by sizeof(PixelType)
- this->m_BpE = ( this->m_Image->GetPixelType().GetBpe() / 8);
-}
-
-bool mitk::OclImage::IsModified(int _type)
-{
- if (_type) return m_cpuModified;
- else return m_gpuModified;
-}
-
-void mitk::OclImage::Modified(int _type)
-{
- // defines... GPU: 0, CPU: 1
- m_cpuModified = _type;
- m_gpuModified = !_type;
-}
-
-int mitk::OclImage::TransferDataToGPU(cl_command_queue gpuComQueue)
-{
- cl_int clErr = 0;
-
- // check whether an image present
- if (!m_Image->IsInitialized()){
- MITK_ERROR("ocl.Image") << "(mitk) Image not initialized!\n";
- return -1;
- }
-
- // there is a need for copy only if RAM-Data newer then GMEM data
- if (m_cpuModified)
- {
- //check the buffer
- if(m_gpuImage == nullptr)
- {
- clErr = this->AllocateGPUImage();
- }
-
- if (m_Image->IsInitialized() &&
- (clErr == CL_SUCCESS))
- {
- const size_t origin[3] = {0, 0, 0};
- const size_t region[3] = {m_Dims[0], m_Dims[1], m_Dims[2]};
-
- if( this->m_formatSupported )
- {
- mitk::ImageReadAccessor accessor(m_Image);
- clErr = clEnqueueWriteImage( gpuComQueue, m_gpuImage, CL_TRUE, origin, region, 0, 0, accessor.GetData(), 0, nullptr, nullptr);
- }
- else
- {
- MITK_ERROR << "Selected image format currently not supported...";
- }
-
- CHECK_OCL_ERR(clErr);
- }
- m_gpuModified = true;
- }
-
- return clErr;
-}
-
-cl_int mitk::OclImage::AllocateGPUImage()
-{
- cl_int clErr = 0;
-
- us::ServiceReference<OclResourceService> ref = GetModuleContext()->GetServiceReference<OclResourceService>();
- OclResourceService* resources = GetModuleContext()->GetService<OclResourceService>(ref);
-
- cl_context gpuContext = resources->GetContext();
-
- // initialize both proposed and supported format variables to same value
- this->m_proposedFormat = this->ConvertPixelTypeToOCLFormat();
- this->m_supportedFormat = this->m_proposedFormat;
-
- // test the current format for HW support
- this->m_formatSupported = resources->GetIsFormatSupported( &(this->m_supportedFormat) );
-
- // create an transfer kernel object in case the proposed format is not supported
- if( !(this->m_formatSupported) )
- {
- mitkThrowException(mitk::ImageTypeIsNotSupportedByGPU) << "Original format not supported on the installed graphics card.";
- }
-
-
- _cl_image_desc imageDescriptor;
-
- imageDescriptor.image_width = *(m_Dims);
- imageDescriptor.image_height = *(m_Dims + 1);
- imageDescriptor.image_depth = *(m_Dims + 2);
- imageDescriptor.image_array_size = 0;
- imageDescriptor.image_row_pitch = 0;
- imageDescriptor.image_slice_pitch = 0;
- imageDescriptor.num_mip_levels = 0;
- imageDescriptor.num_samples = 0;
- imageDescriptor.buffer = nullptr;
- // create new buffer
- if( this->m_dim > 2)
- {
- //Create a 3D Image
- imageDescriptor.image_type = CL_MEM_OBJECT_IMAGE3D;
- }
- else
- {
- //Create a 2D Image
- imageDescriptor.image_type = CL_MEM_OBJECT_IMAGE2D;
- }
- m_gpuImage = clCreateImage(gpuContext, CL_MEM_READ_ONLY, &m_supportedFormat, &imageDescriptor, nullptr, &clErr);
-
- CHECK_OCL_ERR(clErr);
-
- return clErr;
-}
-
-cl_mem mitk::OclImage::GetGPUImage(cl_command_queue gpuComQueue)
-{
- // clGetMemObjectInfo()
- cl_mem_object_type memInfo;
- cl_int clErr = 0;
-
- // query image object info only if already initialized
- if( this->m_gpuImage )
- {
- clErr = clGetMemObjectInfo(this->m_gpuImage, CL_MEM_TYPE, sizeof(cl_mem_object_type), &memInfo, nullptr );
- CHECK_OCL_ERR(clErr);
- }
-
- MITK_INFO << "Querying info for object, recieving: " << memInfo;
-
- // test if m_gpuImage CL_MEM_IMAGE_2/3D
- // if not, copy buffer to image
- if (memInfo == CL_MEM_OBJECT_BUFFER)
- {
- MITK_WARN << " Passed oclImage is a buffer-object, creating image";
-
- //hold a copy of the buffer gmem pointer
- cl_mem tempBuffer = this->m_gpuImage;
-
- const size_t origin[3] = {0, 0, 0};
- size_t region[3] = {this->m_Dims[0], this->m_Dims[1], 1};
-
- clErr = this->AllocateGPUImage();
-
- this->m_dim = 3;
-
- //copy last data to the image data
- clErr = clEnqueueCopyBufferToImage( gpuComQueue, tempBuffer, m_gpuImage, 0, origin, region, 0, nullptr, nullptr);
- CHECK_OCL_ERR(clErr);
-
- //release pointer
- clReleaseMemObject(tempBuffer);
- }
- return m_gpuImage;
-}
-
-void mitk::OclImage::SetPixelType(const cl_image_format *_image)
-{
- this->m_proposedFormat.image_channel_data_type = _image->image_channel_data_type;
- this->m_proposedFormat.image_channel_order = _image->image_channel_order;
-}
-
-void* mitk::OclImage::TransferDataToCPU(cl_command_queue gpuComQueue)
-{
- cl_int clErr = 0;
-
- // if image created on GPU, needs to create mitk::Image
- if( m_Image.IsNull() ){
- MITK_INFO << "Image not initialized, creating new one.";
- m_Image = mitk::Image::New();
- }
-
- // check buffersize/image size
- char* data = new char[m_bufferSize * m_BpE];
-
- // debug info
- oclPrintMemObjectInfo( m_gpuImage );
-
- clErr = clEnqueueReadBuffer( gpuComQueue, m_gpuImage, CL_FALSE, 0, m_bufferSize * m_BpE, data ,0, nullptr, nullptr);
- CHECK_OCL_ERR(clErr);
-
- clFlush( gpuComQueue );
- // the cpu data is same as gpu
- this->m_gpuModified = false;
-
- return (void*) data;
-}
-
-cl_image_format mitk::OclImage::ConvertPixelTypeToOCLFormat()
-{
- cl_image_format texFormat;
- //single channel Gray-Valued Images
- texFormat.image_channel_order = CL_R;
-
- MITK_INFO << "Class own value: " << this->m_BpE;
-
- switch ( this->m_BpE )
- {
- case 1:
- texFormat.image_channel_data_type = CL_UNSIGNED_INT8;
- MITK_INFO<< "PixelType: UCHAR => CLFormat: [CL_UNORM_INT8, CL_R]";
- break;
- case 2:
- texFormat.image_channel_data_type = CL_SIGNED_INT16;
- // texFormat.image_channel_order = CL_R;
- MITK_INFO<< "PixelType: SHORT => CLFormat: [CL_SIGNED_INT16, CL_R]";
- break;
- case 4:
- texFormat.image_channel_data_type = CL_FLOAT;
- MITK_INFO<< "Choosing CL_FLOAT";
- break;
- default:
- texFormat.image_channel_data_type = CL_UNORM_INT8;
- texFormat.image_channel_order = CL_RG;
- MITK_INFO<< "Choosing (default) short: 2-Channel UCHAR";
- break;
- }
-
- return texFormat;
-}
-
-int mitk::OclImage::GetDimension(int idx) const
-{
- if (this->m_dim > idx)
- {
- return m_Dims[idx];
- }
- else
- {
- MITK_WARN << "Trying to access non-existing dimension.";
- return 1;
- }
-}
-
-void mitk::OclImage::SetDimensions(unsigned int* Dims)
-{
- m_Dims = Dims;
-}
-
-void mitk::OclImage::SetDimension(unsigned short dim)
-{
- m_dim = dim;
-}
-
-float mitk::OclImage::GetSpacing(int idx)
-{
- if (this->m_dim > idx)
- {
- const mitk::Vector3D imSpacing = m_Image->GetSlicedGeometry()->GetSpacing();
-
- return imSpacing[idx];
- }
- else
- {
- MITK_WARN << "Trying to access non-existing dimension.";
- return 1;
- }
-}
-
-void mitk::OclImage::InitializeMITKImage()
-{
- this->m_Image = mitk::Image::New();
-}
-
-void mitk::OclImage::GetOffset(float* _imOffset) const
-{
- itk::Vector<float, 3> result2;
- result2.Fill(0.0f);
-
- result2 = this->m_Image->GetGeometry()->GetIndexToWorldTransform()->GetOffset();
-
- _imOffset[0] = result2[0];
- _imOffset[1] = result2[1];
- _imOffset[2] = result2[2];
-}
diff --git a/Modules/OpenCL/mitkOclImage.h b/Modules/OpenCL/mitkOclImage.h
deleted file mode 100644
index f42eff6dce..0000000000
--- a/Modules/OpenCL/mitkOclImage.h
+++ /dev/null
@@ -1,201 +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 mitkOclImage_h
-#define mitkOclImage_h
-
-#define GPU_DATA 0
-#define CPU_DATA 1
-
-#define MAX_DIMS 20
-
-#include <mitkImage.h>
-#include "MitkOpenCLExports.h"
-
-#include "mitkOclBaseData.h"
-#include "mitkOclImageFormats.h"
-#include "mitkOpenCLActivator.h"
-
-#include <mitkException.h>
-
-
-#define SHORT_IM mitk::MakeScalarPixelType<short>()
-#define FLOAT_IM mitk::MakeScalarPixelType<float>()
-
-namespace mitk {
-
-/*!
- * \brief Class implementing the image format for GPU Image Processing
- *
- * The class holds a pointer to the mitk::Image stored in RAM and performs an
- * on-demand-copy to the graphics memory. It is the basic data structure for all
- * mitk::oclImageToImageFilter classes
- * @throw This class may throw an ImageTypeIsNotSupportedByGPU, if the image
- * format is supported by the GPU.
- */
-class MITKOPENCL_EXPORT OclImage : public OclBaseData
-{
-public:
- mitkClassMacro(OclImage, OclBaseData);
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- /*! \brief Copies the RAM-stored data to GMEM */
- virtual int TransferDataToGPU(cl_command_queue);
-
- /*! \brief Copies the in GMEM stored data to RAM */
- virtual void* TransferDataToCPU(cl_command_queue);
-
- /*! \brief Returns the pointer to the referenced mitk::Image */
- Image::Pointer GetMITKImage()
- {
- return m_Image;
- }
-
- /*! \brief Checks whether gpuImage is a valid clImage object
-
- when an oclImage gets created by an image to image filter, the output image is created
- by clCreateBuffer() because it is not in general possible to write to clImage directly
- */
- cl_mem GetGPUImage(cl_command_queue);
-
- /** Returns the pointer to the GPU buffer */
- cl_mem GetGPUBuffer()
- {
- return this->m_gpuImage;
- }
-
- /** Create the GPU buffer for image
- *
- */
- cl_mem CreateGPUImage(unsigned int, unsigned int, unsigned int, unsigned int);
-
- /** \brief Returns the status of the image buffer
- *
- * @param _type The flag to specify the buffer type ( GPU / CPU )
- */
- bool IsModified(int _type);
-
- using OclBaseData::Modified;
- /** \brief Set the modified flag for one of the buffers
- *
- * @param _type The flag to specify the buffer type ( GPU / CPU )
- */
- void Modified(int _type);
-
- /** @brief Initialize the internal variable of type mitk::Image.
- */
- void InitializeMITKImage();
-
- /** \brief Initialze the OclImage with an mitkImage. */
- void InitializeByMitkImage(mitk::Image::Pointer _image);
-
- /*! \brief returns the specified image dimension size */
- int GetDimension(int) const;
-
- /*! \brief returns the dimensionality of the image */
- int GetDimension() const
- {
- return this->m_dim;
- }
-
- /*! \brief returns the pointer to the array of image sizes */
- unsigned int* GetDimensions(){ return this->m_Dims; }
-
- /*! \brief returns the spacing of the image for specified dimension */
- float GetSpacing(int);
-
- /*! \brief Returns the image offset (needed for WorldToIndex Transform */
- void GetOffset(float*) const;
-
- /** @brief Set the pixel type for the image to be used
- */
- void SetPixelType(const cl_image_format*);
-
- short GetBytesPerPixel() const
- {
- return this->m_BpE;
- }
-
- /** @brief Get the currently used pixel type
-
- @returns OpenCL Image Format struct
- */
- const cl_image_format* GetPixelType() const
- {
- return &(this->m_proposedFormat);
- }
-
- /** @brief Set the image dimensions through an unsigned int array */
- void SetDimensions(unsigned int* Dims);
-
- /** @brief Set the dimensionality of the image */
- void SetDimension(unsigned short dim);
-
-protected:
- /*! \brief Constructor */
- OclImage();
-
- /** @brief Destructor */
- virtual ~OclImage();
-
- /*! GMEM Image buffer */
- cl_mem m_gpuImage;
-
- /*! GPU Context the Image Buffer was created in, needed for access */
- cl_context m_context;
-
- /*! GMEM Buffer Size */
- unsigned int m_bufferSize;
-
-private:
-
- cl_image_format ConvertPixelTypeToOCLFormat();
-
- bool m_gpuModified;
- bool m_cpuModified;
-
- /*! Reference to mitk::Image */
- Image::Pointer m_Image;
-
- unsigned short m_dim;
-
- unsigned int* m_Dims;
-
- unsigned short m_BpE;
-
- cl_int AllocateGPUImage();
-
- /** Bool flag to signalize if the proposed format is supported on currend HW.
- For value 'false', the transfer kernel has to be called to fit the data to
- the supported format */
- bool m_formatSupported;
-
- /** Supported format, defined using oclImageFormats */
- cl_image_format m_supportedFormat;
-
- /** Proposed format for image */
- cl_image_format m_proposedFormat;
-};
-
-/**
- * @brief The ImageTypeIsNotSupportedByGPU class specialized exception class for unsupported
- * image formats. If this exception is thrown, try other graphics device.
- */
-class ImageTypeIsNotSupportedByGPU : public Exception
-{
-public:
- mitkExceptionClassMacro(ImageTypeIsNotSupportedByGPU,Exception)
-};
-
-}
-#endif
diff --git a/Modules/OpenCL/mitkOclImageFilter.cpp b/Modules/OpenCL/mitkOclImageFilter.cpp
deleted file mode 100644
index fabd1b473b..0000000000
--- a/Modules/OpenCL/mitkOclImageFilter.cpp
+++ /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.
-
-============================================================================*/
-
-#include "mitkOclImageFilter.h"
-#include "mitkOclFilter.h"
-#include "mitkOclImage.h"
-
-mitk::OclImageFilter::OclImageFilter()
-{
- // set the filter type to default value = SHORT
- this->m_CurrentType = FILTER_SHORT;
-}
-
-mitk::OclImageFilter::~OclImageFilter()
-{
-}
-
-void mitk::OclImageFilter::SetInput(mitk::OclImage::Pointer image)
-{
- m_Input = image;
-}
-
-void mitk::OclImageFilter::SetInput(mitk::Image::Pointer image)
-{
- m_Input = mitk::OclImage::New();
- m_Input->InitializeByMitkImage(image);
-
- // update current size
- MITK_DEBUG << "Current Type was: " << this->m_CurrentType;
- this->m_CurrentType = m_Input->GetBytesPerPixel() - 1;
- MITK_DEBUG << "Current Type is: " << this->m_CurrentType;
-}
-
diff --git a/Modules/OpenCL/mitkOclImageFilter.h b/Modules/OpenCL/mitkOclImageFilter.h
deleted file mode 100644
index 4cdc41f939..0000000000
--- a/Modules/OpenCL/mitkOclImageFilter.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 mitkOclImageFilter_h
-#define mitkOclImageFilter_h
-
-#include "mitkOclFilter.h"
-#include "mitkOclImage.h"
-
-#define FILTER_UCHAR 0
-#define FILTER_SHORT 1
-
-namespace mitk
-{
-class OclFilter;
-class OclImageFilter;
-
- /**
- * \brief The OclImageFilter is the topmost class for all filter which take images as input.
- *
- * The input image can be intialized via an oclImage or an mitk::Image.
- * This makes it possible to create a filter pipeline of GPU-based filters
- * and to bind this part into the CPU (ITK) filter pipeline.
- */
-class MITKOPENCL_EXPORT OclImageFilter: public OclFilter
-{
-public:
- /**
- * @brief SetInput SetInput Set the input image (as mitk::OclImage).
- * @param image The image in mitk::OclImage.
- */
- void SetInput(mitk::OclImage::Pointer image);
-
- /**
- * @brief SetInput Set the input image (as mitk::Image).
- * @param image The image in mitk::Image.
- */
- void SetInput(mitk::Image::Pointer image);
-
-protected:
- OclImageFilter();
-
- virtual ~OclImageFilter();
-
- /** The input image */
- mitk::OclImage::Pointer m_Input;
-
- /*! Current (last used) image pixel type */
- short m_CurrentType;
-};
-}
-#endif
diff --git a/Modules/OpenCL/mitkOclImageFormats.cpp b/Modules/OpenCL/mitkOclImageFormats.cpp
deleted file mode 100644
index 89f3a1a002..0000000000
--- a/Modules/OpenCL/mitkOclImageFormats.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 "mitkOclImageFormats.h"
-
-mitk::OclImageFormats::OclImageFormats()
- :m_Image2DSupport( nullptr ), m_Image3DSupport( nullptr ),
- m_GpuContext( nullptr )
-{
- //todo: what happens here?
- const unsigned int matrixSize = MAX_FORMATS * MAX_DATA_TYPES;
-
- this->m_Image2DSupport = new unsigned char[matrixSize];
- this->m_Image3DSupport = new unsigned char[matrixSize];
-
- for( unsigned int i = 0; i<matrixSize; i++ )
- {
- this->m_Image2DSupport[i] = 0;
- this->m_Image3DSupport[i] = 0;
- }
-}
-
-mitk::OclImageFormats::~OclImageFormats()
-{
-}
-
-void mitk::OclImageFormats::PrintSelf()
-{
- std::stringstream outputstream;
- outputstream << "Values: Read-Write(1) ReadOnly(2) , WriteOnly(4) \n";
- outputstream << "ROWS: [CL_A, CL_R, CL_RA, CL_RG, CL_RGB, CL_RGBA, CL_ARGB, CL_BGRA, CL_LUM, CL_INT] \n";
-
- const unsigned int matrixSize = MAX_FORMATS * MAX_DATA_TYPES;
-
- for( unsigned int i = 0; i<matrixSize; i++ )
- {
- outputstream << (int) this->m_Image2DSupport[i] << ", \t";
- if( (i+1) % MAX_DATA_TYPES == 0 )
- outputstream << " \n";
- }
- outputstream << "========================== \n";
-
- for( unsigned int i = 0; i<matrixSize; i++ )
- {
- outputstream << (int) this->m_Image3DSupport[i] << ", \t";
- if( (i+1) % MAX_DATA_TYPES == 0 )
- outputstream << " \n";
- }
- MITK_INFO << outputstream.str();
-}
-
-unsigned int mitk::OclImageFormats::GetOffset(cl_image_format format)
-{
- //todo: what happens here?
- unsigned int offset = 0;
-
- switch( format.image_channel_order )
- {
- case CL_A:
- break;
- case CL_R:
- offset += 1 * MAX_DATA_TYPES;
- break;
- case CL_RA:
- offset += 2 * MAX_DATA_TYPES;
- break;
- case CL_RG:
- offset += 3 * MAX_DATA_TYPES;
- break;
- case CL_RGB:
- offset += 4 * MAX_DATA_TYPES;
- break;
- case CL_RGBA:
- offset += 5 * MAX_DATA_TYPES;
- break;
- case CL_ARGB:
- offset += 6 * MAX_DATA_TYPES;
- break;
- case CL_BGRA:
- offset += 7 * MAX_DATA_TYPES;
- break;
- case CL_LUMINANCE:
- offset += 8 * MAX_DATA_TYPES;
- break;
- case CL_INTENSITY:
- offset += 9 * MAX_DATA_TYPES;
- break;
- }
-
- switch ( format.image_channel_data_type )
- {
- case CL_SNORM_INT8:
- break;
- case CL_SNORM_INT16:
- offset += 1;
- break;
- case CL_UNORM_INT8:
- offset += 2;
- break;
- case CL_UNORM_INT16:
- offset += 3;
- break;
- case CL_SIGNED_INT8:
- offset += 4;
- break;
- case CL_SIGNED_INT16:
- offset += 5;
- break;
- case CL_SIGNED_INT32:
- offset += 6;
- break;
- case CL_UNSIGNED_INT8:
- offset += 7;
- break;
- case CL_UNSIGNED_INT16:
- offset += 8;
- break;
- case CL_UNSIGNED_INT32:
- offset += 9;
- break;
- case CL_HALF_FLOAT:
- offset += 10;
- break;
- case CL_FLOAT:
- offset += 11;
- break;
- }
-
- return offset;
-}
-
-bool mitk::OclImageFormats::IsFormatSupported(cl_image_format* format)
-{
- bool retVal = false;
-
- // FIXME needs finer subdivision...
- //todo: Comment above???
- if ( this->m_Image2DSupport[ GetOffset(*format)] > 4 )
- retVal = true;
-
- return retVal;
-}
-
-bool mitk::OclImageFormats::GetNearestSupported(cl_image_format *inputformat, cl_image_format *outputformat)
-{
- bool returnValue = false;
-
- // init output format
- outputformat->image_channel_data_type = inputformat->image_channel_data_type;
- outputformat->image_channel_order = inputformat->image_channel_order;
-
- // the input format is supported, just copy the information into out
- if( this->IsFormatSupported(inputformat) )
- {
- returnValue = true;
- }
- else
- {
- // get the 'nearest' format
- // try RGBA first
- //todo: It seems like ONLY RGBA is considered to be near?!? Either code or docu should be adapted.
- cl_image_format test;
- test.image_channel_order = CL_RGBA;
- test.image_channel_data_type = inputformat->image_channel_data_type;
-
- if(this->IsFormatSupported( &test) )
- {
- outputformat->image_channel_order = CL_RGBA;
- }
- }
- return returnValue;
-}
-
-void mitk::OclImageFormats::SetGPUContext(cl_context context)
-{
- this->m_GpuContext = context;
- //collect available formats can now be called
- this->CollectAvailableFormats();
-}
-
-void mitk::OclImageFormats::SortFormats(cl_image_format *formats, cl_uint count, int val, int dims)
-{
- //todo what happens here?
- unsigned char *target = this->m_Image2DSupport;
- if (dims == 3)
- {
- target = this->m_Image3DSupport;
- }
-
- for( unsigned int i=0; i<count; i++)
- {
- // each supported format => +1
- target[ this->GetOffset( formats[i] ) ]+=val;
- }
-}
-
-void mitk::OclImageFormats::CollectAvailableFormats()
-{
- if( this->m_GpuContext == nullptr)
- {
- mitkThrow() << "No GPU context was set! Use SetGPUContext() before calling this method!";
- }
- //todo what happens here?
- const unsigned int entries = 100;
- cl_image_format* formats = new cl_image_format[entries];
-
- cl_uint written = 0;
- cl_int clErr = 0;
-
- // GET formats for R/W, 2D
- clErr = clGetSupportedImageFormats( m_GpuContext, CL_MEM_READ_WRITE, CL_MEM_OBJECT_IMAGE2D, entries, formats, &written);
- CHECK_OCL_ERR( clErr );
-
- this->SortFormats( formats, written, 1 );
-
- // GET formats for R/-, 2D
- written = 0;
- clErr = clGetSupportedImageFormats( m_GpuContext, CL_MEM_READ_ONLY, CL_MEM_OBJECT_IMAGE2D, entries, formats, &written);
- CHECK_OCL_ERR( clErr );
-
- this->SortFormats( formats, written, 2 );
-
- // GET formats for -/W, 2D
- written = 0;
- clErr = clGetSupportedImageFormats( m_GpuContext, CL_MEM_WRITE_ONLY, CL_MEM_OBJECT_IMAGE2D, entries, formats, &written);
- CHECK_OCL_ERR( clErr );
-
- this->SortFormats( formats, written, 4 );
- //-----------------------
-
-
- // GET formats for R/W, 3D
- written = 0;
- clErr = clGetSupportedImageFormats( m_GpuContext, CL_MEM_READ_WRITE, CL_MEM_OBJECT_IMAGE3D, entries, formats, &written);
- CHECK_OCL_ERR( clErr );
-
- this->SortFormats( formats, written, 1, 3 );
-
- // GET formats for R/-, 3D
- written = 0;
- clErr = clGetSupportedImageFormats( m_GpuContext, CL_MEM_READ_ONLY, CL_MEM_OBJECT_IMAGE3D, entries, formats, &written);
- CHECK_OCL_ERR( clErr );
-
- this->SortFormats( formats, written, 2, 3 );
-
- // GET formats for -/W, 3D
- written = 0;
- clErr = clGetSupportedImageFormats( m_GpuContext, CL_MEM_WRITE_ONLY, CL_MEM_OBJECT_IMAGE3D, entries, formats, &written);
- CHECK_OCL_ERR( clErr );
-
- this->SortFormats( formats, written, 4, 3 );
-}
diff --git a/Modules/OpenCL/mitkOclImageFormats.h b/Modules/OpenCL/mitkOclImageFormats.h
deleted file mode 100644
index 08b5a4cd8d..0000000000
--- a/Modules/OpenCL/mitkOclImageFormats.h
+++ /dev/null
@@ -1,118 +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 mitkOclImageFormats_h
-#define mitkOclImageFormats_h
-
-//mitk
-#include <mitkCommon.h>
-#include <mitkLog.h>
-
-//itk
-#include <itkLightObject.h>
-#include <itkObjectFactory.h>
-
-//ocl
-#include "mitkOclUtils.h"
-#include <MitkOpenCLExports.h>
-
-#define MAX_FORMATS 10
-#define MAX_DATA_TYPES 12
-
-namespace mitk
-{
-
-/**
- @class oclImageFormats
- @brief A class handling the (un)supported OpenCL Image formats.
-
- This class checks whether a format is supported or not and acts accordingly.
- */
-class MITKOPENCL_EXPORT OclImageFormats : public itk::LightObject
-{
-public:
- mitkClassMacroItkParent(OclImageFormats, itk::LightObject);
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- /** @brief Checks if format supported.
- @param format The image format to be checked for support.
- @return True if the parameter is supported.
- */
- bool IsFormatSupported(cl_image_format* format);
-
- /** @brief Finds one supported image format similar to the given format.
-
- In case the input format is supported, the output format will contain the same value.
-
- @param inputformat The (unsupported) image format
- @param outputformat A supported image format
-
- @return True if a supported format was changed.
- */
- bool GetNearestSupported(cl_image_format* inputformat, cl_image_format* outputformat);
-
- /**
- * @brief SetGPUContext Set the GPU context. Must be called before using this class!
- * @param context GPU context in cl format.
- */
- void SetGPUContext( cl_context context );
-
-
-protected:
- /** @brief Get and store all available infos
- * @throw Throws an mitk::Exception if the GPU context was not defined.
- */
- void CollectAvailableFormats();
-
- /**
- * @brief OclImageFormats Constructor
- */
- OclImageFormats();
-
- /** @brief Destructor (default) */
- virtual ~OclImageFormats();
-
-private:
-
- /** @brief Store the given format into the table
- * Todo: what table? Where? Why is it called sort?
- @param formats A pointer to an array of image formats
- Todo: What formats?
- @param count Size of the formats array (i.e. how many formats are to be sorted).
- @param val an intern value to distinguish between read/write/readwrite type
- Todo: what is val?
- @param dim Specifies the target image dimension (default IMAGE_2D).
- */
- void SortFormats( cl_image_format* formats, cl_uint count, int val=1 , int dims = 2);
-
- /** @brief Get the byte offset to the image support fields.
- Todo: What means support field? What is this offset used for? In what unit is it returned?*/
- unsigned int GetOffset( cl_image_format format );
-
- using itk::LightObject::PrintSelf;
- /** @brief Print all supported formats (in a table) for both 2D and 3D IMAGE */
- void PrintSelf();
-
- /** An array to hold the information about IMAGE_2D supported formats. */
- unsigned char* m_Image2DSupport;
-
- /** An array to hold the information about IMAGE_3D supported formats. */
- unsigned char* m_Image3DSupport;
-
- /** the OpenCL context */
- cl_context m_GpuContext;
-};
-
-}
-
-#endif
diff --git a/Modules/OpenCL/mitkOclImageToImageFilter.cpp b/Modules/OpenCL/mitkOclImageToImageFilter.cpp
deleted file mode 100644
index 014a62b45f..0000000000
--- a/Modules/OpenCL/mitkOclImageToImageFilter.cpp
+++ /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.
-
-============================================================================*/
-
-#include "mitkOclImageToImageFilter.h"
-#include "mitkOclImage.h"
-
-#include "mitkException.h"
-
-mitk::OclImageToImageFilter::OclImageToImageFilter()
-{
- m_Output = mitk::OclImage::New();
-}
-
-
-mitk::OclImageToImageFilter::~OclImageToImageFilter()
-{
-}
-
-mitk::OclImage::Pointer mitk::OclImageToImageFilter::GetGPUOutput()
-{
- // initialize some variables
- m_Output->SetPixelType(m_Input->GetPixelType());
-
- // create new image, for passing the essential information to the output
- m_Output->InitializeMITKImage();
-
- const unsigned int dimension = m_Input->GetDimension();
- unsigned int* dimensions = m_Input->GetDimensions();
-
- m_Output->SetDimensions( dimensions );
- m_Output->SetDimension( (unsigned short)dimension );
-
- m_Output->GetMITKImage()->Initialize( this->GetOutputType(), dimension, dimensions);
- const mitk::SlicedGeometry3D::Pointer p_slg = m_Input->GetMITKImage()->GetSlicedGeometry(0);
- m_Output->GetMITKImage()->SetSpacing( p_slg->GetSpacing() );
- m_Output->GetMITKImage()->SetGeometry( m_Input->GetMITKImage()->GetGeometry() );
-
- return this->m_Output;
-
-}
-
-mitk::Image::Pointer mitk::OclImageToImageFilter::GetOutput()
-{
- if (m_Output->IsModified(GPU_DATA))
- {
- void* pData = m_Output->TransferDataToCPU(m_CommandQue);
-
- const unsigned int dimension = m_Input->GetDimension();
- unsigned int* dimensions = m_Input->GetDimensions();
-
- const mitk::SlicedGeometry3D::Pointer p_slg = m_Input->GetMITKImage()->GetSlicedGeometry();
-
- MITK_DEBUG << "Creating new MITK Image.";
-
- m_Output->GetMITKImage()->Initialize( this->GetOutputType(), dimension, dimensions);
- m_Output->GetMITKImage()->SetSpacing( p_slg->GetSpacing());
- m_Output->GetMITKImage()->SetGeometry( m_Input->GetMITKImage()->GetGeometry() );
- m_Output->GetMITKImage()->SetImportVolume( pData, 0, 0, mitk::Image::ReferenceMemory);
- }
-
- MITK_DEBUG << "Image Initialized.";
-
- return m_Output->GetMITKImage();
-}
-
-mitk::PixelType mitk::OclImageToImageFilter::GetOutputType()
-{
- // get the current image format from the input image
- const cl_image_format* currentImFormat = this->m_Input->GetPixelType();
-
- // return the value according to the current channel type
- switch( currentImFormat->image_channel_data_type )
- {
- case CL_UNORM_INT8:
- return mitk::MakeScalarPixelType<unsigned char>();
- case CL_UNSIGNED_INT8:
- return mitk::MakeScalarPixelType<unsigned char>();
- case CL_UNORM_INT16:
- return mitk::MakeScalarPixelType<short>();
- default:
- return mitk::MakeScalarPixelType<short>();
- }
-}
-
-int mitk::OclImageToImageFilter::GetBytesPerElem()
-{
- return (this->m_CurrentType + 1);
-}
-
-bool mitk::OclImageToImageFilter::InitExec(cl_kernel ckKernel)
-{
- cl_int clErr = 0;
-
- if( m_Input.IsNull() )
- mitkThrow() << "Input image is null.";
-
- // get image size once
- const unsigned int uiImageWidth = m_Input->GetDimension(0);
- const unsigned int uiImageHeight = m_Input->GetDimension(1);
- const unsigned int uiImageDepth = m_Input->GetDimension(2);
-
- // compute work sizes
- this->SetWorkingSize( 8, uiImageWidth, 8, uiImageHeight , 8, uiImageDepth );
-
- cl_mem clBuffIn = m_Input->GetGPUImage(this->m_CommandQue);
- cl_mem clBuffOut = m_Output->GetGPUBuffer();
-
- if (!clBuffIn)
- {
- if ( m_Input->TransferDataToGPU(m_CommandQue) != CL_SUCCESS )
- {
- mitkThrow()<< "Could not create / initialize gpu image.";
- }
-
- clBuffIn = m_Input->GetGPUImage(m_CommandQue);
- }
-
- // output image not initialized
- if (!clBuffOut)
- {
- //TODO bpp, or SetImageWidth/Height/...
- MITK_DEBUG << "Create GPU Image call " << uiImageWidth<< "x"<<uiImageHeight<< "x"<<uiImageDepth;
- clBuffOut = m_Output->CreateGPUImage(uiImageWidth, uiImageHeight, uiImageDepth, this->m_CurrentType + 1);
- }
-
- clErr = 0;
- clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffIn);
- clErr |= clSetKernelArg(ckKernel, 1, sizeof(cl_mem), &clBuffOut);
- CHECK_OCL_ERR( clErr );
-
- if( clErr != CL_SUCCESS )
- mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr);
-
- return( clErr == CL_SUCCESS );
-}
-
- bool mitk::OclImageToImageFilter::InitExec(cl_kernel ckKernel, unsigned int* dimensions)
- {
- cl_int clErr = 0;
-
- if( m_Input.IsNull() )
- mitkThrow() << "Input image is null.";
-
- // get image size once
- const unsigned int uiImageWidth = dimensions[0];
- const unsigned int uiImageHeight = dimensions[1];
- const unsigned int uiImageDepth = dimensions[2]+1;
-
- // compute work sizes
- this->SetWorkingSize( 8, uiImageWidth, 8, uiImageHeight , 8, uiImageDepth );
-
- cl_mem clBuffIn = m_Input->GetGPUImage(this->m_CommandQue);
- cl_mem clBuffOut = m_Output->GetGPUBuffer();
-
- if (!clBuffIn)
- {
- if ( m_Input->TransferDataToGPU(m_CommandQue) != CL_SUCCESS )
- {
- mitkThrow()<< "Could not create / initialize gpu image.";
- }
-
- clBuffIn = m_Input->GetGPUImage(m_CommandQue);
- }
-
- // output image not initialized
- //TODO bpp, or SetImageWidth/Height/...
- MITK_INFO << "Create GPU Image call " << uiImageWidth<< "x"<<uiImageHeight<< "x"<<uiImageDepth;
- clBuffOut = m_Output->CreateGPUImage(uiImageWidth, uiImageHeight, uiImageDepth, this->m_CurrentType + 1);
-
-
- clErr = 0;
- clErr = clSetKernelArg(ckKernel, 0, sizeof(cl_mem), &clBuffIn);
- clErr |= clSetKernelArg(ckKernel, 1, sizeof(cl_mem), &clBuffOut);
- CHECK_OCL_ERR( clErr );
-
- if( clErr != CL_SUCCESS )
- mitkThrow() << "OpenCL Part initialization failed with " << GetOclErrorAsString(clErr);
-
- return( clErr == CL_SUCCESS );
-}
diff --git a/Modules/OpenCL/mitkOclImageToImageFilter.h b/Modules/OpenCL/mitkOclImageToImageFilter.h
deleted file mode 100644
index 9e0af08e72..0000000000
--- a/Modules/OpenCL/mitkOclImageToImageFilter.h
+++ /dev/null
@@ -1,78 +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 mitkOclImageToImageFilter_h
-#define mitkOclImageToImageFilter_h
-
-#include "mitkOclImageFilter.h"
-
-namespace mitk
-{
-class OclImageFilter;
-class OclImageToImageFilter;
-
-/** @class OclImageToImageFilter
- * @brief The OclImageToImageFilter is the base class for all OpenCL image filter generating images.
- */
-class MITKOPENCL_EXPORT OclImageToImageFilter: public OclImageFilter
-{
-public:
- /*!
- * \brief Returns an mitk::Image::Pointer containing the filtered data.
- */
- mitk::Image::Pointer GetOutput();
-
- /*!
- * \brief Returns a pointer to the graphics memory.
- *
- * Use this method when executing two and more filters on the GPU for fast access.
- * This method does not copy the data to RAM. It returns only a pointer.
- */
- mitk::OclImage::Pointer GetGPUOutput();
-
-protected:
- /**
- * @brief OclImageToImageFilter Default constructor.
- */
- OclImageToImageFilter();
-
- /** @brief Destructor */
- virtual ~OclImageToImageFilter();
-
- /** Output Image */
- mitk::OclImage::Pointer m_Output;
-
- /** @brief (Virtual) method Update() to be implemented in derived classes. */
- virtual void Update() = 0;
-
- /** @brief (Virtual) method returning the format in which the output image will be returned */
- virtual mitk::PixelType GetOutputType();
-
- /**
- * @brief InitExec Initialize the execution
- * @param ckKernel The GPU kernel.
- * @throws mitk::Exception if something goes wrong.
- * @return True for success.
- */
- bool InitExec(cl_kernel ckKernel);
- bool InitExec(cl_kernel ckKernel, unsigned int* dimensions);
-
- /** @brief Get the memory size needed for each element */
- virtual int GetBytesPerElem();
-
-private:
- /** Block dimensions */
- unsigned int m_BlockDims[3];
-
-};
-}
-#endif
diff --git a/Modules/OpenCL/mitkOclResourceService.h b/Modules/OpenCL/mitkOclResourceService.h
deleted file mode 100644
index cc4762bbf1..0000000000
--- a/Modules/OpenCL/mitkOclResourceService.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 mitkOclResourceService_h
-#define mitkOclResourceService_h
-
-#include <mitkServiceInterface.h>
-
-#include <mitkOpenCL.h>
-
-/**
- * @brief Declaration of the OpenCL Resources micro-service
- *
- * The OclResourceService defines an service interface for providing access to the
- * essential OpenCL-related variables. In addition the service can also store compiled
- * OpenCL Programs in order to avoid multiple compiling of a single program source
- */
-class OclResourceService
-{
-public:
- /** @brief Returns a valid OpenCL Context (if applicable) or nullptr if none present */
- virtual cl_context GetContext() const = 0;
-
- /** @brief Returns a valid cl_command_queue related to the (one) OpenCL context */
- virtual cl_command_queue GetCommandQueue() const = 0;
-
- /** @brief Returns the identifier of an OpenCL device related to the current context */
- virtual cl_device_id GetCurrentDevice() const = 0;
-
- /** @brief Checks if an OpenCL image format passed in is supported on current device */
- virtual bool GetIsFormatSupported( cl_image_format* format ) = 0;
-
- /** @brief Puts the OpenCL Context info in std::cout */
- virtual void PrintContextInfo() const = 0;
-
- /** @brief Insert program into the internal program storage
- *
- * @param program A cl_program object.
- * @param string Text identifier of the inserted program. Used for getting the program.
- * @param flag
- */
- virtual void InsertProgram(cl_program program, std::string string, bool flag) = 0;
-
- /** @brief Get the cl_program by name
- * @param name Text identifier of the program.
- * @throws an mitk::Exception in case the program cannot be found
- */
- virtual cl_program GetProgram(const std::string& name) = 0;
-
- /** @brief Remove all invalid (=do not compile) programs from the internal storage */
- virtual void InvalidateStorage() = 0;
-
- /** @brief Remove given program from storage
- * @param name Text identifier of the program.
- */
- virtual void RemoveProgram(const std::string& name) = 0;
-
- /** @brief Get the maximum size of an image
- *
- * @param dimension (unsigned int) identifier of the image diemsion in {0,1,2}
- * @param image object type, either CL_MEM_OBJECT_IMAGE2D, CL_MEM_OBJECT_IMAGE3D
- */
- virtual unsigned int GetMaximumImageSize(unsigned int dimension, cl_mem_object_type image) = 0;
-
- virtual ~OclResourceService() = 0;
-
-};
-
-MITK_DECLARE_SERVICE_INTERFACE(OclResourceService, "OpenCLResourceService/1.0")
-#endif
diff --git a/Modules/OpenCL/mitkOclResourceServiceImpl_Private.cpp b/Modules/OpenCL/mitkOclResourceServiceImpl_Private.cpp
deleted file mode 100644
index 7de7e51e4d..0000000000
--- a/Modules/OpenCL/mitkOclResourceServiceImpl_Private.cpp
+++ /dev/null
@@ -1,256 +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 "mitkOclResourceServiceImpl_p.h"
-
-OclResourceService::~OclResourceService()
-{
-}
-
-OclResourceServiceImpl::OclResourceServiceImpl()
- : m_ContextCollection(nullptr), m_ProgramStorage()
-{
- m_ProgramStorageMutex = itk::FastMutexLock::New();
-}
-
-OclResourceServiceImpl::~OclResourceServiceImpl()
-{
- // if map non-empty, release all remaining
- if( m_ProgramStorage.size() )
- {
- ProgramMapType::iterator it = m_ProgramStorage.begin();
- while(it != m_ProgramStorage.end() )
- {
- clReleaseProgram( it->second.program );
- m_ProgramStorage.erase( it++ );
- }
- }
-
- if( m_ContextCollection )
- delete m_ContextCollection;
-}
-
-cl_context OclResourceServiceImpl::GetContext() const
-{
- if( m_ContextCollection == nullptr )
- {
- m_ContextCollection = new OclContextCollection();
- }
- else if( !m_ContextCollection->CanProvideContext() )
- {
- return nullptr;
- }
-
- return m_ContextCollection->m_Context;
-}
-
-cl_command_queue OclResourceServiceImpl::GetCommandQueue() const
-{
- // check if queue valid
- cl_context clQueueContext;
-
- // check if there is a context available
- // if not create one
- if( ! m_ContextCollection )
- {
- m_ContextCollection = new OclContextCollection();
- }
-
- cl_int clErr = clGetCommandQueueInfo( m_ContextCollection->m_CommandQueue, CL_QUEUE_CONTEXT, sizeof(clQueueContext), &clQueueContext, nullptr );
- if( clErr != CL_SUCCESS || clQueueContext != m_ContextCollection->m_Context )
- {
- MITK_WARN << "Have no valid command queue. Query returned : " << GetOclErrorAsString( clErr );
- return nullptr;
- }
-
- return m_ContextCollection->m_CommandQueue;
-}
-
-cl_device_id OclResourceServiceImpl::GetCurrentDevice() const
-{
- return m_ContextCollection->m_Devices[0];
-}
-
-bool OclResourceServiceImpl::GetIsFormatSupported(cl_image_format *fmt)
-{
- cl_image_format temp;
- temp.image_channel_data_type = fmt->image_channel_data_type;
- temp.image_channel_order = fmt->image_channel_order;
-
- return (this->m_ContextCollection->m_ImageFormats->GetNearestSupported(&temp, fmt));
-}
-
-void OclResourceServiceImpl::PrintContextInfo() const
-{
- // context and devices available
- if( m_ContextCollection->CanProvideContext() )
- {
- oclPrintDeviceInfo( m_ContextCollection->m_Devices[0] );
- }
-}
-
-void OclResourceServiceImpl::InsertProgram(cl_program _program_in, std::string name, bool forceOverride)
-{
- typedef std::pair < std::string, ProgramData > MapElemPair;
- std::pair< ProgramMapType::iterator, bool> retValue;
-
- ProgramData data;
- data.counter = 1;
- data.program = _program_in;
- data.mutex = itk::FastMutexLock::New();
-
- // program is not stored, insert first instance (count = 1)
- m_ProgramStorageMutex->Lock();
- retValue = m_ProgramStorage.insert( MapElemPair(name, data) );
- m_ProgramStorageMutex->Unlock();
-
- // insertion failed, i.e. a program with same name exists
- if( !retValue.second )
- {
- std::string overrideMsg("");
- if( forceOverride )
- {
- // overwrite old instance
- m_ProgramStorage[name].program = _program_in;
- overrideMsg +=" The old program was overwritten!";
- }
-
- MITK_WARN("OpenCL.ResourceService") << "The program " << name << " already exists." << overrideMsg;
- }
-}
-
-cl_program OclResourceServiceImpl::GetProgram(const std::string &name)
-{
- ProgramMapType::iterator it = m_ProgramStorage.find(name);
-
- if( it != m_ProgramStorage.end() )
- {
- it->second.mutex->Lock();
- // first check if the program was deleted
- // while waiting on the mutex
- if ( it->second.counter == 0 )
- mitkThrow() << "Requested OpenCL Program (" << name <<") not found."
- << "(deleted while waiting on the mutex)";
- // increase the reference counter
- // by one if the program is requestet
- it->second.counter += 1;
- it->second.mutex->Unlock();
-
- // return the cl_program
- return it->second.program;
- }
-
- mitkThrow() << "Requested OpenCL Program (" << name <<") not found.";
-}
-
-void OclResourceServiceImpl::InvalidateStorage()
-{
- // do nothing if no context present, there is also no storage
- if( !m_ContextCollection->CanProvideContext() )
- return;
-
- // query the map
- ProgramMapType::iterator it = m_ProgramStorage.begin();
-
- while(it != m_ProgramStorage.end() )
- {
- // query the program build status
- cl_build_status status;
- unsigned int query = clGetProgramBuildInfo( it->second.program, m_ContextCollection->m_Devices[0], CL_PROGRAM_BUILD_STATUS, sizeof(cl_int), &status, nullptr );
- CHECK_OCL_ERR( query )
-
- MITK_DEBUG << "Quering status for " << it->first << std::endl;
-
- // remove program if no succesfull build
- // we need to pay attention to the increment of the iterator when erasing current element
- if( status != CL_BUILD_SUCCESS )
- {
- MITK_DEBUG << " +-- Build failed " << std::endl;
- m_ProgramStorage.erase( it++ );
- }
- else
- {
- ++it;
- }
- }
-}
-
-void OclResourceServiceImpl::RemoveProgram(const std::string& name)
-{
- ProgramMapType::iterator it = m_ProgramStorage.find(name);
- cl_int status = 0;
- cl_program program = nullptr;
-
- if( it != m_ProgramStorage.end() )
- {
- it->second.mutex->Lock();
- // decrease reference by one
- it->second.counter -= 1;
- it->second.mutex->Unlock();
-
- // remove from the storage
- if( it->second.counter == 0 )
- {
- program = it->second.program;
-
- m_ProgramStorageMutex->Lock();
- m_ProgramStorage.erase(it);
- m_ProgramStorageMutex->Unlock();
- }
-
- // delete the program
- if( program )
- {
- status = clReleaseProgram(program);
- CHECK_OCL_ERR( status );
- }
- }
- else
- {
- MITK_WARN("OpenCL.ResourceService") << "Program name [" <<name <<"] passed for deletion not found.";
- }
-}
-
-unsigned int OclResourceServiceImpl::GetMaximumImageSize(unsigned int dimension, cl_mem_object_type _imagetype)
-{
- if( ! m_ContextCollection->CanProvideContext() )
- return 0;
-
- size_t retValue = 0;
-
- switch(dimension)
- {
- case 0:
- if ( _imagetype == CL_MEM_OBJECT_IMAGE2D)
- clGetDeviceInfo( m_ContextCollection->m_Devices[0], CL_DEVICE_IMAGE2D_MAX_WIDTH, sizeof( size_t ), &retValue, nullptr );
- else
- clGetDeviceInfo( m_ContextCollection->m_Devices[0], CL_DEVICE_IMAGE3D_MAX_WIDTH, sizeof( size_t ), &retValue, nullptr );
-
- break;
- case 1:
- if ( _imagetype == CL_MEM_OBJECT_IMAGE2D)
- clGetDeviceInfo( m_ContextCollection->m_Devices[0], CL_DEVICE_IMAGE2D_MAX_HEIGHT, sizeof( size_t ), &retValue, nullptr );
- else
- clGetDeviceInfo( m_ContextCollection->m_Devices[0], CL_DEVICE_IMAGE3D_MAX_HEIGHT, sizeof( size_t ), &retValue, nullptr );
- break;
- case 2:
- if ( _imagetype == CL_MEM_OBJECT_IMAGE3D)
- clGetDeviceInfo( m_ContextCollection->m_Devices[0], CL_DEVICE_IMAGE3D_MAX_DEPTH, sizeof( size_t ), &retValue, nullptr);
- break;
- default:
- MITK_WARN << "Could not recieve info. Desired dimension or object type does not exist. ";
- break;
- }
-
- return retValue;
-}
-
diff --git a/Modules/OpenCL/mitkOclResourceServiceImpl_p.h b/Modules/OpenCL/mitkOclResourceServiceImpl_p.h
deleted file mode 100644
index f95707f0c5..0000000000
--- a/Modules/OpenCL/mitkOclResourceServiceImpl_p.h
+++ /dev/null
@@ -1,182 +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 mitkOclResourceServiceImpl_p_h
-#define mitkOclResourceServiceImpl_p_h
-
-#include <map>
-
-//Micro Services
-#include <usModuleActivator.h>
-#include <usModuleContext.h>
-#include <usGetModuleContext.h>
-#include <usServiceProperties.h>
-
-//ocl
-#include "mitkOclResourceService.h"
-#include "mitkOclUtils.h"
-#include "mitkOclImageFormats.h"
-
-#include <itkFastMutexLock.h>
-
-US_USE_NAMESPACE
-
-//todo add docu!
-
-/** @struct OclContextCollection
- * @brief An capsulation of all OpenCL context related variables needed for the OclResourceService implementation
- *
- * The struct gets created on first call to GetContext in the OclResourceService and attepts to initialize all
- * relevant parts, i.e. the context itself, the device and the command queue
- */
-struct OclContextCollection{
-public:
- OclContextCollection()
- : m_Context(nullptr), m_Devices(nullptr), m_CreateContextFailed(false)
- {
- cl_int clErr = 0;
- size_t szParmDataBytes;
- cl_platform_id cpPlatform;
- cl_device_id m_cdDevice;
-
- try{
- clErr = oclGetPlatformID( &cpPlatform);
- CHECK_OCL_ERR( clErr );
-
- clErr = clGetDeviceIDs( cpPlatform, CL_DEVICE_TYPE_GPU, 1, &m_cdDevice, nullptr);
- CHECK_OCL_ERR( clErr );
-
- this->m_Context = clCreateContext( 0, 1, &m_cdDevice, nullptr, nullptr, &clErr);
- m_CreateContextFailed = (clErr != CL_SUCCESS);
-
- // get the info size
- clErr = clGetContextInfo(m_Context, CL_CONTEXT_DEVICES, 0,nullptr, &szParmDataBytes );
- this->m_Devices = (cl_device_id*) malloc(szParmDataBytes);
-
- // get device info
- clErr = clGetContextInfo(m_Context, CL_CONTEXT_DEVICES, szParmDataBytes, m_Devices, nullptr);
- CHECK_OCL_ERR( clErr );
-
- // create command queue
- m_CommandQueue = clCreateCommandQueue(m_Context, m_Devices[0], 0, &clErr);
- CHECK_OCL_ERR( clErr );
-
- this->PrintContextInfo( );
-
- // collect available image formats for current context
- this->m_ImageFormats = mitk::OclImageFormats::New();
- this->m_ImageFormats->SetGPUContext(m_Context);
- }
- catch( std::exception& e)
- {
- MITK_ERROR("OpenCL.ResourceService") << "Exception while creating context: \n" << e.what();
- }
- }
-
- ~OclContextCollection()
- {
- // if devices were allocated, delete
- if(m_Devices)
- {
- // TODO: Available first in OpenCL 1.2 : query the device for CL_PLATFORM_VERSION
- // through clGetPlatformInfo
- // clReleaseDevice(m_Devices[0]);
-
- delete [] m_Devices;
- }
-
- // if context was created release it
- if( m_Context )
- clReleaseContext( this->m_Context );
- }
-
- bool CanProvideContext() const
- {
- return ( m_Context != nullptr && !m_CreateContextFailed );
- }
-
- void PrintContextInfo() const
- {
- if( m_Devices )
- {
- oclPrintDeviceInfo( m_Devices[0] );
- }
- }
-
- /** The context */
- cl_context m_Context;
-
- /** Available OpenCL devices */
- cl_device_id* m_Devices;
-
- /** Class for handling (un)supported GPU image formats **/
- mitk::OclImageFormats::Pointer m_ImageFormats;
-
- /** The command queue*/
- cl_command_queue m_CommandQueue;
-
- bool m_CreateContextFailed;
-};
-
-class OclResourceServiceImpl
- : public OclResourceService
-{
-
-private:
- // define programmdata private class
- struct ProgramData
- {
- int counter;
- cl_program program;
- itk::FastMutexLock::Pointer mutex;
- ProgramData() :counter(1), program(nullptr)
- {}
- };
-
- typedef std::map< std::string, ProgramData > ProgramMapType;
- //typedef std::map< std::string, std::pair< int, cl_program> > ProgramMapType;
-
- mutable OclContextCollection* m_ContextCollection;
-
- /** Map containing all available (allready compiled) OpenCL Programs */
- ProgramMapType m_ProgramStorage;
- /** mutex for manipulating the program storage */
- itk::FastMutexLock::Pointer m_ProgramStorageMutex;
-
-public:
-
- OclResourceServiceImpl();
-
- ~OclResourceServiceImpl();
-
- cl_context GetContext() const;
-
- cl_command_queue GetCommandQueue() const;
-
- cl_device_id GetCurrentDevice() const;
-
- bool GetIsFormatSupported(cl_image_format *);
-
- void PrintContextInfo() const;
-
- void InsertProgram(cl_program _program_in, std::string name, bool forceOverride=true);
-
- cl_program GetProgram(const std::string&name);
-
- void InvalidateStorage();
-
- void RemoveProgram(const std::string&name);
-
- unsigned int GetMaximumImageSize(unsigned int dimension, cl_mem_object_type _imagetype);
-};
-
-#endif
diff --git a/Modules/OpenCL/mitkOclUtils.cpp b/Modules/OpenCL/mitkOclUtils.cpp
deleted file mode 100644
index c12b659173..0000000000
--- a/Modules/OpenCL/mitkOclUtils.cpp
+++ /dev/null
@@ -1,579 +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 "mitkOclUtils.h"
-#include "mitkLog.h"
-#include <cstdio>
-#include <cstring>
-
-
-unsigned int iDivUp(unsigned int dividend, unsigned int divisor){
- return (dividend % divisor == 0) ? (dividend / divisor) : (dividend / divisor + 1);
-}
-
-cl_int oclGetPlatformID(cl_platform_id* selectedPlatform)
-{
- cl_uint num_platforms = 0;
- cl_platform_id* clPlatformIDs;
- cl_int ciErrNum = 0;
-
- ciErrNum = clGetPlatformIDs( 0, nullptr, &num_platforms);
- if ( ciErrNum != CL_SUCCESS)
- {
- MITK_ERROR<<" Error " << ciErrNum << " in clGetPlatformIDs() \n";
- throw std::bad_exception();
- }
- else
- {
- clPlatformIDs = new cl_platform_id[num_platforms];
-
- ciErrNum = clGetPlatformIDs( num_platforms, clPlatformIDs, nullptr);
- if(ciErrNum == CL_SUCCESS)
- {
- *selectedPlatform = clPlatformIDs[0];
- }
- }
-
- return CL_SUCCESS;
-
-}
-
-void oclPrintMemObjectInfo(cl_mem memobj)
-{
- cl_int clErr = 0;
-
- MITK_INFO << "Examining cl_mem object: " << memobj
- << "\n------------------\n";
-
- // CL_MEM_TYPE
- cl_mem_object_type objtype;
- clErr = clGetMemObjectInfo( memobj, CL_MEM_TYPE, sizeof(cl_mem_object_type),&objtype, nullptr);
- CHECK_OCL_ERR( clErr );
-
- switch(objtype)
- {
- case CL_MEM_OBJECT_BUFFER:
- MITK_INFO << "CL_MEM_TYPE \t" << "BUFFER_OBJ" << "\n";
- break;
- case CL_MEM_OBJECT_IMAGE2D:
- MITK_INFO << "CL_MEM_TYPE \t" << "2D IMAGE" << "\n";
- break;
- case CL_MEM_OBJECT_IMAGE3D:
- MITK_INFO << "CL_MEM_TYPE \t" << "3D IMAGE" << "\n";
- break;
- default:
- MITK_INFO << "CL_MEM_TYPE \t" << "[could not resolve]" << "\n";
- break;
- }
-
- // CL_MEM_FLAGS
- cl_mem_flags flags;
- clErr = clGetMemObjectInfo( memobj, CL_MEM_FLAGS, sizeof(cl_mem_flags),&flags, nullptr);
- CHECK_OCL_ERR( clErr );
-
- switch(flags)
- {
- case CL_MEM_READ_ONLY:
- MITK_INFO << "CL_MEM_FLAGS \t" << "CL_MEM_READ_ONLY" << "\n";
- break;
- case CL_MEM_WRITE_ONLY:
- MITK_INFO << "CL_MEM_FLAGS \t" << "CL_MEM_WRITE_ONLY" << "\n";
- break;
- case CL_MEM_READ_WRITE:
- MITK_INFO << "CL_MEM_FLAGS \t" << "CL_MEM_READ_WRITE" << "\n";
- break;
- default:
- MITK_INFO << "CL_MEM_FLAGS \t" << "not resolved, " << flags << "\n";
- break;
- }
-
- // get CL_MEM_SIZE
- size_t memsize;
- clErr = clGetMemObjectInfo( memobj, CL_MEM_SIZE, sizeof(memsize),&memsize, nullptr);
- CHECK_OCL_ERR( clErr );
-
- MITK_INFO << "CL_MEM_SIZE \t" << memsize << "\n";
-
- // get CL_MEM_HOST_PTR
- float *hostptr;
- clErr = clGetMemObjectInfo( memobj, CL_MEM_HOST_PTR, sizeof(void*), (void*) &hostptr, nullptr);
- CHECK_OCL_ERR( clErr );
-
- MITK_INFO << "CL_MEM_HOST_PTR \t" << hostptr << "\n";
-
- // get CL_CONTEXT
- cl_context gpuctxt;
- clErr = clGetMemObjectInfo( memobj, CL_MEM_CONTEXT, sizeof(cl_context), &gpuctxt, nullptr);
- CHECK_OCL_ERR( clErr );
-
- MITK_INFO << "CL_CONTEXT \t\t" << gpuctxt << "\n";
-
- // get CL_MEM_REFERENCE_COUNT
- cl_uint refs;
- clErr = clGetMemObjectInfo( memobj, CL_MEM_REFERENCE_COUNT, sizeof(cl_uint), &refs, nullptr);
- CHECK_OCL_ERR(clErr);
-
- MITK_INFO << "CL_REF_COUNT \t" << refs << "\n";
-
- MITK_INFO << "================== \n" << std::endl;
-}
-
-void oclPrintDeviceInfo(cl_device_id device)
-{
- char device_string[1024];
-
- clGetDeviceInfo(device, CL_DEVICE_NAME, sizeof(device_string), &device_string, nullptr);
- MITK_INFO("ocl.log")<< " Device : " << device_string;
-
- // CL_DEVICE_INFO
- cl_device_type type;
- clGetDeviceInfo(device, CL_DEVICE_TYPE, sizeof(type), &type, nullptr);
- if( type & CL_DEVICE_TYPE_CPU )
- MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_CPU";
- if( type & CL_DEVICE_TYPE_GPU )
- MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_GPU";
- if( type & CL_DEVICE_TYPE_ACCELERATOR )
- MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_ACCELERATOR";
- if( type & CL_DEVICE_TYPE_DEFAULT )
- MITK_INFO("ocl.log")<<" CL_DEVICE_TYPE: CL_DEVICE_TYPE_DEFAULT";
-
- // CL_DEVICE_MAX_COMPUTE_UNITS
- cl_uint compute_units;
- clGetDeviceInfo(device, CL_DEVICE_MAX_COMPUTE_UNITS, sizeof(compute_units), &compute_units, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_COMPUTE_UNITS:" << compute_units;
-
- // CL_DEVICE_MAX_WORK_GROUP_SIZE
- size_t workitem_size[3];
- clGetDeviceInfo(device, CL_DEVICE_MAX_WORK_ITEM_SIZES, sizeof(workitem_size), &workitem_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_WORK_ITEM_SIZES:\t"<< workitem_size[0]<< workitem_size[1]<< workitem_size[2];
-
- // CL_DEVICE_MAX_WORK_GROUP_SIZE
- size_t workgroup_size;
- clGetDeviceInfo(device, CL_DEVICE_MAX_WORK_GROUP_SIZE, sizeof(workgroup_size), &workgroup_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_WORK_GROUP_SIZE:" << workgroup_size;
-
- // CL_DEVICE_MAX_CLOCK_FREQUENCY
- cl_uint clock_frequency;
- clGetDeviceInfo(device, CL_DEVICE_MAX_CLOCK_FREQUENCY, sizeof(clock_frequency), &clock_frequency, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_MAX_CLOCK_FREQUENCY:"<< clock_frequency / 1000;
-
- // CL_DEVICE_IMAGE_SUPPORT
- cl_bool image_support;
- clGetDeviceInfo(device, CL_DEVICE_IMAGE_SUPPORT, sizeof(image_support), &image_support, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE_SUPPORT:\t" << image_support;
-
- // CL_DEVICE_GLOBAL_MEM_SIZE
- cl_ulong mem_size;
- clGetDeviceInfo(device, CL_DEVICE_GLOBAL_MEM_SIZE, sizeof(mem_size), &mem_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_GLOBAL_MEM_SIZE:\t\t"<<(unsigned int)(mem_size / (1024 * 1024))<<"Mbytes";
-
- // CL_DEVICE_LOCAL_MEM_SIZE
- clGetDeviceInfo(device, CL_DEVICE_LOCAL_MEM_SIZE, sizeof(mem_size), &mem_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_LOCAL_MEM_SIZE:\t\t"<< (unsigned int)(mem_size / (1024)) <<"KByte\n";
-
- // CL_DEVICE_MAX_CONSTANT_BUFFER_SIZE
- clGetDeviceInfo(device, CL_DEVICE_MAX_CONSTANT_BUFFER_SIZE, sizeof(mem_size), &mem_size, nullptr);
- MITK_INFO("ocl.log") << " CL_DEVICE_MAX_CONSTANT_BUFFER_SIZE:\t\t" << (unsigned int)(mem_size / (1024)) << "KByte";
-
- //check for image support properties
- clGetDeviceInfo(device, CL_DEVICE_IMAGE2D_MAX_WIDTH, sizeof(workgroup_size), &workgroup_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE2D_MAX_WIDTH:\t" << workgroup_size;
-
- clGetDeviceInfo(device, CL_DEVICE_IMAGE2D_MAX_HEIGHT, sizeof(workgroup_size), &workgroup_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE2D_MAX_HEIGHT:\t" << workgroup_size;
-
- clGetDeviceInfo(device, CL_DEVICE_IMAGE3D_MAX_WIDTH, sizeof(workgroup_size), &workgroup_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE3D_MAX_WIDTH:\t" << workgroup_size;
-
- clGetDeviceInfo(device, CL_DEVICE_IMAGE3D_MAX_HEIGHT, sizeof(workgroup_size), &workgroup_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE3D_MAX_HEIGHT:\t" << workgroup_size;
-
- clGetDeviceInfo(device, CL_DEVICE_IMAGE3D_MAX_DEPTH, sizeof(workgroup_size), &workgroup_size, nullptr);
- MITK_INFO("ocl.log")<<" CL_DEVICE_IMAGE3D_MAX_DEPTH:\t" << workgroup_size;
-
-
- // CL_DEVICE_QUEUE_PROPERTIES
- cl_command_queue_properties queue_properties;
- clGetDeviceInfo(device, CL_DEVICE_QUEUE_PROPERTIES, sizeof(queue_properties), &queue_properties, nullptr);
- if( queue_properties & CL_QUEUE_OUT_OF_ORDER_EXEC_MODE_ENABLE )
- MITK_INFO("ocl.log")<<" CL_DEVICE_QUEUE_PROPERTIES:\t\t"<< "CL_QUEUE_OUT_OF_ORDER_EXEC_MODE_ENABLE";
- if( queue_properties & CL_QUEUE_PROFILING_ENABLE )
- MITK_INFO("ocl.log")<<" CL_DEVICE_QUEUE_PROPERTIES:\t\t"<< "CL_QUEUE_PROFILING_ENABLE";
-
-}
-
-cl_ulong oclGetGlobalMemSize(cl_device_id device)
-{
- cl_ulong mem_size;
- clGetDeviceInfo(device, CL_DEVICE_GLOBAL_MEM_SIZE, sizeof(mem_size), &mem_size, nullptr);
- return mem_size;
-}
-
-std::string GetOclErrorAsString( int _clErr )
-{
- std::string returnString("unkown error number: "+std::to_string(_clErr)+" \n");
-
- switch(_clErr)
- {
- case CL_SUCCESS:
- returnString = "CL_SUCCESS\n";
- break;
- case CL_DEVICE_NOT_FOUND:
- returnString = "CL_DEVICE_NOT_FOUND\n";
- break;
- case CL_DEVICE_NOT_AVAILABLE:
- returnString = "CL_DEVICE_NOT_AVAILABLE\n";
- break;
- /*case CL_DEVICE_COMPILER_NOT_AVAILABLE:
- returnString = "CL_DEVICE_COMPILER_NOT_AVAILABLE\n";
- break; */
- case CL_MEM_OBJECT_ALLOCATION_FAILURE :
- returnString = "CL_MEM_OBJECT_ALLOCATION_FAILURE\n";
- break;
- case CL_OUT_OF_RESOURCES:
- returnString = "CL_OUT_OF_RESOURCES\n";
- break;
- case CL_OUT_OF_HOST_MEMORY:
- returnString = "CL_OUT_OF_HOST_MEMORY\n";
- break;
- case CL_PROFILING_INFO_NOT_AVAILABLE:
- returnString = "CL_PROFILING_INFO_NOT_AVAILABLE\n";
- break;
- case CL_MEM_COPY_OVERLAP:
- returnString = "CL_MEM_COPY_OVERLAP\n";
- break;
- case CL_IMAGE_FORMAT_MISMATCH:
- returnString = "CL_IMAGE_FORMAT_MISMATCH\n";
- break;
- case CL_IMAGE_FORMAT_NOT_SUPPORTED:
- returnString = "CL_IMAGE_FORMAT_NOT_SUPPORTED\n";
- break;
- case CL_BUILD_PROGRAM_FAILURE:
- returnString = "CL_BUILD_PROGRAM_FAILURE\n";
- break;
- case CL_MAP_FAILURE:
- returnString = "CL_MAP_FAILURE\n";
- break;
- case CL_INVALID_VALUE:
- returnString = "CL_INVALID_VALUE\n";
- break;
- case CL_INVALID_DEVICE_TYPE:
- returnString = "CL_INVALID_DEVICE_TYPE\n";
- break;
- case CL_INVALID_PLATFORM:
- returnString = "CL_INVALID_PLATFORM\n";
- break;
- case CL_INVALID_DEVICE:
- returnString = "CL_INVALID_DEVICE\n";
- break;
- case CL_INVALID_CONTEXT :
- returnString = "CL_INVALID_CONTEXT\n";
- break;
- case CL_INVALID_QUEUE_PROPERTIES:
- returnString = "CL_INVALID_QUEUE_PROPERTIES\n";
- break;
- case CL_INVALID_COMMAND_QUEUE:
- returnString = "CL_INVALID_COMMAND_QUEUE\n";
- break;
- case CL_INVALID_HOST_PTR:
- returnString = "CL_INVALID_HOST_PTR\n";
- break;
- case CL_INVALID_MEM_OBJECT:
- returnString = "CL_INVALID_MEM_OBJECT\n";
- break;
- case CL_INVALID_IMAGE_FORMAT_DESCRIPTOR:
- returnString = "CL_INVALID_IMAGE_FORMAT_DESCRIPTOR\n";
- break;
- case CL_INVALID_IMAGE_SIZE:
- returnString = "CL_INVALID_IMAGE_SIZE\n";
- break;
- case CL_INVALID_SAMPLER :
- returnString = "CL_INVALID_SAMPLER\n";
- break;
- case CL_INVALID_BINARY:
- returnString = "CL_INVALID_BINARY\n";
- break;
- case CL_INVALID_BUILD_OPTIONS:
- returnString = "CL_INVALID_BUILD_OPTIONS\n";
- break;
- case CL_INVALID_PROGRAM:
- returnString = "CL_INVALID_PROGRAM\n";
- break;
- case CL_INVALID_PROGRAM_EXECUTABLE:
- returnString = "CL_INVALID_PROGRAM_EXECUTABLE\n";
- break;
- case CL_INVALID_KERNEL_NAME:
- returnString = "CL_INVALID_KERNEL_NAME\n";
- break;
- case CL_INVALID_KERNEL_DEFINITION:
- returnString = "CL_INVALID_KERNEL_DEFINITION\n";
- break;
- case CL_INVALID_KERNEL :
- returnString = "CL_INVALID_KERNEL\n";
- break;
- case CL_INVALID_ARG_INDEX :
- returnString = "CL_INVALID_ARG_INDEX\n";
- break;
- case CL_INVALID_ARG_VALUE :
- returnString = "CL_INVALID_ARG_VALUE\n";
- break;
- case CL_INVALID_ARG_SIZE :
- returnString = "CL_INVALID_ARG_SIZE\n";
- break;
- case CL_INVALID_KERNEL_ARGS :
- returnString = "CL_INVALID_KERNEL_ARGS\n";
- break;
- case CL_INVALID_WORK_DIMENSION:
- returnString = "CL_INVALID_WORK_DIMENSION\n";
- break;
- case CL_INVALID_WORK_GROUP_SIZE:
- returnString = "CL_INVALID_WORK_GROUP_SIZE\n";
- break;
- case CL_INVALID_WORK_ITEM_SIZE:
- returnString = "CL_INVALID_WORK_ITEM_SIZE\n";
- break;
- case CL_INVALID_GLOBAL_OFFSET:
- returnString = "CL_INVALID_GLOBAL_OFFSET\n";
- break;
- case CL_INVALID_EVENT_WAIT_LIST:
- returnString = "CL_INVALID_EVENT_WAIT_LIST\n";
- break;
- case CL_INVALID_EVENT:
- returnString = "CL_INVALID_EVENT\n";
- break;
- case CL_INVALID_OPERATION:
- returnString = "CL_INVALID_OPERATION\n";
- break;
- case CL_INVALID_GL_OBJECT:
- returnString = "CL_INVALID_GL_OBJECT\n";
- break;
- case CL_INVALID_BUFFER_SIZE :
- returnString = "CL_INVALID_BUFFER_SIZE\n";
- break;
- case CL_INVALID_MIP_LEVEL :
- returnString = "CL_INVALID_MIP_LEVEL\n";
- break;
- default:
- break;
- }
-
- return returnString;
-}
-
-void GetOclError(int _clErr)
-{
- if(_clErr == CL_SUCCESS)
- MITK_WARN << "Called GetOclErr() with no error value: [CL_SUCCESS]";
- else
- MITK_ERROR << GetOclErrorAsString(_clErr);
-}
-
-bool oclCheckError(int _err, const char* filepath, int lineno)
-{
- if (_err)
- {
- MITK_ERROR<< "OpenCL Error at " << filepath <<":"<< lineno;
- GetOclError(_err);
-
- return 0;
- }
-
- return 1;
-}
-
-void GetSupportedImageFormats(cl_context _context, cl_mem_object_type _type)
-{
- const unsigned int entries = 500;
- cl_image_format* formats = new cl_image_format[entries];
-
- cl_uint _written = 0;
-
- // OpenCL constant to catch error IDs
- cl_int ciErr1;
- // Get list of supported image formats for READ_ONLY access
- ciErr1 = clGetSupportedImageFormats( _context, CL_MEM_READ_ONLY, _type, entries, formats, &_written);
- CHECK_OCL_ERR(ciErr1);
-
- MITK_INFO << "Supported Image Formats, Image: CL_MEM_READ_ONLY \n";
-
- for (unsigned int i=0; i<_written; i++)
- {
- MITK_INFO<< "ChannelType: " << GetImageTypeAsString(formats[i].image_channel_data_type) << "| ChannelOrder: "<< GetImageTypeAsString(formats[i].image_channel_order) <<"\n";
- }
-
- _written = 0;
-
- // Get list of supported image formats for READ_WRITE access
- ciErr1 = clGetSupportedImageFormats( _context, CL_MEM_READ_WRITE, _type, entries, formats, &_written);
- CHECK_OCL_ERR(ciErr1);
-
- MITK_INFO << "Supported Image Formats, Image: CL_MEM_READ_WRITE (found: " << _written <<") \n";
-
- for (unsigned int i=0; i<_written; i++)
- {
- MITK_INFO<< "ChannelType: " << GetImageTypeAsString(formats[i].image_channel_data_type) << "| ChannelOrder: "<< GetImageTypeAsString(formats[i].image_channel_order) <<"\n";
- }
-
- _written = 0;
-
- // Get list of supported image formats for WRITE_ONLY access
- ciErr1 = clGetSupportedImageFormats( _context, CL_MEM_WRITE_ONLY, _type, entries, formats, &_written);
- CHECK_OCL_ERR(ciErr1);
-
- MITK_INFO << "Supported Image Formats, Image: CL_MEM_WRITE_ONLY (found: " << _written <<") \n";
-
- for (unsigned int i=0; i<_written; i++)
- {
- MITK_INFO<< "ChannelType: " << GetImageTypeAsString(formats[i].image_channel_data_type) << "| ChannelOrder: "<< GetImageTypeAsString(formats[i].image_channel_order) <<"\n";
- }
-}
-
-std::string GetImageTypeAsString( const unsigned int _in)
-{
- switch(_in)
- {
- case CL_R:
- return "CL_R ";
- break;
- case CL_A:
- return "CL_A ";
- break;
- case CL_RG:
- return "CL_RG ";
- break;
- case CL_RA:
- return "CL_RA ";
- break;
- case CL_RGB:
- return "CL_RGB ";
- break;
- case CL_RGBA:
- return "CL_RGBA ";
- break;
- case CL_BGRA:
- return "CL_BGRA ";
- break;
- case CL_ARGB:
- return "CL_ARGB ";
- break;
- case CL_INTENSITY:
- return "CL_INTENSITY ";
- break;
- case CL_LUMINANCE:
- return "CL_LUMINANCE ";
- break;
- case CL_SNORM_INT8:
- return "CL_SNORM_INT8 ";
- break;
- case CL_SNORM_INT16:
- return "CL_SNORM_INT16 ";
- break;
- case CL_UNORM_INT8:
- return "CL_UNORM_INT8 ";
- break;
- case CL_UNORM_INT16:
- return "CL_UNORM_INT16 ";
- break;
- case CL_UNORM_SHORT_565:
- return "CL_UNORM_SHORT_565 ";
- break;
- case CL_UNORM_SHORT_555:
- return "CL_UNORM_SHORT_555 ";
- break;
- case CL_UNORM_INT_101010:
- return "CL_UNORM_INT_101010 ";
- break;
- case CL_SIGNED_INT8:
- return "CL_SIGNED_INT8 ";
- break;
- case CL_SIGNED_INT16:
- return "CL_SIGNED_INT16 ";
- break;
- case CL_SIGNED_INT32:
- return "CL_SIGNED_INT32 ";
- break;
- case CL_UNSIGNED_INT8:
- return "CL_UNSIGNED_INT8 ";
- break;
- case CL_UNSIGNED_INT16:
- return "CL_UNSIGNED_INT16 ";
- break;
- case CL_UNSIGNED_INT32:
- return "CL_UNSIGNED_INT32 ";
- break;
- case CL_HALF_FLOAT:
- return "CL_HALF_FLOAT ";
- break;
- case CL_FLOAT:
- return "CL_FLOAT ";
- break;
- default:
- return "--";
- break;
- }
-}
-
-
-
-void oclLogBinary(cl_program clProg, cl_device_id clDev)
-{
- // Grab the number of devices associated with the program
- cl_uint num_devices;
- clGetProgramInfo(clProg, CL_PROGRAM_NUM_DEVICES, sizeof(cl_uint), &num_devices, nullptr);
-
- // Grab the device ids
- cl_device_id* devices = (cl_device_id*) malloc(num_devices * sizeof(cl_device_id));
- clGetProgramInfo(clProg, CL_PROGRAM_DEVICES, num_devices * sizeof(cl_device_id), devices, 0);
-
- // Grab the sizes of the binaries
- size_t* binary_sizes = (size_t*)malloc(num_devices * sizeof(size_t));
- clGetProgramInfo(clProg, CL_PROGRAM_BINARY_SIZES, num_devices * sizeof(size_t), binary_sizes, nullptr);
-
- // Now get the binaries
- char** ptx_code = (char**)malloc(num_devices * sizeof(char*));
- for( unsigned int i=0; i<num_devices; ++i)
- {
- ptx_code[i] = (char*)malloc(binary_sizes[i]);
- }
- clGetProgramInfo(clProg, CL_PROGRAM_BINARIES, 0, ptx_code, nullptr);
-
- // Find the index of the device of interest
- unsigned int idx = 0;
- while((idx < num_devices) && (devices[idx] != clDev))
- {
- ++idx;
- }
-
- // If the index is associated, log the result
- if( idx < num_devices )
- {
- MITK_INFO<< "\n ---------------- \n Program Binary: \n -----------------------\n";
- MITK_INFO<< ptx_code[idx];
- }
-
- free( devices );
- free( binary_sizes );
- for(unsigned int i=0; i<num_devices; ++i)
- {
- free(ptx_code[i]);
- }
- free( ptx_code );
-}
-
-void oclLogBuildInfo(cl_program clProg, cl_device_id clDev)
-{
- char cBuildLog[10240];
-
- clGetProgramBuildInfo(clProg, clDev, CL_PROGRAM_BUILD_LOG, sizeof(cBuildLog), cBuildLog, nullptr);
- MITK_INFO<< "\n Program Build Log: \n -----------------------\n";
- MITK_INFO<< cBuildLog;
-}
diff --git a/Modules/OpenCL/mitkOclUtils.h b/Modules/OpenCL/mitkOclUtils.h
deleted file mode 100644
index 1c5d221389..0000000000
--- a/Modules/OpenCL/mitkOclUtils.h
+++ /dev/null
@@ -1,95 +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 mitkOclUtils_h
-#define mitkOclUtils_h
-
-#include "mitkOpenCL.h"
-
-#include <string>
-#include <MitkOpenCLExports.h>
-
-#define CHECK_OCL_ERR(_er) oclCheckError(_er, __FILE__, __LINE__);
-
-/**
- @brief Method to estimate an integer quotient C from given dividend and divisor higher or equal to
- the corresponding floating quotient
-
- If the divisor is a factor of the dividend, the dividend/divisor is an integer value and is returned. If not,
- the nearest higher integer is returned. So it holds for the return value C that C * divisor is equal or greater then
- the dividend. In OpenCL context useful for estimating the local/global working dimension of a NDRange so that all
- image data is covered by the parallelisation scheme.
- */
-MITKOPENCL_EXPORT unsigned int iDivUp(unsigned int dividend, unsigned int divisor);
-
-/**
- @brief Returns the name of an OpenCL Error as a string
-
- Most of the OpenCL Methods ( cl<NAME> ) return an integer error code. This method translates the
- error value given as parameter to the corresponding error name. For example the value -30 will be translated
- to CL_INVALID_VALUE
- */
-MITKOPENCL_EXPORT std::string GetOclErrorAsString( int _clErr );
-
-/**
- @brief Checks whether the given value corresponds to an OpenCL Error value and prints this message out as MITK_ERROR if yes
- */
-MITKOPENCL_EXPORT void GetOclError(int _clErr);
-
-/**
- @brief Returns a platform ID of an OpenCL-capable GPU, or throws an exception
-*/
-MITKOPENCL_EXPORT cl_int oclGetPlatformID(cl_platform_id* selectedPlatform);
-
-/*! \brief Prints out the essential support information about current device */
-MITKOPENCL_EXPORT void oclPrintDeviceInfo(cl_device_id);
-
-/*! \brief Returns the Global memory size of the current device */
-MITKOPENCL_EXPORT cl_ulong oclGetGlobalMemSize(cl_device_id device);
-
-/*! @brief Prints the available memory info about the given object to std::cout
- */
-MITKOPENCL_EXPORT void oclPrintMemObjectInfo( cl_mem memobj);
-
-/*! \brief Checks the given code for errors and produces a std::cout output if
- the _err does not equal CL_SUCCESS. The output includes also the filename and the line
- number of the method call.
- */
-MITKOPENCL_EXPORT bool oclCheckError(int _err, const char*, int);
-
-/*! \brief Logs the GPU Program binary code
-
-@param clProg: the OpenCL Program to log
-@param clDev: the OpenCL-capable device the program was tried to be compiled for
-*/
-MITKOPENCL_EXPORT void oclLogBinary(cl_program clProg, cl_device_id clDev);
-
-/*! \brief Shows the OpenCL-Program build info, called if clBuildProgram != CL_SUCCES
-
-@param clProg: the OpenCL Program to log
-@param clDev: the OpenCL-capable device the program was tried to be compiled for
-*/
-MITKOPENCL_EXPORT void oclLogBuildInfo(cl_program clProg, cl_device_id clDev);
-
-/** \brief Print out all supported image formats for given image type
-
- @param _type the image type ( CL_MEM_OBJECT_2D or CL_MEM_OBJECT_3D )
- @param _context the OpenCL context to be examined
- */
-MITKOPENCL_EXPORT void GetSupportedImageFormats(cl_context _context, cl_mem_object_type _type);
-
-/**
- @brief Translates the internal image type identifier to a human readable description string
-*/
-MITKOPENCL_EXPORT std::string GetImageTypeAsString( const unsigned int _in);
-
-#endif
diff --git a/Modules/OpenCL/mitkOpenCL.h b/Modules/OpenCL/mitkOpenCL.h
deleted file mode 100644
index 32eea4f91d..0000000000
--- a/Modules/OpenCL/mitkOpenCL.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkOpenCL_h
-#define mitkOpenCL_h
-
-#if defined (__APPLE__) || defined(MACOSX)
-#include <OpenCL/cl.h>
-#else
-#define CL_USE_DEPRECATED_OPENCL_1_2_APIS
-#include <CL/cl.h>
-#endif
-
-#endif
diff --git a/Modules/OpenCL/mitkOpenCLActivator.cpp b/Modules/OpenCL/mitkOpenCLActivator.cpp
deleted file mode 100644
index 3ea84f430d..0000000000
--- a/Modules/OpenCL/mitkOpenCLActivator.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 "mitkOpenCLActivator.h"
-
-void OpenCLActivator::Load(us::ModuleContext *context)
-{
- // generate context
- m_ResourceService.reset(new OclResourceServiceImpl);
- us::ServiceProperties props;
-
- context->RegisterService<OclResourceService>(m_ResourceService.get(), props);
-}
-
-void OpenCLActivator::Unload(us::ModuleContext *)
-{
- m_ResourceService.release();
-}
-
-US_EXPORT_MODULE_ACTIVATOR(OpenCLActivator )
diff --git a/Modules/OpenCL/mitkOpenCLActivator.h b/Modules/OpenCL/mitkOpenCLActivator.h
deleted file mode 100644
index 8500ca3eb4..0000000000
--- a/Modules/OpenCL/mitkOpenCLActivator.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 mitkOpenCLActivator_h
-#define mitkOpenCLActivator_h
-
-#include "mitkOclResourceServiceImpl_p.h"
-
-#include <usModuleActivator.h>
-#include <usModuleContext.h>
-#include <usGetModuleContext.h>
-#include <usServiceProperties.h>
-
-#include <set>
-#include <algorithm>
-#include <memory>
-
-/**
- * @class OpenCLActivator
- *
- * @brief Custom activator for the OpenCL Module in order to register
- * and provide the OclResourceService
- */
-class US_ABI_LOCAL OpenCLActivator : public us::ModuleActivator
-{
-private:
-
- std::unique_ptr<OclResourceServiceImpl> m_ResourceService;
-
-public:
- /** @brief Load module context */
- void Load(us::ModuleContext *context);
-
- /** @brief Unload module context */
- void Unload(us::ModuleContext* );
-
-};
-
-
-
-#endif
diff --git a/Modules/SemanticRelations/CMakeLists.txt b/Modules/SemanticRelations/CMakeLists.txt
deleted file mode 100644
index f4c3c2d50f..0000000000
--- a/Modules/SemanticRelations/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-MITK_CREATE_MODULE(
- DEPENDS MitkSceneSerializationBase MitkDICOM MitkMultilabel MitkPersistence MitkImageStatisticsUI
-)
-
-if(BUILD_TESTING)
- ADD_SUBDIRECTORY(Test)
-endif(BUILD_TESTING)
diff --git a/Modules/SemanticRelations/Test/CMakeLists.txt b/Modules/SemanticRelations/Test/CMakeLists.txt
deleted file mode 100644
index 153cd81e2e..0000000000
--- a/Modules/SemanticRelations/Test/CMakeLists.txt
+++ /dev/null
@@ -1 +0,0 @@
-MITK_CREATE_MODULE_TESTS()
diff --git a/Modules/SemanticRelations/Test/files.cmake b/Modules/SemanticRelations/Test/files.cmake
deleted file mode 100644
index 3e491291c0..0000000000
--- a/Modules/SemanticRelations/Test/files.cmake
+++ /dev/null
@@ -1,7 +0,0 @@
-set(MODULE_TESTS
- mitkSemanticRelationsTest.cpp
-)
-
-set(CPP_FILES
- mitkSemanticRelationsTestHelper.cpp
-)
diff --git a/Modules/SemanticRelations/Test/mitkSemanticRelationsTest.cpp b/Modules/SemanticRelations/Test/mitkSemanticRelationsTest.cpp
deleted file mode 100644
index 70ff2f25e6..0000000000
--- a/Modules/SemanticRelations/Test/mitkSemanticRelationsTest.cpp
+++ /dev/null
@@ -1,947 +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.
-
-============================================================================*/
-
-// mitk semantic relations
-#include "mitkSemanticRelationException.h"
-#include "mitkSemanticRelationsInference.h"
-#include "mitkSemanticRelationsIntegration.h"
-#include "mitkSemanticRelationsDataStorageAccess.h"
-#include "mitkRelationStorage.h"
-#include "mitkControlPointManager.h"
-#include "mitkDICOMHelper.h"
-#include "mitkLesionManager.h"
-#include "mitkSemanticRelationsTestHelper.h"
-#include "mitkUIDGeneratorBoost.h"
-
-// mitk core
-#include <mitkStandaloneDataStorage.h>
-#include <mitkTestFixture.h>
-#include <mitkTestingMacros.h>
-#include <mitkPropertyNameHelper.h>
-
-// mitk persistence
-#include <mitkPersistenceService.h>
-
-class mitkSemanticRelationsTestSuite : public mitk::TestFixture
-{
- CPPUNIT_TEST_SUITE(mitkSemanticRelationsTestSuite);
- MITK_TEST(IntegrationTest);
- MITK_TEST(InferenceTest);
- MITK_TEST(DataStorageAccessTest);
- MITK_TEST(RemoveAndUnlinkTest);
- MITK_TEST(LesionAndControlPointTest);
- CPPUNIT_TEST_SUITE_END();
-
-private:
-
- mitk::DataStorage::Pointer m_DataStorage;
-
-public:
-
- void setUp() override
- {
- mitk::PersistenceService::LoadModule();
- m_DataStorage = mitk::StandaloneDataStorage::New();
- }
-
- void tearDown() override
- {
- // clear semantic relations storage
- mitk::SemanticRelationsTestHelper::ClearRelationStorage();
- }
-
- //////////////////////////////////////////////////////////////////////////
- // SPECIFIC TEST GROUPS
- //////////////////////////////////////////////////////////////////////////
- void IntegrationTest()
- {
- MITK_INFO << "=== IntegrationTest start ===";
- AddNewData();
- ExaminationPeriod();
- SegmentationAndLesion();
- InvalidData();
- MITK_INFO << "=== IntegrationTest end ===";
- }
-
- void InferenceTest()
- {
- MITK_INFO << "=== InferenceTest start ===";
- CombinedQueries();
- InstanceExistences();
- MITK_INFO << "=== InferenceTest end ===";
- }
-
- void DataStorageAccessTest()
- {
- MITK_INFO << "=== DataStorageAccessTest start ===";
- DataStorageAccess();
- MITK_INFO << "=== DataStorageAccessTest end ===";
- }
-
- void RemoveAndUnlinkTest()
- {
- MITK_INFO << "=== RemoveAndUnlinkTest start ===";
- CPRemoveAndUnlink();
- LesionRemoveAndUnlink();
- RemoveImagesAndSegmentation();
- MITK_INFO << "=== RemoveAndUnlinkTest end ===";
- }
-
- void LesionAndControlPointTest()
- {
- MITK_INFO << "=== LesionAndControlPointTest start ===";
- LesionDataTest();
- LesionOverwriteTest();
- MITK_INFO << "=== LesionAndControlPointTest end ===";
- }
-
- //////////////////////////////////////////////////////////////////////////
- // SPECIFIC TESTS
- //////////////////////////////////////////////////////////////////////////
- // IntegrationTest
- void AddNewData()
- {
- MITK_INFO << "=== AddNewData";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
-
- auto image = mitk::SemanticRelationsTestHelper::GetPatientOneCTImage();
- m_DataStorage->Add(image);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", image.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", image->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(image);
-
- // start test
- auto allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- CPPUNIT_ASSERT_MESSAGE("CaseID not correctly stored", allCaseIDs.front() == "Patient1");
- auto caseID = allCaseIDs.front();
-
- // test control point
- auto allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One control point should be stored", allControlPoints.size() == 1);
-
- auto controlPointOfImage = mitk::SemanticRelationsInference::GetControlPointOfImage(image);
- mitk::SemanticTypes::ControlPoint controlPointToCompare;
- controlPointToCompare.date = boost::gregorian::date(2019, 01, 01);
- CPPUNIT_ASSERT_MESSAGE("Control point not correctly stored", controlPointOfImage.date == controlPointToCompare.date);
-
- // test information type
- auto allInformationTypes = mitk::RelationStorage::GetAllInformationTypesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One information type should be stored", allInformationTypes.size() == 1);
-
- auto informationType = mitk::SemanticRelationsInference::GetInformationTypeOfImage(image);
- CPPUNIT_ASSERT_MESSAGE("Information type not correctly stored", informationType == "CT");
-
- semanticRelationsIntegration.SetInformationType(image, "MR");
- informationType = mitk::SemanticRelationsInference::GetInformationTypeOfImage(image);
- CPPUNIT_ASSERT_MESSAGE("Information type not correctly stored", informationType == "MR");
- }
-
- void ExaminationPeriod()
- {
- MITK_INFO << "=== ExaminationPeriod";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
-
- auto MRImage = mitk::SemanticRelationsTestHelper::GetPatientOneMRImage();
- m_DataStorage->Add(MRImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", MRImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", MRImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(MRImage);
-
- // start test
- auto allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- CPPUNIT_ASSERT_MESSAGE("One CaseID should be stored", allCaseIDs.size() == 1);
- auto caseID = allCaseIDs.front();
-
- auto allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One control point should be stored", allControlPoints.size() == 1);
-
- auto controlPointOfImage = mitk::SemanticRelationsInference::GetControlPointOfImage(MRImage);
- mitk::SemanticTypes::ControlPoint controlPoint;
- controlPoint.date = boost::gregorian::date(2019, 01, 01);
- CPPUNIT_ASSERT_MESSAGE("Control point not correctly stored", controlPointOfImage.date == controlPoint.date);
-
- auto allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be stored", allExaminationPeriods.size() == 1);
-
- auto allImageIDs = mitk::RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPointOfImage);
- CPPUNIT_ASSERT_MESSAGE("Two images should reference the same control point", allImageIDs.size() == 2);
-
- // add additional control point to the same examination period
- // load data
- auto CTImage = mitk::SemanticRelationsTestHelper::GetPatientOneOtherCTImage();
- m_DataStorage->Add(CTImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", CTImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", CTImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(CTImage);
-
- // start test
- allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two control points should be stored", allControlPoints.size() == 2);
-
- allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be stored", allExaminationPeriods.size() == 1);
-
- // modify control point to create new examination period
- // current control point is 2019, 01, 31
- // new control point should exceed threshold (30 days) and create new examination period
- // new control point is 2019, 02, 01
- controlPoint.UID = mitk::UIDGeneratorBoost::GenerateUID();
- controlPoint.date = boost::gregorian::date(2019, 02, 01);
- semanticRelationsIntegration.UnlinkImageFromControlPoint(CTImage);
- semanticRelationsIntegration.SetControlPointOfImage(CTImage, controlPoint);
-
- allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two control points should be stored", allControlPoints.size() == 2);
-
- allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two examination periods should be stored", allExaminationPeriods.size() == 2);
-
- auto examinationPeriod = allExaminationPeriods.front();
- CPPUNIT_ASSERT_MESSAGE("Examination period name should be 'New examination period'", examinationPeriod.name == "New examination period");
-
- examinationPeriod.name = "ExaminationPeriod_01";
- semanticRelationsIntegration.RenameExaminationPeriod(caseID, examinationPeriod);
-
- examinationPeriod = mitk::FindFittingExaminationPeriod(MRImage);
- CPPUNIT_ASSERT_MESSAGE("Examination period name should be 'ExaminationPeriod_01'", examinationPeriod.name == "ExaminationPeriod_01");
-
- examinationPeriod = mitk::FindFittingExaminationPeriod(CTImage);
- CPPUNIT_ASSERT_MESSAGE("Examination period name should be 'New examination period'", examinationPeriod.name == "New examination period");
-
- // modify control point to remove examination period and create new one before the first one
- controlPoint.UID = mitk::UIDGeneratorBoost::GenerateUID();
- controlPoint.date = boost::gregorian::date(2018, 01, 01);
- semanticRelationsIntegration.UnlinkImageFromControlPoint(CTImage);
- semanticRelationsIntegration.SetControlPointOfImage(CTImage, controlPoint);
-
- allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Examination period name should be 'ExaminationPeriod_01'", allExaminationPeriods.front().name == "ExaminationPeriod_01");
- CPPUNIT_ASSERT_MESSAGE("Examination period name should be 'New examination period'", allExaminationPeriods.back().name == "New examination period");
-
- mitk::SortAllExaminationPeriods(caseID, allExaminationPeriods);
- CPPUNIT_ASSERT_MESSAGE("Examination period name should be 'New examination period'", allExaminationPeriods.front().name == "New examination period");
- CPPUNIT_ASSERT_MESSAGE("Examination period name should be 'ExaminationPeriod_01'", allExaminationPeriods.back().name == "ExaminationPeriod_01");
- CPPUNIT_ASSERT_MESSAGE("Two examination periods should be stored", allExaminationPeriods.size() == 2);
- }
-
- void SegmentationAndLesion()
- {
- MITK_INFO << "=== SegmentationAndLesion";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
-
- // Patient2
- auto image = mitk::SemanticRelationsTestHelper::GetPatientTwoPETImage();
- m_DataStorage->Add(image);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", image.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", image->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(image);
-
- auto segmentation = mitk::SemanticRelationsTestHelper::GetPatientTwoSegmentation();
- m_DataStorage->Add(segmentation, image);
- CPPUNIT_ASSERT_MESSAGE("Not a valid segmentation data node", segmentation.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Segmentation data is empty", segmentation->GetData() != nullptr);
- semanticRelationsIntegration.AddSegmentation(segmentation, image);
-
- // start test
- auto allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- CPPUNIT_ASSERT_MESSAGE("Two CaseIDs should be stored", allCaseIDs.size() == 2);
-
- // test lesion (add and link)
- auto lesion = mitk::GenerateNewLesion();
- semanticRelationsIntegration.AddLesionAndLinkSegmentation(segmentation, lesion);
-
- auto representedLesion = mitk::SemanticRelationsInference::GetLesionOfSegmentation(segmentation);
- CPPUNIT_ASSERT_MESSAGE("Represented lesion should be the only stored lesion", lesion.UID == representedLesion.UID);
- }
-
- void InvalidData()
- {
- MITK_INFO << "=== InvalidData";
-
- // TEST INVALID CASE ID
- std::string caseID = "invalidID";
- auto allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No lesion should be stored, given a non-existing CaseID", allLesions.size() == 0);
-
- auto allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No control point should be stored, given a non-existing CaseID", allControlPoints.size() == 0);
-
- auto allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No examination periods should be stored, given a non-existing CaseID", allExaminationPeriods.size() == 0);
-
- auto allInformationTypes = mitk::RelationStorage::GetAllInformationTypesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No information type should be stored, given a non-existing CaseID", allInformationTypes.size() == 0);
-
- auto allImageIDsOfCase = mitk::RelationStorage::GetAllImageIDsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No image ID should be stored, given a non-existing CaseID", allControlPoints.size() == 0);
-
- bool instanceExists = mitk::RelationStorage::InstanceExists(caseID);
- CPPUNIT_ASSERT_MESSAGE("CaseID should not exist", !instanceExists);
-
- // TEST INVALID DATE
- mitk::DataNode::Pointer invalidDateImage = mitk::SemanticRelationsTestHelper::GetInvalidDate();
- m_DataStorage->Add(invalidDateImage);
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", invalidDateImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", invalidDateImage->GetData() != nullptr);
-
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: AddImage",
- semanticRelationsIntegration.AddImage(invalidDateImage),
- mitk::SemanticRelationException);
-
- auto controlPointOfImage = mitk::SemanticRelationsInference::GetControlPointOfImage(invalidDateImage);
- CPPUNIT_ASSERT_MESSAGE("No control point should be stored for an invalid DICOM date", controlPointOfImage.UID.empty());
-
- // set invalid date format for current image
- // 0x0008, 0x0022 (AcquisitionDate), should be 20180101
- invalidDateImage->GetData()->SetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0022).c_str(),
- mitk::StringProperty::New("201811"));
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: GenerateControlPoint",
- mitk::GenerateControlPoint(invalidDateImage),
- mitk::SemanticRelationException);
-
- // set valid date format for current image and add image again (only control point should be updated)
- // 0x0008, 0x0022 (AcquisitionDate), should be 20180101
- invalidDateImage->GetData()->SetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0022).c_str(),
- mitk::StringProperty::New("20180101"));
- semanticRelationsIntegration.AddImage(invalidDateImage);
-
- controlPointOfImage = mitk::SemanticRelationsInference::GetControlPointOfImage(invalidDateImage);
- mitk::SemanticTypes::ControlPoint controlPointToCompare;
- controlPointToCompare.date = boost::gregorian::date(2018, 01, 01);
- CPPUNIT_ASSERT_MESSAGE("Control point not correctly stored", controlPointOfImage.date == controlPointToCompare.date);
-
- // TEST INVALID MODALITY
- mitk::DataNode::Pointer invalidModalityImage = mitk::SemanticRelationsTestHelper::GetInvalidModality();
- m_DataStorage->Add(invalidModalityImage);
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", invalidModalityImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", invalidModalityImage->GetData() != nullptr);
-
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: AddImage",
- semanticRelationsIntegration.AddImage(invalidModalityImage),
- mitk::SemanticRelationException);
-
- auto informationTypeOfImage = mitk::SemanticRelationsInference::GetInformationTypeOfImage(invalidModalityImage);
- CPPUNIT_ASSERT_MESSAGE("No information type should be stored for an invalid DICOM date", informationTypeOfImage.empty());
-
- // set valid modality for current image and add image again
- // 0x0008, 0x0060 (Modality), should be CT
- invalidModalityImage->GetData()->SetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0060).c_str(),
- mitk::StringProperty::New("CT"));
- semanticRelationsIntegration.AddImage(invalidModalityImage);
-
- auto informationType = mitk::SemanticRelationsInference::GetInformationTypeOfImage(invalidModalityImage);
- CPPUNIT_ASSERT_MESSAGE("Information type not correctly stored", informationType == "CT");
-
- // TEST INVALID ID
- mitk::DataNode::Pointer invalidIDImage = mitk::SemanticRelationsTestHelper::GetInvalidID();
- m_DataStorage->Add(invalidIDImage);
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", invalidModalityImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", invalidModalityImage->GetData() != nullptr);
-
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: AddImage",
- semanticRelationsIntegration.AddImage(invalidIDImage),
- mitk::SemanticRelationException);
-
- // set valid ID for current image and add image again
- // 0x0020, 0x000e (SeriesInstanceUID)
- auto generatedUID = mitk::UIDGeneratorBoost::GenerateUID();
- invalidIDImage->GetData()->SetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0020, 0x000e).c_str(),
- mitk::StringProperty::New(generatedUID));
- semanticRelationsIntegration.AddImage(invalidIDImage);
-
- auto IDFromNode = mitk::GetIDFromDataNode(invalidIDImage);
- CPPUNIT_ASSERT_MESSAGE("ID not correctly stored", IDFromNode == generatedUID);
-
- // TEST INVALID CASE ID
- mitk::DataNode::Pointer invalidCaseIDImage = mitk::SemanticRelationsTestHelper::GetInvalidCaseID();
- m_DataStorage->Add(invalidCaseIDImage);
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", invalidModalityImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", invalidModalityImage->GetData() != nullptr);
-
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: AddImage",
- semanticRelationsIntegration.AddImage(invalidCaseIDImage),
- mitk::SemanticRelationException);
-
- // set valid case ID for current image and add image again
- // 0x0010, 0x0010 (PatientName)
- invalidCaseIDImage->GetData()->SetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0010, 0x0010).c_str(),
- mitk::StringProperty::New("Patient7"));
- semanticRelationsIntegration.AddImage(invalidCaseIDImage);
-
- auto caseIDFromNode = mitk::GetCaseIDFromDataNode(invalidCaseIDImage);
- CPPUNIT_ASSERT_MESSAGE("Case ID not correctly stored", caseIDFromNode == "Patient7");
- }
-
- // InferenceTest
- void CombinedQueries()
- {
- MITK_INFO << "=== CombinedQueries";
-
- // add image with segmentation and lesion
- auto image = mitk::SemanticRelationsTestHelper::GetPatientTwoPETImage();
- m_DataStorage->Add(image);
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", image.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", image->GetData() != nullptr);
-
- auto segmentation = mitk::SemanticRelationsTestHelper::GetPatientTwoSegmentation();
- m_DataStorage->Add(segmentation, image);
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid segmentation data node", segmentation.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Segmentation data is empty", segmentation->GetData() != nullptr);
-
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- semanticRelationsIntegration.AddImage(image);
- semanticRelationsIntegration.AddSegmentation(segmentation, image);
-
- auto caseID = mitk::GetCaseIDFromDataNode(image);
-
- auto lesion = mitk::GenerateNewLesion();
- semanticRelationsIntegration.AddLesionAndLinkSegmentation(segmentation, lesion);
-
- auto allLesionsOfImage = mitk::SemanticRelationsInference::GetAllLesionsOfImage(image);
- CPPUNIT_ASSERT_MESSAGE("One lesion should be stored", allLesionsOfImage.size() == 1);
-
- auto controlPoint = mitk::SemanticRelationsInference::GetControlPointOfImage(image);
- auto allLesionsOfControlPoint = mitk::SemanticRelationsInference::GetAllLesionsOfControlPoint(caseID, controlPoint);
- CPPUNIT_ASSERT_MESSAGE("Lesions should be the same", (allLesionsOfImage.size() == allLesionsOfControlPoint.size())
- && (allLesionsOfImage.front().UID == allLesionsOfControlPoint.front().UID));
-
- auto allImageIDsOfLesion = mitk::SemanticRelationsInference::GetAllImageIDsOfLesion(caseID, allLesionsOfControlPoint.front());
- CPPUNIT_ASSERT_MESSAGE("Image IDs should be the same", (allImageIDsOfLesion.size() == 1)
- && (allImageIDsOfLesion.front() == mitk::GetIDFromDataNode(image)));
-
- auto allControlPointsOfLesion = mitk::SemanticRelationsInference::GetAllControlPointsOfLesion(caseID, allLesionsOfImage.front());
- CPPUNIT_ASSERT_MESSAGE("Control points should be the same", (allControlPointsOfLesion.size() == 1)
- && (allControlPointsOfLesion.front().date == controlPoint.date));
-
- auto informationType = mitk::SemanticRelationsInference::GetInformationTypeOfImage(image);
- auto allLesionsOfInformationType = mitk::SemanticRelationsInference::GetAllLesionsOfInformationType(caseID, informationType);
- CPPUNIT_ASSERT_MESSAGE("Lesions should be the same", (allLesionsOfImage.size() == allLesionsOfInformationType.size())
- && (allLesionsOfImage.front().UID == allLesionsOfInformationType.front().UID));
-
- auto allControlPointsOfInformationType = mitk::SemanticRelationsInference::GetAllControlPointsOfInformationType(caseID, informationType);
- CPPUNIT_ASSERT_MESSAGE("Control points should be the same", (allControlPointsOfLesion.size() == 1)
- && (allControlPointsOfLesion.front().date == controlPoint.date));
-
- auto allInformationTypesOfControlPoint = mitk::SemanticRelationsInference::GetAllInformationTypesOfControlPoint(caseID, controlPoint);
- CPPUNIT_ASSERT_MESSAGE("Information types should be the same", (allInformationTypesOfControlPoint.size() == 1)
- && (allInformationTypesOfControlPoint.front() == informationType));
-
- auto allSpecificLesions = mitk::SemanticRelationsInference::GetAllSpecificLesions(caseID, controlPoint, informationType);
- CPPUNIT_ASSERT_MESSAGE("Lesions should be the same", (allLesionsOfImage.size() == allSpecificLesions.size())
- && (allLesionsOfImage.front().UID == allSpecificLesions.front().UID));
- }
-
- void InstanceExistences()
- {
- MITK_INFO << "=== InstanceExistences";
-
- mitk::SemanticRelationsDataStorageAccess semanticRelationsDataStorageAccess(m_DataStorage);
- auto allSegmentationsOfCase = semanticRelationsDataStorageAccess.GetAllSegmentationsOfCase("Patient2");
- CPPUNIT_ASSERT_MESSAGE("One segmentation should be stored", allSegmentationsOfCase.size() == 1);
-
- auto segmentation = allSegmentationsOfCase.front();
- CPPUNIT_ASSERT_MESSAGE("Not a valid segmentation data node", segmentation.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Segmentation data is empty", segmentation->GetData() != nullptr);
-
- bool valid = mitk::SemanticRelationsInference::IsRepresentingALesion(segmentation);
- CPPUNIT_ASSERT_MESSAGE("Segmentation node should represent a lesion", valid);
-
- auto caseID = "Patient2";
- valid = mitk::SemanticRelationsInference::IsRepresentingALesion(caseID, mitk::GetIDFromDataNode(segmentation));
- CPPUNIT_ASSERT_MESSAGE("Segmentation (via ID) should represent a lesion", valid);
-
- auto allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesion should be stored", allLesions.size() == 1);
-
- auto lesion = allLesions.front();
- valid = mitk::SemanticRelationsInference::IsLesionPresent(lesion, segmentation);
- CPPUNIT_ASSERT_MESSAGE("Lesion should be present on segmentation", valid);
-
- auto allImagesOfCase = semanticRelationsDataStorageAccess.GetAllImagesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One image should be stored", allImagesOfCase.size() == 1);
-
- auto image = allImagesOfCase.front();
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", image.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", image->GetData() != nullptr);
-
- valid = mitk::SemanticRelationsInference::IsLesionPresent(lesion, image);
- CPPUNIT_ASSERT_MESSAGE("Lesion should be present on image", valid);
-
- valid = mitk::SemanticRelationsInference::IsLesionPresentOnImage(caseID, lesion, mitk::GetIDFromDataNode(image));
- CPPUNIT_ASSERT_MESSAGE("Lesion should be present on segmentation", valid);
-
- valid = mitk::SemanticRelationsInference::IsLesionPresentOnSegmentation(caseID, lesion, mitk::GetIDFromDataNode(segmentation));
- CPPUNIT_ASSERT_MESSAGE("Lesion should be present on image", valid);
-
- auto controlPoint = mitk::SemanticRelationsInference::GetControlPointOfImage(image);
- valid = mitk::SemanticRelationsInference::IsLesionPresentAtControlPoint(caseID, lesion, controlPoint);
- CPPUNIT_ASSERT_MESSAGE("Lesion should be present at control point", valid);
-
- controlPoint.date = boost::gregorian::date(2019, 01, 01);
- valid = mitk::SemanticRelationsInference::IsLesionPresentAtControlPoint(caseID, lesion, controlPoint);
- CPPUNIT_ASSERT_MESSAGE("No lesion should be present at control point", !valid);
-
- valid = mitk::SemanticRelationsInference::InstanceExists(image);
- CPPUNIT_ASSERT_MESSAGE("Image should exist", valid);
-
- valid = mitk::SemanticRelationsInference::InstanceExists(segmentation);
- CPPUNIT_ASSERT_MESSAGE("Segmentation should exist", valid);
-
- valid = mitk::SemanticRelationsInference::InstanceExists(caseID, lesion);
- CPPUNIT_ASSERT_MESSAGE("Lesion should exist", valid);
-
- auto emptyLesion = mitk::GenerateNewLesion("ExampleLesionClass");
- valid = mitk::SemanticRelationsInference::InstanceExists(caseID, emptyLesion);
- CPPUNIT_ASSERT_MESSAGE("Lesion should not exist", !valid);
-
- auto newControlPoint = mitk::SemanticTypes::ControlPoint();
- valid = mitk::SemanticRelationsInference::InstanceExists(caseID, newControlPoint);
- CPPUNIT_ASSERT_MESSAGE("Control point should not exist for this case", !valid);
-
- valid = mitk::SemanticRelationsInference::InstanceExists(caseID, controlPoint);
- CPPUNIT_ASSERT_MESSAGE("Control point should exist for this case", valid);
-
- auto allExaminationPeriod = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be stored", allExaminationPeriod.size() == 1);
- auto examinationPeriod = allExaminationPeriod.front();
-
- valid = mitk::SemanticRelationsInference::InstanceExists(caseID, examinationPeriod);
- CPPUNIT_ASSERT_MESSAGE("Examination period should exist for this case", valid);
-
- auto informationType = mitk::SemanticRelationsInference::GetInformationTypeOfImage(image);
- valid = mitk::SemanticRelationsInference::InstanceExists(caseID, informationType);
- CPPUNIT_ASSERT_MESSAGE("Control point should exist for this case", valid);
-
- valid = mitk::SemanticRelationsInference::InstanceExists(caseID, "CT");
- CPPUNIT_ASSERT_MESSAGE("Control point should not exist for this case", !valid);
-
- valid = mitk::SemanticRelationsInference::SpecificImageExists(caseID, lesion, informationType);
- CPPUNIT_ASSERT_MESSAGE("Specific image should exist for this case", valid);
-
- valid = mitk::SemanticRelationsInference::SpecificImageExists(caseID, lesion, controlPoint);
- CPPUNIT_ASSERT_MESSAGE("Specific image should exist for this case", valid);
-
- valid = mitk::SemanticRelationsInference::SpecificImageExists(caseID, informationType, controlPoint);
- CPPUNIT_ASSERT_MESSAGE("Specific image should exist for this case", valid);
- }
-
- // DataStorageAccessTest
- void DataStorageAccess()
- {
- MITK_INFO << "=== DataStorageAccess";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
-
- // Patient1
- auto CTImage = mitk::SemanticRelationsTestHelper::GetPatientOneCTImage();
- m_DataStorage->Add(CTImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", CTImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", CTImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(CTImage);
-
- auto MRImage = mitk::SemanticRelationsTestHelper::GetPatientOneMRImage();
- m_DataStorage->Add(MRImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", MRImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", MRImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(MRImage);
-
- auto otherCTImage = mitk::SemanticRelationsTestHelper::GetPatientOneOtherCTImage();
- m_DataStorage->Add(otherCTImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", otherCTImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", otherCTImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(otherCTImage);
-
- // Patient2
- auto PETImage = mitk::SemanticRelationsTestHelper::GetPatientTwoPETImage();
- m_DataStorage->Add(PETImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", PETImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", PETImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(PETImage);
-
- auto PETSegmentation = mitk::SemanticRelationsTestHelper::GetPatientTwoSegmentation();
- m_DataStorage->Add(PETSegmentation, PETImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid segmentation data node", PETSegmentation.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Segmentation data is empty", PETSegmentation->GetData() != nullptr);
- semanticRelationsIntegration.AddSegmentation(PETSegmentation, PETImage);
-
- auto lesion = mitk::GenerateNewLesion();
- semanticRelationsIntegration.AddLesionAndLinkSegmentation(PETSegmentation, lesion);
-
- // start test
- mitk::SemanticRelationsDataStorageAccess semanticRelationsDataStorageAccess(m_DataStorage);
-
- auto caseID = "Patient1";
- auto allSegmentationsOfCase = semanticRelationsDataStorageAccess.GetAllSegmentationsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No segmentation should be stored", allSegmentationsOfCase.size() == 0);
-
- auto allImagesOfCase = semanticRelationsDataStorageAccess.GetAllImagesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Three images should be stored", allImagesOfCase.size() == 3);
-
- auto allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No lesion should be stored", allLesions.size() == 0);
-
- auto emptyLesion = mitk::GenerateNewLesion("ExampleLesionClass");
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: GetAllSegmentationsOfLesion",
- semanticRelationsDataStorageAccess.GetAllSegmentationsOfLesion(caseID, emptyLesion),
- mitk::SemanticRelationException);
-
- auto examinationPeriod = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be stored", examinationPeriod.size() == 1);
- auto allSpecificImages = semanticRelationsDataStorageAccess.GetAllSpecificImages(caseID, "CT", examinationPeriod.front());
- CPPUNIT_ASSERT_MESSAGE("Two CT images should be stored", allSpecificImages.size() == 2);
-
- caseID = "Patient2";
- allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesion should be stored", allLesions.size() == 1);
-
- lesion = allLesions.front();
- auto allSegmentationsOfLesion = semanticRelationsDataStorageAccess.GetAllSegmentationsOfLesion(caseID, lesion);
- CPPUNIT_ASSERT_MESSAGE("One segmentation should be stored", allSegmentationsOfLesion.size() == 1);
-
- auto allImagesOfLesion = semanticRelationsDataStorageAccess.GetAllImagesOfLesion(caseID, lesion);
- CPPUNIT_ASSERT_MESSAGE("One image should be stored", allImagesOfLesion.size() == 1);
-
- auto allControlPointsOfLesion = mitk::SemanticRelationsInference::GetAllControlPointsOfLesion(caseID, lesion);
- CPPUNIT_ASSERT_MESSAGE("One control point should be stored", allControlPointsOfLesion.size() == 1);
- auto controlPoint = allControlPointsOfLesion.front();
-
- allSpecificImages = semanticRelationsDataStorageAccess.GetAllSpecificImages(caseID, controlPoint, "PT");
- CPPUNIT_ASSERT_MESSAGE("One image should be stored", allSpecificImages.size() == 1);
-
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: GetAllSpecificImages",
- semanticRelationsDataStorageAccess.GetAllSpecificImages(caseID, controlPoint, "CT"),
- mitk::SemanticRelationException);
-
- auto allSpecificSegmentations = semanticRelationsDataStorageAccess.GetAllSpecificSegmentations(caseID, controlPoint, "PT");
- CPPUNIT_ASSERT_MESSAGE("One segmentation should be stored", allSpecificSegmentations.size() == 1);
-
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: GetAllSpecificSegmentations",
- semanticRelationsDataStorageAccess.GetAllSpecificSegmentations(caseID, controlPoint, "MR"),
- mitk::SemanticRelationException);
-
- auto specificSegmentation = semanticRelationsDataStorageAccess.GetSpecificSegmentation(caseID, controlPoint, "PT", lesion);
- CPPUNIT_ASSERT_MESSAGE("One segmentation should be stored", specificSegmentation == PETSegmentation);
-
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: GetAllSpecificSegmentations",
- semanticRelationsDataStorageAccess.GetSpecificSegmentation(caseID, controlPoint, "CT", lesion),
- mitk::SemanticRelationException);
- }
-
- // RemoveAndUnlinkTest
- void CPRemoveAndUnlink()
- {
- MITK_INFO << "=== RemoveAndUnlink";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
-
- auto CTImage = mitk::SemanticRelationsTestHelper::GetPatientThreeCTImage();
- m_DataStorage->Add(CTImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", CTImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", CTImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(CTImage);
-
- auto MRImage = mitk::SemanticRelationsTestHelper::GetPatientThreeMRImage();
- m_DataStorage->Add(MRImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", MRImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", MRImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(MRImage);
-
- // start test
- auto allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- CPPUNIT_ASSERT_MESSAGE("One CaseID should be stored", allCaseIDs.size() == 1);
-
- auto caseID = allCaseIDs.front();
- CPPUNIT_ASSERT_MESSAGE("CaseID should be Patient3", caseID == "Patient3");
-
- auto allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be sored", allExaminationPeriods.size() == 1);
-
- auto allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two control points should be stored", allControlPoints.size() == 2);
-
- // control points
- auto CTControlPoint = mitk::SemanticRelationsInference::GetControlPointOfImage(CTImage);
- semanticRelationsIntegration.UnlinkImageFromControlPoint(CTImage);
-
- allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be stored", allExaminationPeriods.size() == 1);
-
- allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One control point should be stored since one has been removed", allControlPoints.size() == 1);
-
- CTControlPoint = mitk::SemanticRelationsInference::GetControlPointOfImage(CTImage);
- CPPUNIT_ASSERT_MESSAGE("Control point should be removed", CTControlPoint.UID.empty());
-
- CTControlPoint = mitk::GenerateControlPoint(CTImage);
- semanticRelationsIntegration.SetControlPointOfImage(CTImage, CTControlPoint);
-
- allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be sored", allExaminationPeriods.size() == 1);
-
- allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two control points should be stored", allControlPoints.size() == 2);
-
- mitk::SemanticTypes::ControlPoint newCTControlPoint;
- newCTControlPoint.UID = mitk::UIDGeneratorBoost::GenerateUID();
- newCTControlPoint.date = boost::gregorian::date(2019, 03, 01);
- semanticRelationsIntegration.SetControlPointOfImage(CTImage, newCTControlPoint);
-
- allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One examination period should be sored", allExaminationPeriods.size() == 1);
-
- allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two control points should be stored", allControlPoints.size() == 2);
-
- newCTControlPoint.UID = mitk::UIDGeneratorBoost::GenerateUID();
- newCTControlPoint.date = boost::gregorian::date(2019, 01, 01);
- semanticRelationsIntegration.SetControlPointOfImage(CTImage, newCTControlPoint);
-
- allExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two examination periods should be stored", allExaminationPeriods.size() == 2);
-
- allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two control points should be stored", allControlPoints.size() == 2);
- }
-
- void LesionRemoveAndUnlink()
- {
- MITK_INFO << "=== LesionRemoveAndUnlink";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- mitk::SemanticRelationsDataStorageAccess semanticRelationsDataStorageAccess(m_DataStorage);
-
- auto allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- CPPUNIT_ASSERT_MESSAGE("One CaseID should be stored", allCaseIDs.size() == 1);
- auto caseID = allCaseIDs.front();
-
- auto allImages = semanticRelationsDataStorageAccess.GetAllImagesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two images should be stored", allImages.size() == 2);
-
- auto allCTImageIDs = mitk::RelationStorage::GetAllImageIDsOfInformationType(caseID, "CT");
- CPPUNIT_ASSERT_MESSAGE("One image should be stored", allCTImageIDs.size() == 1);
-
- auto allMRImageIDs = mitk::RelationStorage::GetAllImageIDsOfInformationType(caseID, "MR");
- CPPUNIT_ASSERT_MESSAGE("One image should be stored", allMRImageIDs.size() == 1);
-
- mitk::DataNode::Pointer CTImage;
- mitk::DataNode::Pointer MRImage;
- for (const auto& image : allImages)
- {
- auto imageID = mitk::GetIDFromDataNode(image);
- if (imageID == allCTImageIDs.front())
- {
- CTImage = image;
- }
- else if (imageID == allMRImageIDs.front())
- {
- MRImage = image;
- }
- }
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", CTImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", CTImage->GetData() != nullptr);
-
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", MRImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", MRImage->GetData() != nullptr);
-
- auto CTSegmentation = mitk::SemanticRelationsTestHelper::GetPatientThreeCTSegmentation();
- m_DataStorage->Add(CTSegmentation, CTImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid segmentation data node", CTSegmentation.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Segmentation data is empty", CTSegmentation->GetData() != nullptr);
- semanticRelationsIntegration.AddSegmentation(CTSegmentation, CTImage);
-
- auto MRSegmentation = mitk::SemanticRelationsTestHelper::GetPatientThreeMRSegmentation();
- m_DataStorage->Add(MRSegmentation, MRImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid segmentation data node", MRSegmentation.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Segmentation data is empty", MRSegmentation->GetData() != nullptr);
- semanticRelationsIntegration.AddSegmentation(MRSegmentation, MRImage);
-
- auto newLesion = mitk::GenerateNewLesion();
- semanticRelationsIntegration.AddLesionAndLinkSegmentation(CTSegmentation, newLesion);
- newLesion = mitk::GenerateNewLesion();
- semanticRelationsIntegration.AddLesionAndLinkSegmentation(MRSegmentation, newLesion);
-
- // start test
- auto allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two lesions should be stored", allLesions.size() == 2);
-
- auto MRLesion = mitk::SemanticRelationsInference::GetLesionOfSegmentation(MRSegmentation);
- semanticRelationsIntegration.UnlinkSegmentationFromLesion(MRSegmentation);
-
- allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two lesions should be stored", allLesions.size() == 2);
-
- auto emptyLesion = mitk::SemanticRelationsInference::GetLesionOfSegmentation(MRSegmentation);
- CPPUNIT_ASSERT_MESSAGE("Lesion should be removed", emptyLesion.UID.empty());
-
- semanticRelationsIntegration.LinkSegmentationToLesion(MRSegmentation, MRLesion);
- allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two lesions should be stored", allLesions.size() == 2);
-
- auto CTLesion = mitk::SemanticRelationsInference::GetLesionOfSegmentation(CTSegmentation);
- CPPUNIT_ASSERT_THROW_MESSAGE("Semantic relation exception not thrown: RemoveLesion",
- semanticRelationsIntegration.RemoveLesion(caseID, CTLesion),
- mitk::SemanticRelationException);
-
- semanticRelationsIntegration.UnlinkSegmentationFromLesion(CTSegmentation);
- semanticRelationsIntegration.RemoveLesion(caseID, CTLesion);
-
- allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesions should be stored since one has been removed", allLesions.size() == 1);
-
- CTLesion = mitk::SemanticRelationsInference::GetLesionOfSegmentation(CTSegmentation);
- CPPUNIT_ASSERT_MESSAGE("Lesion should be removed", CTLesion.UID.empty());
- }
-
- void RemoveImagesAndSegmentation()
- {
- MITK_INFO << "=== RemoveImagesAndSegmentation";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- mitk::SemanticRelationsDataStorageAccess semanticRelationsDataStorageAccess(m_DataStorage);
-
- auto allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- CPPUNIT_ASSERT_MESSAGE("One CaseID should be stored", allCaseIDs.size() == 1);
- auto caseID = allCaseIDs.front();
-
- auto allImages = semanticRelationsDataStorageAccess.GetAllImagesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two images should be stored", allImages.size() == 2);
-
- auto allSegmentations = semanticRelationsDataStorageAccess.GetAllSegmentationsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("Two segmentations should be stored", allSegmentations.size() == 2);
-
- for (const auto& image : allImages)
- {
- semanticRelationsIntegration.RemoveImage(image);
- }
-
- for (const auto& segmentation : allSegmentations)
- {
- semanticRelationsIntegration.RemoveSegmentation(segmentation);
- }
-
- allImages = semanticRelationsDataStorageAccess.GetAllImagesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No images should be stored", allImages.size() == 0);
-
- allSegmentations = semanticRelationsDataStorageAccess.GetAllSegmentationsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No segmentations should be stored", allSegmentations.size() == 0);
-
- auto allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No control point should be stored", allControlPoints.size() == 0);
-
- auto allInformationTypes = mitk::RelationStorage::GetAllInformationTypesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("No information type should be stored", allInformationTypes.size() == 0);
-
- auto allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesions should be stored", allLesions.size() == 1);
- }
-
- // LesionAndControlPointTest
- void LesionDataTest()
- {
- MITK_INFO << "=== LesionDataTest";
-
- // load data
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
-
- // CT image
- auto CTImage = mitk::SemanticRelationsTestHelper::GetPatientThreeCTImage();
- m_DataStorage->Add(CTImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", CTImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", CTImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(CTImage);
-
- // MR image
- auto MRImage = mitk::SemanticRelationsTestHelper::GetPatientThreeMRImage();
- m_DataStorage->Add(MRImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid image data node", MRImage.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Image data is empty", MRImage->GetData() != nullptr);
- semanticRelationsIntegration.AddImage(MRImage);
-
- auto segmentation = mitk::SemanticRelationsTestHelper::GetPatientThreeMRSegmentation();
- m_DataStorage->Add(segmentation, MRImage);
- CPPUNIT_ASSERT_MESSAGE("Not a valid segmentation data node", segmentation.IsNotNull());
- CPPUNIT_ASSERT_MESSAGE("Segmentation data is empty", segmentation->GetData() != nullptr);
- semanticRelationsIntegration.AddSegmentation(segmentation, MRImage);
-
- auto lesion = mitk::GenerateNewLesion();
- semanticRelationsIntegration.AddLesionAndLinkSegmentation(segmentation, lesion);
-
- auto caseID = "Patient3";
- auto allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesions should be stored", allLesions.size() == 1);
-
- lesion = allLesions.front();
- mitk::LesionData lesionData(lesion);
- mitk::ComputeLesionPresence(lesionData, caseID);
-
- auto lesionByUID = mitk::GetLesionByUID(caseID, lesion.UID);
- mitk::LesionData lesionByUIDData;
- lesionByUIDData.SetLesion(lesionByUID);
- mitk::ComputeLesionPresence(lesionByUIDData, caseID);
-
- CPPUNIT_ASSERT_MESSAGE("Lesions should be equal", lesion.UID == lesionByUID.UID && lesionData.GetLesionUID() == lesionByUIDData.GetLesionUID());
- CPPUNIT_ASSERT_MESSAGE("Lesion names should be equal", lesion.name == lesionByUID.name && lesionData.GetLesionName() == lesionByUIDData.GetLesionName());
- CPPUNIT_ASSERT_MESSAGE("Lesion classes should be equal", lesion.lesionClass.UID == lesionByUID.lesionClass.UID);
- CPPUNIT_ASSERT_MESSAGE("Lesion presences should be equal", lesionData.GetLesionPresence() == lesionByUIDData.GetLesionPresence());
- CPPUNIT_ASSERT_MESSAGE("Lesion presence should be 'false' and 'true'", lesionData.GetLesionPresence()[0] == false && lesionData.GetLesionPresence()[1] == true);
- }
-
- void LesionOverwriteTest()
- {
- MITK_INFO << "=== LesionOverwriteTest";
-
- auto caseID = "Patient3";
- auto allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesions should be stored", allLesions.size() == 1);
-
- auto lesion = allLesions.front();
- CPPUNIT_ASSERT_MESSAGE("Lesion name should be 'New lesion'", lesion.name == "New lesion");
- CPPUNIT_ASSERT_MESSAGE("Lesion class type should be empty", lesion.lesionClass.classType == "");
-
- lesion.name = "Lesion_01";
- lesion.lesionClass.classType = "Class_01";
-
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- semanticRelationsIntegration.OverwriteLesion(caseID, lesion);
-
- CPPUNIT_ASSERT_MESSAGE("Lesion name should be 'Lesion_01'", lesion.name == "Lesion_01");
-
- auto foundLesionClass = mitk::FindExistingLesionClass(caseID, "Class_01");
- CPPUNIT_ASSERT_MESSAGE("Lesion class type should be 'Class_01'", foundLesionClass.classType == "Class_01");
-
- allLesions = mitk::RelationStorage::GetAllLesionsOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesions should be stored", allLesions.size() == 1);
-
- auto allLesionClasses = mitk::SemanticRelationsInference::GetAllLesionClassesOfCase(caseID);
- CPPUNIT_ASSERT_MESSAGE("One lesion class should be stored", allLesionClasses.size() == 1);
- }
-};
-
-MITK_TEST_SUITE_REGISTRATION(mitkSemanticRelations)
diff --git a/Modules/SemanticRelations/Test/mitkSemanticRelationsTestHelper.cpp b/Modules/SemanticRelations/Test/mitkSemanticRelationsTestHelper.cpp
deleted file mode 100644
index e81fac00df..0000000000
--- a/Modules/SemanticRelations/Test/mitkSemanticRelationsTestHelper.cpp
+++ /dev/null
@@ -1,331 +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 "mitkSemanticRelationsTestHelper.h"
-
-// mitk semantic relations
-#include "mitkDICOMHelper.h"
-#include "mitkRelationStorage.h"
-#include "mitkUIDGeneratorBoost.h"
-
-// mitk core
-#include <mitkImage.h>
-#include <mitkIPersistenceService.h>
-#include <mitkTemporoSpatialStringProperty.h>
-
-// mitk multilabel
-#include <mitkLabelSetImage.h>
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientOneCTImage()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient1"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20190101"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("CT"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientOneMRImage()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient1"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20190101"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("MR"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientOneOtherCTImage()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient1"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20190131"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("CT"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientTwoPETImage()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient2"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20180101"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("PT"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientTwoSegmentation()
-{
- // create new empty segmentation
- LabelSetImage::Pointer segmentation = LabelSetImage::New();
-
- // set properties of segmentation (base data)
- segmentation->SetProperty(GetCaseIDDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New("Patient2"));
- segmentation->SetProperty(GetNodeIDDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New(UIDGeneratorBoost::GenerateUID()));
- segmentation->SetProperty(GetDateDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New("20180101"));
- // segmentation modality is 'SEG'
-
- // create new data node and add segmentation as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(segmentation);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientThreeCTImage()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient3"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20190201"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("CT"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientThreeCTSegmentation()
-{
- // create new empty segmentation
- LabelSetImage::Pointer segmentation = LabelSetImage::New();
-
- // set properties of segmentation (base data)
- segmentation->SetProperty(GetCaseIDDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New("Patient3"));
- segmentation->SetProperty(GetNodeIDDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New(UIDGeneratorBoost::GenerateUID()));
- segmentation->SetProperty(GetDateDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New("20190201"));
- // segmentation modality is 'SEG'
-
- // create new data node and add segmentation as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(segmentation);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientThreeMRImage()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient3"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20190215"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("MR"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetPatientThreeMRSegmentation()
-{
- // create new empty segmentation
- LabelSetImage::Pointer segmentation = LabelSetImage::New();
-
- // set properties of segmentation (base data)
- segmentation->SetProperty(GetCaseIDDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New("Patient3"));
- segmentation->SetProperty(GetNodeIDDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New(UIDGeneratorBoost::GenerateUID()));
- segmentation->SetProperty(GetDateDICOMProperty().c_str(),
- TemporoSpatialStringProperty::New("20190215"));
- // segmentation modality is 'SEG'
-
- // create new data node and add segmentation as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(segmentation);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetInvalidDate()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient4"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
-
- // no DICOM information for Date
-
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("CT"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetInvalidModality()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient5"));
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20180101"));
-
- // no DICOM information for Modality
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetInvalidID()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- image->SetProperty(GetCaseIDDICOMProperty().c_str(),
- StringProperty::New("Patient6"));
-
- // no DICOM information for NodeID
-
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20180101"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("CT"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsTestHelper::GetInvalidCaseID()
-{
- // create new empty image
- Image::Pointer image = Image::New();
-
- // set properties of image (base data)
- // no DICOM information for CaseID
-
- image->SetProperty(GetNodeIDDICOMProperty().c_str(),
- StringProperty::New(UIDGeneratorBoost::GenerateUID()));
- image->SetProperty(GetDateDICOMProperty().c_str(),
- StringProperty::New("20180101"));
- image->SetProperty(GetModalityDICOMProperty().c_str(),
- StringProperty::New("CT"));
-
- // create new data node and add image as base data
- DataNode::Pointer dataNode = DataNode::New();
- dataNode->SetData(image);
-
- return dataNode;
-}
-
-void mitk::SemanticRelationsTestHelper::ClearRelationStorage()
-{
- // access the storage
- PERSISTENCE_GET_SERVICE_MACRO
- if (nullptr == persistenceService)
- {
- MITK_DEBUG << "Persistence service could not be loaded";
- return;
- }
-
- auto allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- for (auto& caseID : allCaseIDs)
- {
- persistenceService->RemovePropertyList(caseID);
- }
-
- std::string listIdentifier("caseIDs");
- persistenceService->RemovePropertyList(listIdentifier);
-}
diff --git a/Modules/SemanticRelations/Test/mitkSemanticRelationsTestHelper.h b/Modules/SemanticRelations/Test/mitkSemanticRelationsTestHelper.h
deleted file mode 100644
index 64dd853f0b..0000000000
--- a/Modules/SemanticRelations/Test/mitkSemanticRelationsTestHelper.h
+++ /dev/null
@@ -1,71 +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 mitkSemanticRelationsTestHelper_h
-#define mitkSemanticRelationsTestHelper_h
-
-#include <mitkDataNode.h>
-
-namespace mitk
-{
- namespace SemanticRelationsTestHelper
- {
- //////////////////////////////////////////////////////////////////////////
- // VALID DATA NODES
- //////////////////////////////////////////////////////////////////////////
- DataNode::Pointer GetPatientOneCTImage();
-
- DataNode::Pointer GetPatientOneMRImage();
-
- DataNode::Pointer GetPatientOneOtherCTImage();
-
- DataNode::Pointer GetPatientTwoPETImage();
-
- DataNode::Pointer GetPatientTwoSegmentation();
-
- DataNode::Pointer GetPatientThreeCTImage();
-
- DataNode::Pointer GetPatientThreeCTSegmentation();
-
- DataNode::Pointer GetPatientThreeMRImage();
-
- DataNode::Pointer GetPatientThreeMRSegmentation();
-
- //////////////////////////////////////////////////////////////////////////
- // INVALID DATA NODES
- //////////////////////////////////////////////////////////////////////////
- /**
- * @brief Date is 0x0008, 0x0022 (AcquisitionDate)
- */
- DataNode::Pointer GetInvalidDate();
- /**
- * @brief Modality is 0x0008, 0x0060(Modality)
- */
- DataNode::Pointer GetInvalidModality();
- /**
- * @brief ID is 0x0020, 0x000e (SeriesInstanceUID)
- */
- DataNode::Pointer GetInvalidID();
- /**
- * @brief CaseID is 0x0010, 0x0010 (PatientName)
- */
- DataNode::Pointer GetInvalidCaseID();
-
- //////////////////////////////////////////////////////////////////////////
- // AUXILIARY FUNCTIONS
- //////////////////////////////////////////////////////////////////////////
- void ClearRelationStorage();
-
- } // end SemanticRelationsTestHelper
-} // end mitk
-
-#endif
diff --git a/Modules/SemanticRelations/files.cmake b/Modules/SemanticRelations/files.cmake
deleted file mode 100644
index b5e1bddd7a..0000000000
--- a/Modules/SemanticRelations/files.cmake
+++ /dev/null
@@ -1,14 +0,0 @@
-file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*")
-
-set(CPP_FILES
- mitkControlPointManager.cpp
- mitkDICOMHelper.cpp
- mitkLesionData.cpp
- mitkLesionManager.cpp
- mitkNodePredicates.cpp
- mitkRelationStorage.cpp
- mitkSemanticRelationsDataStorageAccess.cpp
- mitkSemanticRelationsInference.cpp
- mitkSemanticRelationsIntegration.cpp
- mitkUIDGeneratorBoost.cpp
-)
diff --git a/Modules/SemanticRelations/include/mitkControlPointManager.h b/Modules/SemanticRelations/include/mitkControlPointManager.h
deleted file mode 100644
index bf3def64bc..0000000000
--- a/Modules/SemanticRelations/include/mitkControlPointManager.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.
-
-============================================================================*/
-
-#ifndef mitkControlPointManager_h
-#define mitkControlPointManager_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-// mitk core
-#include <mitkDataNode.h>
-
-namespace mitk
-{
- /**
- * @brief Provides helper functions that are needed to work with control points.
- *
- * These functions help to generate new control points, check for overlapping / containing control points or provide functionality
- * to find a fitting control point or even extend an already existing control point.
- */
- /**
- * @brief Generates a control point from a given data node.
- * The date is extracted from the data node by using the 'DICOMHelper::GetDICOMDateFromDataNode'-function.
- *
- * @param datanode A data node pointer, whose date should be included in the newly generated control point.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GenerateControlPoint(const mitk::DataNode* datanode);
- /**
- * @brief Find and return a whole control point including its date given a specific control point UID.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPointUID The control point UID as string.
- *
- * @return The control point with its UID and the date.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GetControlPointByUID(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& controlPointUID);
- /**
- * @brief Returns an already existing control point from the given vector of control points. This existing control point has the
- * the same date (year, month, day) as the given single control point.
- * If no existing control point can be found an empty control point is returned.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint The control point to check for existence.
- *
- * @return The existing control point.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindExistingControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Returns an already existing close control point from the given vector of control points. This closest control point has a
- * date that is within a certain distance-in-days to the given control point.
- * If no closest control point can be found within the distance threshold an empty control point is returned.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint The control point to check for distance.
- *
- * @return The closest control point.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint FindClosestControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Returns the examination period to which the given control point belongs.
- * Each examination point holds a vector of control point UIDs so that the UID of the given control point can be compared against the UIDs of the vector.
- * An empty examination period is returned if,
- * - the given vector of examination periods is empty
- * - the examination periods do not contain any control point UIDs
- * - the UID of the given control point is not contained in any examination period
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint The control point of which the examination period should be found.
- *
- * @return The examination period that contains the given control point.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ExaminationPeriod FindContainingExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Return the examination period to which the given data node belongs.
- * The control point is used to find an already existing or the closest control point in the semantic relations storage.
- * If such a control point is found, the 'FindClosestControlPoint'-function with this control point as an argument is used
- * to actually find the corresponding examination period.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint The control point of which the examination period should be found.
- *
- * @return The examination period that fits the given data node.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ExaminationPeriod FindFittingExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Return the examination period to which the given data node belongs.
- * The DICOM date of the data node is used to find an already existing or the closest control point in the semantic relations storage.
- * If such a control point is found, the 'FindFittingExaminationPeriod'-function with this control point as an argument is used
- * to actually find the corresponding examination period.
- *
- * @param dataNode A data node pointer, whose date should be included in the newly generated control point.
- *
- * @return The examination period that contains the given data node.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ExaminationPeriod FindFittingExaminationPeriod(const DataNode* dataNode);
- /**
- * @brief Sort the given vector of examination periods.
- * Each examination period has a vector of control point UIDs (stored in chronological order).
- * The examination periods can be sorted by comparing the first control points of the examination periods.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param allExaminationPeriods The examination periods to sort.
- */
- MITKSEMANTICRELATIONS_EXPORT void SortAllExaminationPeriods(const SemanticTypes::CaseID& caseID, SemanticTypes::ExaminationPeriodVector& allExaminationPeriods);
-
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkDICOMHelper.h b/Modules/SemanticRelations/include/mitkDICOMHelper.h
deleted file mode 100644
index 656ba88ca5..0000000000
--- a/Modules/SemanticRelations/include/mitkDICOMHelper.h
+++ /dev/null
@@ -1,126 +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 mitkDICOMHelper_h
-#define mitkDICOMHelper_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-// mitk core
-#include <mitkDataNode.h>
-#include <mitkDICOMTagPath.h>
-
-// c++
-#include <string>
-
-/*
-* @brief Provides helper functions to convert DICOM Tag information.
-*
-* In order to identify the patient of an image or segmentation or to set the control point of DICOM data,
-* these functions are used to retrieve the DICOM tags from the given data nodes and convert them into semantic types
-* that can be used by the SemanticRelations class.
-*/
-namespace mitk
-{
- /**
- * @brief Creates a property name for a DICOM tag.
- * The tag is "0x0010, 0x0010" (PatientName)
- */
- MITKSEMANTICRELATIONS_EXPORT std::string GetCaseIDDICOMProperty();
- /**
- * @brief Creates a property name for a DICOM tag.
- * The tag is "0x0020, 0x000e" (SeriesInstanceUID)
- */
- MITKSEMANTICRELATIONS_EXPORT std::string GetNodeIDDICOMProperty();
- /**
- * @brief Creates a property name for a DICOM tag.
- * The tag is "0x0008, 0x0022" (AcquisitionDate)
- */
- MITKSEMANTICRELATIONS_EXPORT std::string GetDateDICOMProperty();
- /**
- * @brief Creates a property name for a DICOM tag.
- * The tag is "0x0008, 0x0060" (Modality)
- */
- MITKSEMANTICRELATIONS_EXPORT std::string GetModalityDICOMProperty();
- /*
- * @brief Extracts a specific DICOM tag from the node's base data
- * and returns the tag as a string. This tag string is used as an identifier for the patient (case).
- *
- * @pre The given data node or the node's base data has to be valid (!nullptr).
- * @pre The node's base data has to have the specific DICOM Tag property set.
- * @throw mitk::Exception if the given data node, the node's base data or the extracted DICOM tag are invalid (==nullptr).
- *
- * @par dataNode The data node, of which the DICOM tag should be extracted.
- *
- * @return The extracted DICOM tag as string.
- * An empty string, if the DICOM tag can not be extracted (i.e. the data node or
- * the underlying base data is invalid or the DICOM tag does not exist for the given data node).
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::CaseID GetCaseIDFromDataNode(const mitk::DataNode* dataNode);
- /*
- * @brief Extracts a specific DICOM tag (currently "0x0020, 0x000e": SeriesInstanceUID) from the node's base data
- * and returns the tag as a string. This tag string is used as an identifier for the image instance.
- *
- * @pre The given data node or the node's base data has to be valid (!nullptr).
- * @pre The node's base data has to have the "0x0020, 0x000e" DICOM Tag property set.
- * @throw mitk::Exception if the given data node, the node's base data or the extracted DICOM tag are invalid (==nullptr).
- *
- * @par dataNode The data node, of which the DICOM tag should be extracted.
- *
- * @return The extracted DICOM tag as string.
- * An empty string, if the DICOM tag can not be extracted (i.e. the data node or
- * the underlying base data is invalid or the DICOM tag does not exist for the given data node).
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ID GetIDFromDataNode(const mitk::DataNode* dataNode);
- /*
- * @brief Extracts a specific DICOM tag (currently "0x0008, 0x0022": AcquisitionDate) from the node's base data
- * and returns the tag as a control point.
- *
- * @pre The given data node or the node's base data has to be valid (!nullptr).
- * @pre The node's base data has to have the "0x0008, 0x0022" DICOM Tag property set.
- * @throw mitk::Exception if the given data node, the node's base data or the extracted DICOM tag are invalid (==nullptr).
- *
- * @par dataNode The data node, of which the DICOM tag should be extracted.
- *
- * @return The extracted DICOM tag as control point.
- * An empty control point, if the DICOM tag can not be extracted (i.e. the data node or
- * the underlying base data is invalid or the DICOM tag does not exist for the given data node).
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GetDICOMDateFromDataNode(const mitk::DataNode* dataNode);
- /**
- * @brief Extracts a specific DICOM tag from the node's base data and returns the tag as a information type (a string).
- *
- * @pre The given data node or the node's base data has to be valid (!nullptr).
- * @pre The node's base data has to have the "0x0008, 0x0060" DICOM Tag property set.
- * @throw mitk::Exception if the given data node, the node's base data or the extracted DICOM tag are invalid (==nullptr).
- *
- * @par dataNode The data node, of which the DICOM tag should be extracted.
- *
- * @return The extracted DICOM tag as information type (a string).
- * An empty information type, if the DICOM tag can not be extracted (i.e. the data node or
- * the underlying base data is invalid or the DICOM tag does not exist for the given data node).
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::InformationType GetDICOMModalityFromDataNode(const mitk::DataNode* dataNode);
- /*
- * @brief Removes leading and trailing whitespace from the given string.
- *
- * @par identifier The value of a DICOM tag.
- *
- * @return The trimmed DICOM tag
- */
- MITKSEMANTICRELATIONS_EXPORT std::string TrimDICOM(const std::string& identifier);
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkISemanticRelationsObservable.h b/Modules/SemanticRelations/include/mitkISemanticRelationsObservable.h
deleted file mode 100644
index e25acef445..0000000000
--- a/Modules/SemanticRelations/include/mitkISemanticRelationsObservable.h
+++ /dev/null
@@ -1,51 +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 mitkISemanticRelationsObservable_h
-#define mitkISemanticRelationsObservable_h
-
-#include "mitkISemanticRelationsObserver.h"
-
-namespace mitk
-{
- /*
- * @brief This interface declares three functions each observable subject has to implement
- * in order to be observed in the 'Observer pattern' sense.
- * The concrete observable class has to store its observer.
- */
- class ISemanticRelationsObservable
- {
- public:
- /*
- * @brief Adds the given concrete observer to a container that holds all currently registered observer.
- *
- * @param observer The concrete observer to register.
- */
- virtual void AddObserver(ISemanticRelationsObserver* observer) = 0;
- /*
- * @brief Removes the given concrete observer from the container that holds all currently registered observer.
- *
- * @param observer The concrete observer to unregister.
- */
- virtual void RemoveObserver(ISemanticRelationsObserver* observer) = 0;
- /*
- * @brief Updates all concrete observer in the container that holds all currently registered observer.
- * The caseID can be used to only update the observer, if the caseID fulfills a certain condition.
- *
- * @param caseID A caseID that identifies the currently active patient / case.
- */
- virtual void NotifyObserver(const SemanticTypes::CaseID& caseID) const = 0;
-
- }; // class ISemanticRelationsObservable
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkISemanticRelationsObserver.h b/Modules/SemanticRelations/include/mitkISemanticRelationsObserver.h
deleted file mode 100644
index b45f890bfe..0000000000
--- a/Modules/SemanticRelations/include/mitkISemanticRelationsObserver.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkISemanticRelationsObserver_h
-#define mitkISemanticRelationsObserver_h
-
-#include "mitkSemanticTypes.h"
-
-namespace mitk
-{
- /*
- * @brief This interface declares a functions each observer has to implement
- * in order to be notified in the 'Observer pattern' sense.
- */
- class ISemanticRelationsObserver
- {
- public:
- /*
- * @brief Updates the concrete observer.
- * The caseID can be used to get access to a certain patient (case),
- * whose data should be used for updating.
- *
- * @param caseID The current case ID to identify the currently active patient / case.
- */
- virtual void Update(const mitk::SemanticTypes::CaseID& caseID) = 0;
-
- }; // class ISemanticRelationsObserver
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkLesionData.h b/Modules/SemanticRelations/include/mitkLesionData.h
deleted file mode 100644
index b9c00cda7d..0000000000
--- a/Modules/SemanticRelations/include/mitkLesionData.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkLesionData_h
-#define mitkLesionData_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// mitk semantic relations module
-#include "mitkSemanticTypes.h"
-
-// c++
-#include <vector>
-
-namespace mitk
-{
- /**
- * @brief This class holds the data of each lesion in the lesion tree view.
- * The data is the lesion itself with its UID, name and lesion class
- * as well as two vectors for
- * - lesion presence: bool value for each control-point
- * inside the semantic relations storage
- * - lesion volume: double value for each control-point - information type pair
- * inside the semantic relations storage
- *
- */
- class MITKSEMANTICRELATIONS_EXPORT LesionData
- {
- public:
- /**
- * @brief sets the data members to their initial values
- */
- LesionData(const SemanticTypes::Lesion& lesion = SemanticTypes::Lesion());
-
- SemanticTypes::Lesion GetLesion() const { return m_Lesion; };
- SemanticTypes::ID GetLesionUID() const { return m_Lesion.UID; }
- std::string GetLesionName() const { return m_Lesion.name; }
-
- const std::vector<bool>& GetLesionPresence() const { return m_LesionPresence; };
- const std::vector<double>& GetLesionVolume() const { return m_LesionVolume; };
-
- void SetLesion(const SemanticTypes::Lesion& lesion);
- void SetLesionPresence(const std::vector<bool>& lesionPresence);
- void SetLesionVolume(const std::vector<double>& lesionVolume);
-
- private:
-
- SemanticTypes::Lesion m_Lesion;
- std::vector<bool> m_LesionPresence;
- std::vector<double> m_LesionVolume;
-
- };
-} // end namespace
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkLesionManager.h b/Modules/SemanticRelations/include/mitkLesionManager.h
deleted file mode 100644
index 24a92dc1e0..0000000000
--- a/Modules/SemanticRelations/include/mitkLesionManager.h
+++ /dev/null
@@ -1,71 +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 mitkLesionManager_h
-#define mitkLesionManager_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// semantic relations module
-#include "mitkLesionData.h"
-
-/*
-* @brief Provides helper functions that are needed to work with lesions.
-*
-* These functions help to generate new lesions, check for existing lesions or provide functionality
-* to generate new and find existing lesion class types.
-*/
-namespace mitk
-{
- typedef std::vector<SemanticTypes::LesionClass> LesionClassVector;
-
- /**
- * @brief Generate a new lesion and lesion class with UIDs and the given string as lesion class type.
- *
- * @param lesionClassType The lesion class type as string. Default parameter is "".
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::Lesion GenerateNewLesion(const std::string& lesionClassType = "");
- /**
- * @brief Generate a new lesion class with UID and the given string as lesion class type.
- *
- * @param lesionClassType The lesion class type as string. Default parameter is "".
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionClass GenerateNewLesionClass(const std::string& lesionClassType = "");
- /**
- * @brief Find and return a whole lesion including its lesion class given a specific lesion UID.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesionUID The lesion UID as string.
- *
- * @return The lesion with its UID and the lesion class.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::Lesion GetLesionByUID(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionUID);
- /**
- * @brief Find and return the whole lesion class including its UID given a specific lesion class type.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesionClassType The lesion class type as string.
- *
- * @return The lesion class with its UID and the class type.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionClass FindExistingLesionClass(const SemanticTypes::CaseID& caseID, const std::string& lesionClassType);
- /**
- * @brief Compute and store lesion presence for all available control points and information types.
- *
- * @param lesionData The lesion data that holds the lesion and will hold the additional lesion data.
- * @param caseID The current case ID.
- */
- MITKSEMANTICRELATIONS_EXPORT void ComputeLesionPresence(LesionData& lesionData, const SemanticTypes::CaseID& caseID);
-
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkNodePredicates.h b/Modules/SemanticRelations/include/mitkNodePredicates.h
deleted file mode 100644
index f9ef91c869..0000000000
--- a/Modules/SemanticRelations/include/mitkNodePredicates.h
+++ /dev/null
@@ -1,43 +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 mitkNodePredicates_h
-#define mitkNodePredicates_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// mitk core
-#include <mitkNodePredicateAnd.h>
-
-namespace mitk
-{
- namespace NodePredicates
- {
- /*
- * @brief Helper function to get a node predicate that can be used to filter images.
- *
- * The images are of type 'mitk::Image' but must not be 'helper objects' or 'segmentation nodes'.
- * For the definition of 'segmentation nodes' see 'GetSegmentationPredicate'.
- */
- MITKSEMANTICRELATIONS_EXPORT NodePredicateAnd::Pointer GetImagePredicate();
- /*
- * @brief Helper function to get a node predicate that can be used to filter segmentations.
- *
- * The segmentations are of type 'mitk::LabelSetImage' or nodes that have their 'binary' property set to true.
- * Segmentations must not be 'helper objects'.
- */
- MITKSEMANTICRELATIONS_EXPORT NodePredicateAnd::Pointer GetSegmentationPredicate();
-
- } // namespace NodePredicates
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkRelationStorage.h b/Modules/SemanticRelations/include/mitkRelationStorage.h
deleted file mode 100644
index f3a580e6bf..0000000000
--- a/Modules/SemanticRelations/include/mitkRelationStorage.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 mitkRelationStorage_h
-#define mitkRelationStorage_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-namespace mitk
-{
- namespace RelationStorage
- {
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID);
- SemanticTypes::Lesion GetLesionOfSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID);
-
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPointVector GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID);
- SemanticTypes::ControlPoint GetControlPointOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID);
-
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ExaminationPeriodVector GetAllExaminationPeriodsOfCase(const SemanticTypes::CaseID& caseID);
-
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::InformationTypeVector GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID);
- SemanticTypes::InformationType GetInformationTypeOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID);
-
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllImageIDsOfCase(const SemanticTypes::CaseID& caseID);
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllImageIDsOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllImageIDsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType);
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllSegmentationIDsOfCase(const SemanticTypes::CaseID& caseID);
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllSegmentationIDsOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID);
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllSegmentationIDsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
-
- SemanticTypes::ID GetImageIDOfSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID);
-
- MITKSEMANTICRELATIONS_EXPORT std::vector<SemanticTypes::CaseID> GetAllCaseIDs();
- MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID);
-
- void AddCase(const SemanticTypes::CaseID& caseID);
- void AddImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID);
- void RemoveImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID);
- void AddSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID, const SemanticTypes::ID& parentID);
- void RemoveSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID);
-
- void AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- void OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- void LinkSegmentationToLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID, const SemanticTypes::Lesion& lesion);
- void UnlinkSegmentationFromLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID);
- void RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- void RemoveLesionClass(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionClassID);
-
- void AddControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- void LinkImageToControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID, const SemanticTypes::ControlPoint& controlPoint);
- void UnlinkImageFromControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID);
- void RemoveControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
-
- void AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- MITKSEMANTICRELATIONS_EXPORT void RenameExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- void AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- void RemoveControlPointFromExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- void RemoveExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod);
-
- void AddInformationTypeToImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID, const SemanticTypes::InformationType& informationType);
- void RemoveInformationTypeFromImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID);
- void RemoveInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType);
-
- } // namespace RelationStorage
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkSemanticRelationException.h b/Modules/SemanticRelations/include/mitkSemanticRelationException.h
deleted file mode 100644
index b091f90d27..0000000000
--- a/Modules/SemanticRelations/include/mitkSemanticRelationException.h
+++ /dev/null
@@ -1,31 +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 mitkSemanticRelationException_h
-#define mitkSemanticRelationException_h
-
-// mitk core
-#include <mitkExceptionMacro.h>
-
-namespace mitk
-{
- class SemanticRelationException : public Exception
- {
-
- public:
-
- mitkExceptionClassMacro(SemanticRelationException, Exception);
-
- };
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkSemanticRelationsDataStorageAccess.h b/Modules/SemanticRelations/include/mitkSemanticRelationsDataStorageAccess.h
deleted file mode 100644
index 6060ebec5d..0000000000
--- a/Modules/SemanticRelations/include/mitkSemanticRelationsDataStorageAccess.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkSemanticRelationsDataStorageAccess_h
-#define mitkSemanticRelationsDataStorageAccess_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-// mitk core
-#include <mitkDataStorage.h>
-#include <mitkWeakPointer.h>
-
-namespace mitk
-{
- /**
- * @brief The API provides functions to query and manipulate image relations and instances,
- * that are helpful during follow-up examination, like control-points (time period),
- * types of the images or lesions that may be visible on multiple images.
- *
- * The class is able to generate IDs from given data nodes using DICOM information.
- * These IDs are used to identify the corresponding instances of a specific case.
- * The case can also be directly identified by the given case ID.
- *
- * In order for most functions to work the case ID has to be used as a parameter.
- * If not, these functions do nothing.
- */
- class MITKSEMANTICRELATIONS_EXPORT SemanticRelationsDataStorageAccess
- {
- public:
-
- using DataNodeVector = std::vector<DataNode::Pointer>;
-
- SemanticRelationsDataStorageAccess(DataStorage* dataStorage);
-
- /************************************************************************/
- /* functions to get instances / attributes */
- /************************************************************************/
- /**
- * @brief Return a vector of all segmentations that are currently available for the given case.
- * The segmentations may be connected / not connected to a lesion of the case.
- * If no segmentations are stored for the current case, an empty vector is returned.
- *
- * @pre The data storage member has to be valid (!nullptr).
- * @throw SemanticRelationException, if the data storage member is invalid (==nullptr).
- *
- * @param caseID The current case identifier is defined by the given string.
- *
- * @return A vector of data nodes representing segmentations.
- */
- DataNodeVector GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) const;
- /**
- * @brief Return a vector of all segmentations that define the given lesion. These segmentations don't have to be linked to the same image.
- * If the lesion is not referred to by any segmentation, an empty vector is returned.
- *
- * @pre The data storage member has to be valid (!nullptr).
- * @throw SemanticRelationException, if the data storage member is invalid (==nullptr).
- * @pre The UID of the lesion has to exist for a lesion instance.
- * @throw SemanticRelationException, if UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- *
- * @return A vector of data nodes representing segmentations that define the given lesion.
- */
- DataNodeVector GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const;
- /**
- * @brief Return a vector of all images that are currently available for the given case.
- *
- * @pre The data storage member has to be valid (!nullptr).
- * @throw SemanticRelationException, if the data storage member is invalid (==nullptr).
- *
- * @param caseID The current case identifier is defined by the given string.
- *
- * @return A vector of data nodes representing images.
- */
- DataNodeVector GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) const;
- /**
- * @brief Return a vector of all images that are specified by the given vector of image IDs.
- *
- * @pre The data storage member has to be valid (!nullptr).
- * @throw SemanticRelationException, if the data storage member is invalid (==nullptr).
- *
- * @param imageIDs A vector of image IDs that represent the images in the data storage.
- *
- * @return A vector of data nodes representing images.
- */
- DataNodeVector GetAllImagesByID(const SemanticTypes::IDVector& imageIDs) const;
- /**
- * @brief Return a vector of all images that are connected to those segmentations that are linked to the given lesion.
- * If the lesion is not referred to by any segmentation, an empty vector is returned.
- *
- * @pre The UID of the lesion has to exist for a lesion instance.
- * @throw SemanticRelationException, if UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- *
- * @return A vector of data nodes representing images on which the lesions are visible.
- */
- DataNodeVector GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const;
- /**
- * @brief Return a vector of all image nodes that are defined with the given control point and the given information type.
- *
- * @pre The UID of the control point has to exist for a control point instance.
- * The information type has to exist for the given case (and is therefore used by at least one data node).
- * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists') or
- * if the information type is not used by any data node (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint A control point with a UID that identifies the corresponding control point instance.
- * @param informationType An information type that identifies the corresponding information type instance.
- *
- * @return A vector of image nodes that are defined with the given control point and the given information type.
- */
- DataNodeVector GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const;
- /**
- * @brief Return a vector of all image nodes that are defined with the given information type and the given examination period.
- * The function uses the 'SemanticRelationsInference::GetAllImageIDsOfExaminationPeriod'-function to retrieve the imageIDs of the examination period and
- * then compares the information type of all these images against the given information type.
- *
- * @param caseID
- * @param informationType An information type that identifies the corresponding information type instance.
- * @param examinationPeriod An examination period that identifies the corresponding examination period instance.
- *
- * @return A vector of image nodes that are defined with the given information type with the given control point.
- */
- DataNodeVector GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ExaminationPeriod& examinationPeriod) const;
- /**
- * @brief Return a vector of all segmentation nodes that are defined with the given control point and the given information type.
- * The function uses the 'GetAllSpecificImages'-function to retrieve the specific images and then searches for the derived nodes (segmentation child nodes).
- *
- * @pre The UID of the control point has to exist for a control point instance.
- * The information type has to exist for the given case (and is therefore used by at least one data node).
- * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists') or
- * if the information type is not used by any data node (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint A control point with a UID that identifies the corresponding control point instance.
- * @param informationType An information type that identifies the corresponding information type instance.
- *
- * @return A vector of segmentation nodes that are defined with the given control point and the given information type.
- */
- DataNodeVector GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const;
- /**
- * @brief Return the single segmentation node that is defined with the given information type, the given control point and is representing the given lesion.
- * The function uses the 'GetAllSpecificSegmentations'-function to retrieve the specific segmentations and then checks for the represented lesion.
- *
- * @pre The UID of the control point has to exist for a control point instance.
- * The information type has to exist for the given case (and is therefore used by at least one data node).
- * The lesion has to exist for the given case.
- * @throw SemanticRelationException, if the UID of the control point does not exist for a control point instance (this can be checked via 'InstanceExists') or
- * if the information type is not used by any data node (this can be checked via 'InstanceExists') or
- * if the lesion does not exist for the given case (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint A control point with a UID that identifies the corresponding control point instance.
- * @param informationType An information type that identifies the corresponding information type instance.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- *
- * @return A single segmentation node that is defined with the given information type, the given control point and is representing the given lesion.
- */
- DataNode::Pointer GetSpecificSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint,
- const SemanticTypes::InformationType& informationType, const SemanticTypes::Lesion& lesion) const;
-
- private:
-
- WeakPointer<DataStorage> m_DataStorage;
-
- };
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkSemanticRelationsInference.h b/Modules/SemanticRelations/include/mitkSemanticRelationsInference.h
deleted file mode 100644
index 67bcf40b3d..0000000000
--- a/Modules/SemanticRelations/include/mitkSemanticRelationsInference.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.
-
-============================================================================*/
-
-#ifndef mitkSemanticRelationsInference_h
-#define mitkSemanticRelationsInference_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-// mitk core
-#include <mitkDataNode.h>
-
-namespace mitk
-{
- /**
- * @brief The API provides functions to query image relations and instances
- * that are helpful during follow-up examination, like control-points (time period),
- * types of the images or lesions that may be visible on multiple images.
- *
- * The class is able to generate IDs from given data nodes using DICOM information.
- * These IDs are used to identify the corresponding instances of a specific case.
- * The case can also be directly identified by the given case ID.
- *
- * In order for most functions to work the case ID has to be used as a parameter.
- * If not, these functions do nothing.
- */
- namespace SemanticRelationsInference
- {
-
- /************************************************************************/
- /* functions to get instances / attributes */
- /************************************************************************/
- /**
- * @brief Return a vector of lesion classes that are currently available for the given case.
- *
- * @param caseID The current case identifier is defined by the given string.
- *
- * @return A vector of lesion classes.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionClassVector GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID);
- /**
- * @brief Return the lesion that is defined by the given segmentation.
- *
- * @pre The given segmentation data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given segmentation is invalid (==nullptr).
- * @pre The segmentation data node has to represent a lesion. If not, the retrieved lesion will be empty, which leads to an exception.
- * @throw SemanticRelationException, if the segmentation does not represent an existing lesion (this can be checked via 'IsRepresentingALesion').
- *
- * @param segmentationNode The segmentation identifier is extracted from the given data node.
- *
- * @return The represented lesion.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::Lesion GetLesionOfSegmentation(const DataNode* segmentationNode);
- /**
- * @brief Returns a vector of all lesions that are currently available for the current case and are connected to the given image (via a segmentation).
- * If no lesions are stored for the current case, an empty vector is returned. If no segmentations are
- * connected with the image node, no lesions for the specific image will be found and an empty vector is returned.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- *
- * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case.
- *
- * @return A vector of lesions.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllLesionsOfImage(const DataNode* imageNode);
- /**
- * @brief Returns a vector of all lesions that are valid for the given case, given a specific control point.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint A specific control point which has to be available at a returned (found) lesion:
- * Only those lesions are returned for which the image of the associated segmentation is linked to the given control point.
- * If the control point instance does not exist, an empty vector is returned.
- *
- * @return A vector of lesions.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllLesionsOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Returns a vector of all lesions that are valid for the given case, given a specific information type.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param informationType A specific information type which has to be available at a returned (found) lesion:
- * Only those lesions are returned for which the image of the associated segmentation is of the given information type.
- * If the information type instance does not exist, an empty vector is returned.
- *
- * @return A vector of lesions.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllLesionsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType);
- /**
- * @brief Returns a vector of all lesions that are valid for the given case, given a specific control point and a specific information type.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint A specific control point which has to be available at a returned (found) lesion:
- * Only those lesions are returned for which the image of the associated segmentation is linked to the given control point.
- * If the control point instance does not exist, an empty vector is returned.
- * @param informationType A specific information type which has to be available at a returned (found) lesion:
- * Only those lesions are returned for which the image of the associated segmentation is of the given information type.
- * If the information type instance does not exist, an empty vector is returned.
- *
- * @return A vector of lesions.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::LesionVector GetAllSpecificLesions(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType);
- /**
- * @brief Check if the given segmentation refers to an existing lesion instance.
- * This function can be used before calling 'GetRepresentedLesion' in order to avoid a possible exception.
- *
- * @param segmentationNode The segmentation identifier is extracted from the given data node.
- *
- * @return True, if the segmentation refers to an existing lesion; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool IsRepresentingALesion(const DataNode* segmentationNode);
- /**
- * @brief Check if the segmentation identified by the given segmentation ID refers to an existing lesion instance.
- * This function can be used before calling 'GetRepresentedLesion' in order to avoid a possible exception.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param segmentationID The segmentation node identifier is defined by the given string.
- *
- * @return True, if the segmentation refers to an existing lesion; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool IsRepresentingALesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID);
- /**
- * @brief Check if the given lesion is present on the given data node.
- * The function receives the case- and the node-ID from the DICOM tags of the node itself.
- * It uses node predicates to decide if the node is an image or a segmentation node.
- *
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- * @param dataNode A data node to check.
- *
- * @return True, if the lesion is present on the data node; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresent(const SemanticTypes::Lesion& lesion, const DataNode* dataNode);
- /**
- * @brief Check if the given lesion is related to the image identified by the given image ID.
- * Each lesion is represented by a segmentation which is connected to its parent image.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- * @param imageID The image node identifier is defined by the given string.
- *
- * @return True, if the lesion is related to image identified by the given image ID; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresentOnImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& imageID);
- /**
- * @brief Check if the given lesion is present on the segmentation identified by the given segmentation ID.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- * @param segmentationID The segmentation node identifier is defined by the given string.
- *
- * @return True, if the lesion is present on the segmentation identified by the given segmentation ID; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresentOnSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& segmentationID);
- /**
- * @brief Check if the given lesion is present at the given control point.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- * @param controlPoint A control point with a UID that identifies the corresponding control point instance.
- *
- * @return True, if the lesion is present at the given control point; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool IsLesionPresentAtControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Check if the given data node exists in the relation storage.
- * The function receives the case- and the node-ID from the DICOM tags of the node itself.
- * It uses node predicates to decide if the node is an image or a segmentation node and searches
- * through the corresponding relations.
- *
- * @param dataNode A data node to check.
- *
- * @return True, if the data node exists; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const DataNode* dataNode);
- /**
- * @brief Check if the given lesion instance exists.
- * This function can be used before calling 'AddLesionInstance' in order to avoid a possible exception.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- *
- * @return True, if the lesion instance exists; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Return a vector of all image IDs that identify images that are related to the given lesion.
- * Each lesion is represented by a segmentation which is connected to its parent image.
- * If the lesion is not represented by any segmentation, an empty vector is returned.
- *
- * @pre The UID of the lesion has to exist for a lesion instance.
- * @throw SemanticRelationException, if UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A lesion with a UID that identifies the corresponding lesion instance.
- *
- * @return A vector of IDs identifying images that are related to the given lesion.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllImageIDsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Return a vector of all image IDs that identify images that are related to the given examination period.
- * If the examination period is not used by and image, an empty vector is returned.
- *
- * @pre The UID of the examination period has to exist for an examination period instance.
- * @throw SemanticRelationException, if UID of the examination period does not exist for an examination period instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param examinationPeriod An examination period with a UID that identifies the corresponding examination period instance.
- *
- * @return A vector of IDs identifying images that are related to the given examination period.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::IDVector GetAllImageIDsOfExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- /**
- * @brief Return the control point of a data node.
- * If the data node is not linked to a control point or the data node refers to a non-existing control point,
- * a control point with an empty UID is returned.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- *
- * @param dataNode The current case identifier is extracted from the given data node, which contains DICOM information about the case.
- *
- * @return The control point of the given data node.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPoint GetControlPointOfImage(const DataNode* dataNode);
- /**
- * @brief Return a vector of all control points that are valid for the given case, given a specific lesion
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A specific lesion which has to be available at a returned (found) control point:
- * Only those control points are returned for which an associated data has a segmentation that references the given lesion.
- * If the lesion does not exists, an empty vector is returned.
- *
- * @return A vector of control points.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPointVector GetAllControlPointsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Return a vector of all control points that are valid for the given case, given a specific information type.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param informationType A specific information type which has to be available at a returned (found) control point:
- * Only those control points are returned for which an associated data has the given information type.
- * If the information type instance does not exists, an empty vector is returned.
- *
- * @return A vector of control points.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::ControlPointVector GetAllControlPointsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType);
- /**
- * @brief Check if the given control point instance exists.
- * This function can be used before adding, linking and unlinking control points to avoid a possible exception.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint A control point with a UID that identifies the corresponding control point instance.
- *
- * @return True, if the control point instance exists; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Check if the given examination period instance exists.
- * This function can be used before calling 'AddExaminationPeriod' in order to avoid a possible exception.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param examinationPeriod An examination period with a UID that identifies the corresponding examination period instance.
- *
- * @return True, if the examination period instance exists; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- /**
- * @brief Return the information type of the given image.
- * If the image does not contain any information type, an empty information type is returned.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- *
- * @param imageNode The current case identifier is extracted from the given data node, which contains DICOM information about the case.
- *
- * @return The information type of the given data node.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::InformationType GetInformationTypeOfImage(const DataNode* imageNode);
- /**
- * @brief Return a vector of all information types that are valid for the given case, given a specific control point.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint A specific control point which has to be available at a returned (found) information type:
- * Only those information types are returned for which an associated data is linked to the given control point.
- * If the control point instance does not exist, an empty vector is returned.
- *
- * @return A vector of information types.
- */
- MITKSEMANTICRELATIONS_EXPORT SemanticTypes::InformationTypeVector GetAllInformationTypesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Check if the given information type exists.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param informationType An information type.
- *
- * @return True, if the information type exists; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType);
- /**
- * @brief Determine if the given information type contains images, which are connected to segmentations that represent the given lesion.
- * If the lesion or the information type are not correctly stored, the function returns false.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A Lesion with a UID that identifies the corresponding lesion instance.
- * @param informationType An information type that identifies the corresponding information type instance.
- *
- * @return True, if the given information type contains data that is related to the given lesion; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::InformationType& informationType);
- /**
- * @brief Determine if the given control point contains images, which are connected to segmentations that represent the given lesion.
- * If the lesion or the control point are not correctly stored, the function returns false.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion A Lesion with a UID that identifies the corresponding lesion instance.
- * @param controlPoint A control point with a UID that identifies the corresponding control point instance.
- *
- * @return True, if the given control point contains data that is related to the given lesion; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Determine if the given control point contains images, which refer to the given information type.
- * If the information type or the control point are not correctly stored, the function returns false.
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param informationType An information type that identifies the corresponding information type instance.
- * @param controlPoint A control point with a UID that identifies the corresponding control point instance.
- *
- * @return True, if the given control point contains data that is related to the given information type; false otherwise.
- */
- MITKSEMANTICRELATIONS_EXPORT bool SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint);
-
- } // namespace SemanticRelationsInference
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkSemanticRelationsIntegration.h b/Modules/SemanticRelations/include/mitkSemanticRelationsIntegration.h
deleted file mode 100644
index 71ee0d4721..0000000000
--- a/Modules/SemanticRelations/include/mitkSemanticRelationsIntegration.h
+++ /dev/null
@@ -1,322 +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 mitkSemanticRelationsIntegration_h
-#define mitkSemanticRelationsIntegration_h
-
-#include <MitkSemanticRelationsExports.h>
-
-// semantic relations module
-#include "mitkISemanticRelationsObservable.h"
-#include "mitkISemanticRelationsObserver.h"
-#include "mitkSemanticTypes.h"
-
-// mitk core
-#include <mitkDataNode.h>
-
-namespace mitk
-{
- /**
- * @brief The API provides functions to manipulate image relations and instances
- * that are helpful during follow-up examination, like control-points (time period),
- * types of the images or lesions that may be visible on multiple images.
- *
- * The class is able to generate IDs from given data nodes using DICOM information.
- * These IDs are used to identify the corresponding instances of a specific case.
- * The case can also be directly identified by the given case ID.
- *
- * In order for most functions to work the case ID has to be used as a parameter.
- * If not, these functions do nothing.
- *
- * The class implements the ISemanticRelationsObservable interface to allow observers to
- * be informed about changes in the semantic relation storage.
- */
- class MITKSEMANTICRELATIONS_EXPORT SemanticRelationsIntegration : public ISemanticRelationsObservable
- {
- public:
-
- /************************************************************************/
- /* functions to implement the observer pattern */
- /************************************************************************/
- /**
- * @brief Adds the given concrete observer to the vector that holds all currently registered observer.
- * If the observer is already registered, it will not be added to the observer vector.
- *
- * @param observer The concrete observer to register.
- */
- void AddObserver(ISemanticRelationsObserver* observer) override;
- /**
- * @brief Removes the given concrete observer from the vector that holds all currently registered observer.
- *
- * @param observer The concrete observer to unregister.
- */
- void RemoveObserver(ISemanticRelationsObserver* observer) override;
-
- virtual ~SemanticRelationsIntegration() {}
-
- /************************************************************************/
- /* functions to add / remove instances / attributes */
- /************************************************************************/
- /**
- * @brief Add the given image to the set of already existing images.
- * The date is extracted from the DICOM data of the image node and is compared to already existing control points in the semantic relations model.
- * The function tries to find a fitting control point or to extend an already existing control point, if the extracted control point is close to
- * any other, already existing control point.
- * Finally, the image is linked to the correct control point.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- *
- * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node.
- */
- void AddImage(const DataNode* imageNode);
- /**
- * @brief Remove the given image from the set of already existing images.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- *
- * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node.
- */
- void RemoveImage(const DataNode* imageNode);
- /**
- * @brief Add a newly created lesion to the set of already existing lesions - with no connection to a specific image / segmentation of the case data.
- *
- * @pre The UID of the lesion must not already exist for a lesion instance.
- * @throw SemanticRelationException, it the UID of the lesion already exists for a lesion instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion The lesion instance to add.
- */
- void AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Overwrite an already existing lesion instance (this may be useful to overwrite the lesion with a different lesion class).
- *
- * @pre The UID of the lesion has to exist for a lesion instance.
- * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion The lesion instance that overwrites an existing lesion.
- */
- void OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Add a newly created lesion to the set of already existing lesions. The lesion is added and a reference to
- * the lesion is added to the segmentation. If the segmentation is already linked to a lesion, the
- * old linkage is overwritten (this can be checked via 'IsRepresentingALesion').
- *
- * @pre The given segmentation data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr).
- * @pre The UID of the lesion must not already exist for a lesion instance.
- * @throw SemanticRelationException, if the UID of the lesion already exists for a lesion instance (this can be checked via 'InstanceExists').
- *
- * @param segmentationNode The segmentation identifier is extracted from the given segmentation data node. The segmentation node has DICOM information from its parent node.
- * @param lesion The lesion instance to add and link.
- */
- void AddLesionAndLinkSegmentation(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Remove the given lesion from the set of already existing lesions.
- *
- * @pre The UID of the lesion has to exist for a lesion instance.
- * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists').
- * @pre The function needs to assure that no segmentation is still representing (linked to) this lesion.
- * @throw SemanticRelationException, if the lesion instance to remove is still linked to by any segmentation (this can be checked via 'GetAllSegmentationsOfLesion').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param lesion The lesion instance to remove.
- */
- void RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Add a segmentation instance to the set of already existing segmentations - with no connection to a specific lesion.
- *
- * @param segmentationNode The segmentation identifier is extracted from the given segmentation data node. The segmentation node has DICOM information from its parent node.
- * @param parentNode The node identifier of the parent node is extracted from the given parent data node.
- */
- void AddSegmentation(const DataNode* segmentationNode, const DataNode* parentNode);
- /**
- * @brief Link the given segmentation instance to an an already existing lesion instance. If the segmentation is already linked to a lesion instance, the
- * old linkage is overwritten (this can be checked via 'IsRepresentingALesion').
- *
- * @pre The given segmentation data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr).
- * @pre The UID of the lesion has to exist for a lesion instance.
- * @throw SemanticRelationException, if the UID of the lesion does not exist for a lesion instance (this can be checked via 'InstanceExists').
- *
- * @param segmentationNode The segmentation identifier is extracted from the given segmentation data node. The segmentation node has DICOM information from its parent node.
- * @param lesion The lesion instance to link.
- */
- void LinkSegmentationToLesion(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion);
- /**
- * @brief Unlink the given segmentation instance from the linked lesion instance.
- * The lesion may stay unlinked to any segmentation.
- *
- * @pre The given segmentation data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr).
- *
- * @param segmentationNode The segmentation identifier is extracted from the given segmentation data node. The segmentation node has DICOM information from its parent node.
- */
- void UnlinkSegmentationFromLesion(const DataNode* segmentationNode);
- /**
- * @brief Remove the given segmentation from the set of already existing segmentations.
- *
- * @pre The given segmentation data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given segmentation data node is invalid (==nullptr).
- *
- * @param segmentationNode The segmentation identifier is extracted from the given segmentation data node. The segmentation node has DICOM information from its parent node.
- */
- void RemoveSegmentation(const DataNode* segmentationNode);
- /**
- * @brief Set the control point for the given image.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- *
- * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node.
- * @param controlPoint The control point instance which is used for the given image.
- */
- void SetControlPointOfImage(const DataNode* imageNode, const SemanticTypes::ControlPoint& controlPoint);
- /**
- * @brief Add a newly created control point to the set of already existing control points. A reference to the control point is added to the given image.
- * This function combines adding a control point and linking it, since a control point with no associated data is not allowed.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- * @pre The UID of the control point must not already exist for a control point instance.
- * @throw SemanticRelationException, if the UID of the control point already exists for a control point instance (this can be checked via 'InstanceExists').
- * @pre The given control point must not already be contained in an existing control point interval.
- * @throw SemanticRelationException, if the given control point is already contained in an existing control point interval (this can be checked via 'CheckContainingControlPoint').
- * @pre The given control point must contain the date of the given image data node (if parameter 'checkConsistence = true').
- * @throw SemanticRelationException, if the given control point does not contain the date of the given image data node and 'checkConsistence = true' (this can be checked via 'ControlPointManager::InsideControlPoint').
- *
- * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node.
- * @param controlPoint The control point instance to add. For a newly added control point always has "startDate = endDate".
- * @param checkConsistence If true, the function checks, whether the date of the image data node actually lies inside the control point to link.
- */
- void AddControlPointAndLinkImage(const DataNode* imageNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence = true);
- /**
- * @brief Link the given image to an already existing control point.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- * @pre The UID of the control point has to exist for a control point instance.
- * @throw SemanticRelationException, if the UID of the control point does not exists for a control point instance (this can be checked via 'InstanceExists').
- * @pre The given control point must contain the date of the given image data node (if parameter 'checkConsistence = true').
- * @throw SemanticRelationException, if the given control point does not contain the date of the given image data node and 'checkConsistence = true' (this can be checked via 'ControlPointManager::InsideControlPoint').
- *
- * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node.
- * @param controlPoint The control point instance to link.
- * @param checkConsistence If true, the function checks, whether the date of the image data node actually lies inside the control point to link.
- */
- void LinkImageToControlPoint(const DataNode* imageNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence = true);
- /**
- * @brief Unlink the given image from the linked control point.
- * If an image is unlinked from a control point, the function needs to check whether the control point is still linked to any other image:
- * - if not, the control point instance will be removed (has to be removed since a control point with no associated image is not allowed).
- * - if so, the function has to make sure that the control point instance is shortened to its minimum time period (e.g. moving the end point to an earlier date).
- *
- * @param imageNode The current case identifier and node identifier is extracted from the given image data node, which contains DICOM information about the case and the node.
- */
- void UnlinkImageFromControlPoint(const DataNode* imageNode);
- /**
- * @brief Add an examination period instance to the set of already existing examination periods - with no connection to a specific control point.
- *
- * @pre The UID of the examination period must not already exist for an examination period instance.
- * @throw SemanticRelationException, if the UID of the examination period already exists for a examination period instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param examinationPeriod The examination period to add.
- */
- void AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- /**
- * @brief Rename an already existing examination period instance.
- *
- * @pre The UID of the examination period has to exist for an examination period instance.
- * @throw SemanticRelationException, if the UID of the examination period does not exist for an examination period instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param examinationPeriod The examination period instance that renames an existing examination period.
- */
- void RenameExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- /**
- * @brief Add a control point to the vector of control point UIDs of an existing examination period.
- *
- * @pre The UID of the control point has to exist for a control point instance.
- * @throw SemanticRelationException, if the UID of the control point does not exists for a control point instance (this can be checked via 'InstanceExists').
- * @pre The UID of the examination period must not already exist for an examination period instance.
- * @throw SemanticRelationException, if the UID of the examination period already exists for a examination period instance (this can be checked via 'InstanceExists').
- *
- * @param caseID The current case identifier is defined by the given string.
- * @param controlPoint The control point instance to add to the examination period.
- * @param examinationPeriod The examination period to which the control point should be added.
- */
- void AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod);
- /**
- * @brief Set (and possibly overwrite) the information type of the given image.
- * An already associated information type might be removed if is not referenced by any other image:
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- * @post If the information type instance did not exist before, it is now added.
- *
- * @param imageNode The current case identifier is extracted from the given image data node, which contains DICOM information about the case.
- * @param informationType An information type that identifies the corresponding information type instance.
- */
- void SetInformationType(const DataNode* imageNode, const SemanticTypes::InformationType& informationType);
- /**
- * @brief Set the information type of the given image.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- * @post If the information type instance did not exist before, it is now added.
- *
- * @param imageNode The current case identifier is extracted from the given image data node, which contains DICOM information about the case.
- * @param informationType An information type that identifies the corresponding information type instance.
- */
- void AddInformationTypeToImage(const DataNode* imageNode, const SemanticTypes::InformationType& informationType);
- /**
- * @brief Remove the information type of the given image.
- * If the information type is removed, the function needs to check whether the information type is referenced by any other image:
- * - if not, the information type instance can be removed (has to be removed since an information type with no associated image is not allowed).
- * - if so, the information type is just removed from the given image.
- *
- * @pre The given image data node has to be valid (!nullptr).
- * @throw SemanticRelationException, if the given image data node is invalid (==nullptr).
- *
- * @param imageNode The current case identifier is extracted from the given image data node, which contains DICOM information about the case.
- */
- void RemoveInformationTypeFromImage(const DataNode* imageNode);
-
- private:
- /**
- * @brief A vector that stores the currently registered observer of this observable subject.
- */
- static std::vector<mitk::ISemanticRelationsObserver*> m_ObserverVector;
- /**
- * @brief The class notifies (updates) the observer with a given case ID.
- * The view's caseID was set before in the GUI. The parts of the view that observe changes in the semantic relations are only updated,
- * if the given case ID is equal to the observer's current caseID and thus the observer currently shows the semantic information of the given case.
- *
- * @param caseID The caseID that identifies the currently active patient / case.
- */
- void NotifyObserver(const mitk::SemanticTypes::CaseID& caseID) const override;
- /**
- * @brief Remove all control points from the storage that are not referenced by any image anymore.
- * This might happen if an image has been removed (and unlinked from the corresponding control point)
- * or if the user sets a new control point for an image manually in the GUI.
- *
- * @param caseID The current case identifier is defined by the given string.
- */
- void ClearControlPoints(const SemanticTypes::CaseID& caseID);
-
- };
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkSemanticTypes.h b/Modules/SemanticRelations/include/mitkSemanticTypes.h
deleted file mode 100644
index 4a1cc4dd68..0000000000
--- a/Modules/SemanticRelations/include/mitkSemanticTypes.h
+++ /dev/null
@@ -1,125 +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 mitkSemanticTypes_h
-#define mitkSemanticTypes_h
-
-#define BOOST_DATE_TIME_NO_LIB
-#if defined(BOOST_ALL_DYN_LINK)
-#undef BOOST_ALL_DYN_LINK
-#endif
-
-// boost
-#include <boost/date_time/gregorian/gregorian.hpp>
-
-// c++
-#include <set>
-#include <tuple>
-#include <vector>
-
-namespace mitk
-{
- namespace SemanticTypes
- {
- using ID = std::string;
- using CaseID = std::string;
- using InformationType = std::string;
-
- /*
- * @brief The concept of a control point.
- */
- struct ControlPoint
- {
- ID UID;
- boost::gregorian::date date;
-
- ControlPoint()
- {
- date = boost::gregorian::date(boost::gregorian::min_date_time);
- }
-
- // less comparison to sort containers of control points
- bool operator<(const ControlPoint& other) const
- {
- return date < other.date;
- }
-
- std::string ToString() const
- {
- std::stringstream controlPointAsString;
- if (date.is_not_a_date())
- {
- return "";
- }
-
- controlPointAsString << std::to_string(date.year()) << "-"
- << std::setfill('0') << std::setw(2) << std::to_string(date.month()) << "-"
- << std::setfill('0') << std::setw(2) << std::to_string(date.day());
-
- return controlPointAsString.str();
- }
-
- void SetDateFromString(const std::string& dateAsString)
- {
- date = boost::gregorian::from_undelimited_string(dateAsString);
- }
-
- int DistanceInDays(const ControlPoint& other) const
- {
- boost::gregorian::date_duration duration = date - other.date;
- return std::abs(duration.days());
- }
- };
-
- /**
- * @brief The concept of an examination period.
- * An examination period holds a vector of control point UIDs.
- * The semantic relation storage stores the UIDs such that
- * the represented control points are in chronological order.
- */
- struct ExaminationPeriod
- {
- ID UID;
- std::string name = "";
- std::vector<ID> controlPointUIDs;
- };
-
- /*
- * @brief The concept of a lesion class.
- */
- struct LesionClass
- {
- ID UID;
- std::string classType = "";
- };
-
- /*
- * @brief The concept of a lesion.
- */
- struct Lesion
- {
- ID UID;
- std::string name = "";
- LesionClass lesionClass;
- };
-
- using IDVector = std::vector<ID>;
- using LesionVector = std::vector<Lesion>;
- using LesionClassVector = std::vector<LesionClass>;
- using ControlPointVector = std::vector<ControlPoint>;
- using ExaminationPeriodVector = std::vector<ExaminationPeriod>;
- using InformationTypeVector = std::vector<InformationType>;
-
- } // namespace SemanticTypes
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/include/mitkUIDGeneratorBoost.h b/Modules/SemanticRelations/include/mitkUIDGeneratorBoost.h
deleted file mode 100644
index 9902e96bd6..0000000000
--- a/Modules/SemanticRelations/include/mitkUIDGeneratorBoost.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkUIDGeneratorBoost_h
-#define mitkUIDGeneratorBoost_h
-
-#include <MitkSemanticRelationsExports.h>
-
-#include <iostream>
-
-namespace mitk
-{
- namespace UIDGeneratorBoost
- {
- MITKSEMANTICRELATIONS_EXPORT std::string GenerateUID();
- } // namespace UIDGeneratorBoost
-} // namespace mitk
-
-#endif
diff --git a/Modules/SemanticRelations/src/mitkControlPointManager.cpp b/Modules/SemanticRelations/src/mitkControlPointManager.cpp
deleted file mode 100644
index 2f31f63a27..0000000000
--- a/Modules/SemanticRelations/src/mitkControlPointManager.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.
-
-============================================================================*/
-
-// semantic relations module
-#include "mitkControlPointManager.h"
-#include "mitkDICOMHelper.h"
-#include "mitkRelationStorage.h"
-#include "mitkSemanticRelationException.h"
-#include "mitkUIDGeneratorBoost.h"
-
-// mitk core
-#include <mitkPropertyNameHelper.h>
-
-mitk::SemanticTypes::ControlPoint mitk::GenerateControlPoint(const DataNode* datanode)
-{
- SemanticTypes::ControlPoint controlPoint;
- try
- {
- controlPoint = GetDICOMDateFromDataNode(datanode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot generate a control point from the DICOM tag of the given data node.";
- }
-
- controlPoint.UID = UIDGeneratorBoost::GenerateUID();
- return controlPoint;
-}
-
-mitk::SemanticTypes::ControlPoint mitk::GetControlPointByUID(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& controlPointUID)
-{
- auto lambda = [&controlPointUID](const SemanticTypes::ControlPoint& currentControlPoint)
- {
- return currentControlPoint.UID == controlPointUID;
- };
-
- SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
- const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), lambda);
-
- mitk::SemanticTypes::ControlPoint controlPoint;
- if (existingControlPoint != allControlPoints.end())
- {
- controlPoint = *existingControlPoint;
- }
-
- return controlPoint;
-}
-
-mitk::SemanticTypes::ControlPoint mitk::FindExistingControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
- for (const auto& currentControlPoint : allControlPoints)
- {
- if (controlPoint.date == currentControlPoint.date)
- {
- return currentControlPoint;
- }
- }
-
- return SemanticTypes::ControlPoint();
-}
-
-mitk::SemanticTypes::ControlPoint mitk::FindClosestControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
- if (allControlPoints.empty())
- {
- return SemanticTypes::ControlPoint();
- }
-
- // sort the vector of control points for easier lookup
- std::sort(allControlPoints.begin(), allControlPoints.end());
- // new control point does not match an existing control point
- // check if the control point is close to an already existing control point
- SemanticTypes::ControlPointVector::const_iterator it;
- for (it = allControlPoints.begin(); it != allControlPoints.end(); ++it)
- {
- if (controlPoint.date < it->date)
- {
- break;
- }
- }
-
- SemanticTypes::ControlPoint nextControlPoint;
- SemanticTypes::ControlPoint previousControlPoint;
- if (it == allControlPoints.begin())
- {
- // new date is smaller ("older") than the smallest already existing control point
- nextControlPoint = *it;
- }
- else if (it != allControlPoints.end())
- {
- // new date is greater ("newer") than an already existing control point,
- // but smaller ("older") than another already existing control point
- nextControlPoint = *it;
- previousControlPoint = *(--it);
- }
- else
- {
- // new date is greater ("newer") than the greatest already existing control point
- previousControlPoint = *(--it);
- }
-
- // test distance to next and previous time period
- double distanceToNextExaminationPeriod = nextControlPoint.DistanceInDays(controlPoint);
- double distanceToPreviousExaminationPeriod = previousControlPoint.DistanceInDays(controlPoint);
-
- SemanticTypes::ControlPoint closestControlPoint;
- int closestDistanceInDays = 0;
- if (distanceToNextExaminationPeriod < distanceToPreviousExaminationPeriod)
- {
- // control point is closer to the next control point
- closestControlPoint = nextControlPoint;
- closestDistanceInDays = distanceToNextExaminationPeriod;
- }
- else
- {
- // control point is closer to the previous control point
- closestControlPoint = previousControlPoint;
- closestDistanceInDays = distanceToPreviousExaminationPeriod;
- }
-
- int THRESHOLD_DISTANCE_IN_DAYS = 30;
- if (closestDistanceInDays <= THRESHOLD_DISTANCE_IN_DAYS)
- {
- return closestControlPoint;
- }
-
- return SemanticTypes::ControlPoint();
-}
-
-mitk::SemanticTypes::ExaminationPeriod mitk::FindContainingExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::ExaminationPeriodVector allExaminationPeriods = RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
- for (const auto& examinationPeriod : allExaminationPeriods)
- {
- for (const auto& UID : examinationPeriod.controlPointUIDs)
- {
- if (controlPoint.UID == UID)
- {
- return examinationPeriod;
- }
- }
- }
-
- return SemanticTypes::ExaminationPeriod();
-}
-
-mitk::SemanticTypes::ExaminationPeriod mitk::FindFittingExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::ExaminationPeriod specificExaminationPeriod;
- SemanticTypes::ControlPoint specificControlPoint;
- // find the closest control point
- SemanticTypes::ControlPoint existingControlPoint = FindExistingControlPoint(caseID, controlPoint);
- if (!existingControlPoint.UID.empty())
- {
- specificControlPoint = existingControlPoint;
- }
- else
- {
- auto closestControlPoint = FindClosestControlPoint(caseID, controlPoint);
- if (!closestControlPoint.UID.empty())
- {
- specificControlPoint = closestControlPoint;
- }
- }
-
- // find the containing examination period
- return FindContainingExaminationPeriod(caseID, specificControlPoint);
-}
-
-mitk::SemanticTypes::ExaminationPeriod mitk::FindFittingExaminationPeriod(const DataNode* dataNode)
-{
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ControlPoint controlPoint;
- try
- {
- caseID = GetCaseIDFromDataNode(dataNode);
- controlPoint = GetDICOMDateFromDataNode(dataNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot find an examination period.";
- }
-
- return FindFittingExaminationPeriod(caseID, controlPoint);
-}
-
-void mitk::SortAllExaminationPeriods(const SemanticTypes::CaseID& caseID, SemanticTypes::ExaminationPeriodVector& allExaminationPeriods)
-{
- SemanticTypes::ControlPointVector controlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
- // sort the vector of control points for the timeline
- std::sort(controlPoints.begin(), controlPoints.end());
-
- auto lambda = [&caseID](const SemanticTypes::ExaminationPeriod& leftExaminationPeriod, const SemanticTypes::ExaminationPeriod& rightExaminationPeriod)
- {
- if (leftExaminationPeriod.controlPointUIDs.empty())
- {
- return true;
- }
-
- if (rightExaminationPeriod.controlPointUIDs.empty())
- {
- return false;
- }
- const auto leftUID = leftExaminationPeriod.controlPointUIDs.front();
- const auto rightUID = rightExaminationPeriod.controlPointUIDs.front();
- const auto& leftControlPoint = GetControlPointByUID(caseID, leftUID);
- const auto& rightControlPoint = GetControlPointByUID(caseID, rightUID);
-
- return leftControlPoint.date < rightControlPoint.date;
- };
-
- std::sort(allExaminationPeriods.begin(), allExaminationPeriods.end(), lambda);
-}
diff --git a/Modules/SemanticRelations/src/mitkDICOMHelper.cpp b/Modules/SemanticRelations/src/mitkDICOMHelper.cpp
deleted file mode 100644
index 726dd9159c..0000000000
--- a/Modules/SemanticRelations/src/mitkDICOMHelper.cpp
+++ /dev/null
@@ -1,186 +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.
-
-============================================================================*/
-
-// semantic relations module
-#include "mitkDICOMHelper.h"
-#include "mitkSemanticRelationException.h"
-#include "mitkUIDGeneratorBoost.h"
-
-// mitk core
-#include <mitkPropertyNameHelper.h>
-
-// c++
-#include <algorithm>
-
-mitk::SemanticTypes::ControlPoint GetControlPointFromString(const std::string& dateAsString)
-{
- // date expected to be YYYYMMDD (8 characters)
- if (dateAsString.size() != 8)
- {
- // string does not represent a DICOM date
- mitkThrowException(mitk::SemanticRelationException) << "Not a valid DICOM date format.";
- }
-
- mitk::SemanticTypes::ControlPoint controlPoint;
- controlPoint.SetDateFromString(dateAsString);
-
- return controlPoint;
-}
-
-std::string mitk::GetCaseIDDICOMProperty()
-{
- // extract suitable DICOM tag to use as the case id
- // two alternatives can be used:
- // - DICOM tag "0x0010, 0x0010" is PatientName
- // - DICOM tag "0x0010, 0x0020" is PatientID
- // in the current implementation the PatientName (0x0010, 0x0010) is used
- return GeneratePropertyNameForDICOMTag(0x0010, 0x0010);
-}
-
-std::string mitk::GetNodeIDDICOMProperty()
-{
- // extract suitable DICOM tag to use as the data node id
- // DICOM tag "0x0020, 0x000e" is SeriesInstanceUID
- return GeneratePropertyNameForDICOMTag(0x0020, 0x000e);
-}
-
-std::string mitk::GetDateDICOMProperty()
-{
- // extract suitable DICOM tag to use as the data node id
- // DICOM tag "0x0008, 0x0022" is AcquisitionDate
- return GeneratePropertyNameForDICOMTag(0x0008, 0x0022);
-}
-
-std::string mitk::GetModalityDICOMProperty()
-{
- // extract suitable DICOM tag to use as the information type
- // DICOM tag "0x0008, 0x0060" is Modality
- return GeneratePropertyNameForDICOMTag(0x0008, 0x0060);
-}
-
-mitk::SemanticTypes::CaseID mitk::GetCaseIDFromDataNode(const DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data node.";
- }
-
- BaseData* baseData = dataNode->GetData();
- if (nullptr == baseData)
- {
- mitkThrowException(SemanticRelationException) << "No valid base data.";
- }
-
- BaseProperty* dicomTag = baseData->GetProperty(GetCaseIDDICOMProperty().c_str());
- if (nullptr == dicomTag)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid DICOM property.";
- }
-
- std::string dicomTagAsString = dicomTag->GetValueAsString();
- return dicomTagAsString;
-}
-
-mitk::SemanticTypes::ID mitk::GetIDFromDataNode(const DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data node.";
- }
-
- BaseData* baseData = dataNode->GetData();
- if (nullptr == baseData)
- {
- mitkThrowException(SemanticRelationException) << "No valid base data.";
- }
-
- BaseProperty* dicomTag = baseData->GetProperty(GetNodeIDDICOMProperty().c_str());
- if (nullptr == dicomTag)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid DICOM property.";
- }
- std::string dicomTagAsString = dicomTag->GetValueAsString();
- return dicomTagAsString;
-}
-
-mitk::SemanticTypes::ControlPoint mitk::GetDICOMDateFromDataNode(const DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data node.";
- }
-
- BaseData* baseData = dataNode->GetData();
- if (nullptr == baseData)
- {
- mitkThrowException(SemanticRelationException) << "No valid base data.";
- }
-
- BaseProperty* acquisitionDateProperty = baseData->GetProperty(GetDateDICOMProperty().c_str());
- if (nullptr == acquisitionDateProperty)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid DICOM property.";
- }
- std::string acquisitionDateAsString = acquisitionDateProperty->GetValueAsString();
-
- SemanticTypes::ControlPoint controlPoint;
- try
- {
- controlPoint = GetControlPointFromString(acquisitionDateAsString);
- }
- catch (SemanticRelationException &e)
- {
- mitkReThrow(e) << "Cannot retrieve a valid DICOM date.";
- }
-
- return controlPoint;
-}
-
-mitk::SemanticTypes::InformationType mitk::GetDICOMModalityFromDataNode(const DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data node.";
- }
-
- BaseData* baseData = dataNode->GetData();
- if (nullptr == baseData)
- {
- mitkThrowException(SemanticRelationException) << "No valid base data.";
- }
-
- BaseProperty* dicomTag = baseData->GetProperty(GetModalityDICOMProperty().c_str());
- if (nullptr == dicomTag)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid DICOM property.";
- }
- std::string dicomTagAsString = dicomTag->GetValueAsString();
- return dicomTagAsString;
-}
-
-std::string mitk::TrimDICOM(const std::string& identifier)
-{
- if (identifier.empty())
- {
- return identifier;
- }
-
- // leading whitespace
- std::size_t first = identifier.find_first_not_of(' ');
- if (std::string::npos == first)
- {
- return "";
- }
- // trailing whitespace
- std::size_t last = identifier.find_last_not_of(' ');
- return identifier.substr(first, last - first + 1);
-}
diff --git a/Modules/SemanticRelations/src/mitkLesionData.cpp b/Modules/SemanticRelations/src/mitkLesionData.cpp
deleted file mode 100644
index 103bfc9675..0000000000
--- a/Modules/SemanticRelations/src/mitkLesionData.cpp
+++ /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.
-
-============================================================================*/
-
-// semantic relations module
-#include "mitkLesionData.h"
-
-mitk::LesionData::LesionData(const SemanticTypes::Lesion& lesion/* = SemanticTypes::Lesion()*/)
-{
- m_Lesion = lesion;
-}
-
-void mitk::LesionData::SetLesion(const SemanticTypes::Lesion& lesion)
-{
- m_Lesion = lesion;
-}
-
-void mitk::LesionData::SetLesionPresence(const std::vector<bool>& lesionPresence)
-{
- m_LesionPresence = lesionPresence;
-}
-
-void mitk::LesionData::SetLesionVolume(const std::vector<double>& lesionVolume)
-{
- m_LesionVolume = lesionVolume;
-}
diff --git a/Modules/SemanticRelations/src/mitkLesionManager.cpp b/Modules/SemanticRelations/src/mitkLesionManager.cpp
deleted file mode 100644
index 725dbfaf6c..0000000000
--- a/Modules/SemanticRelations/src/mitkLesionManager.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.
-
-============================================================================*/
-
-// semantic relations module
-#include "mitkLesionManager.h"
-#include "mitkRelationStorage.h"
-#include "mitkSemanticRelationException.h"
-#include "mitkSemanticRelationsInference.h"
-#include "mitkUIDGeneratorBoost.h"
-
-mitk::SemanticTypes::Lesion mitk::GenerateNewLesion(const std::string& lesionClassType/* = ""*/)
-{
- SemanticTypes::Lesion lesion;
- lesion.UID = UIDGeneratorBoost::GenerateUID();
- lesion.name = "New lesion";
- lesion.lesionClass = GenerateNewLesionClass(lesionClassType);
-
- return lesion;
-}
-
-mitk::SemanticTypes::LesionClass mitk::GenerateNewLesionClass(const std::string& lesionClassType/* = ""*/)
-{
- SemanticTypes::LesionClass lesionClass;
- lesionClass.UID = UIDGeneratorBoost::GenerateUID();
- lesionClass.classType = lesionClassType;
-
- return lesionClass;
-}
-
-mitk::SemanticTypes::Lesion mitk::GetLesionByUID(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionUID)
-{
- auto lambda = [&lesionUID](const SemanticTypes::Lesion& currentLesion)
- {
- return currentLesion.UID == lesionUID;
- };
-
- SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID);
- const auto existingLesion = std::find_if(allLesions.begin(), allLesions.end(), lambda);
-
- SemanticTypes::Lesion lesion;
- if (existingLesion != allLesions.end())
- {
- lesion = *existingLesion;
- }
-
- return lesion;
-}
-
-mitk::SemanticTypes::LesionClass mitk::FindExistingLesionClass(const SemanticTypes::CaseID& caseID, const std::string& lesionClassType)
-{
- auto lambda = [&lesionClassType](const SemanticTypes::LesionClass& currentLesionClass)
- {
- return currentLesionClass.classType == lesionClassType;
- };
-
- SemanticTypes::LesionClassVector allLesionClasses = SemanticRelationsInference::GetAllLesionClassesOfCase(caseID);
- const auto existingLesionClass = std::find_if(allLesionClasses.begin(), allLesionClasses.end(), lambda);
-
- SemanticTypes::LesionClass lesionClass;
- if (existingLesionClass != allLesionClasses.end())
- {
- lesionClass = *existingLesionClass;
- }
-
- return lesionClass;
-}
-
-void mitk::ComputeLesionPresence(LesionData& lesionData, const SemanticTypes::CaseID& caseID)
-{
- std::vector<bool> lesionPresence;
- auto lesion = lesionData.GetLesion();
- bool presence = false;
- auto controlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
- // sort the vector of control points for the timeline
- std::sort(controlPoints.begin(), controlPoints.end());
- for (const auto& controlPoint : controlPoints)
- {
- try
- {
- presence = SemanticRelationsInference::IsLesionPresentAtControlPoint(caseID, lesion, controlPoint);
- }
- catch (SemanticRelationException&)
- {
- presence = false;
- }
-
- lesionPresence.push_back(presence);
- }
-
- lesionData.SetLesionPresence(lesionPresence);
-}
diff --git a/Modules/SemanticRelations/src/mitkNodePredicates.cpp b/Modules/SemanticRelations/src/mitkNodePredicates.cpp
deleted file mode 100644
index 7d92b9e9f6..0000000000
--- a/Modules/SemanticRelations/src/mitkNodePredicates.cpp
+++ /dev/null
@@ -1,51 +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 "mitkNodePredicates.h"
-
-// mitk core
-#include <mitkNodePredicateDataType.h>
-#include <mitkNodePredicateNot.h>
-#include <mitkNodePredicateOr.h>
-#include <mitkNodePredicateProperty.h>
-
-// multi label module
-#include <mitkLabelSetImage.h>
-
-mitk::NodePredicateAnd::Pointer mitk::NodePredicates::GetImagePredicate()
-{
- TNodePredicateDataType<Image>::Pointer isImage = TNodePredicateDataType<Image>::New();
-
- NodePredicateOr::Pointer validImages = NodePredicateOr::New();
- validImages->AddPredicate(isImage);
-
- NodePredicateAnd::Pointer imagePredicate = NodePredicateAnd::New();
- imagePredicate->AddPredicate(validImages);
- imagePredicate->AddPredicate(NodePredicateNot::New(GetSegmentationPredicate()));
- imagePredicate->AddPredicate(NodePredicateNot::New(NodePredicateProperty::New("helper object")));
-
- return imagePredicate;
-}
-
-mitk::NodePredicateAnd::Pointer mitk::NodePredicates::GetSegmentationPredicate()
-{
- NodePredicateAnd::Pointer segmentationPredicate = NodePredicateAnd::New();
-
- NodePredicateProperty::Pointer isBinary = NodePredicateProperty::New("binary", BoolProperty::New(true));
- TNodePredicateDataType<LabelSetImage>::Pointer isLabelSetImage = TNodePredicateDataType<LabelSetImage>::New();
- NodePredicateOr::Pointer allSegmentations = NodePredicateOr::New(isBinary, isLabelSetImage);
-
- segmentationPredicate->AddPredicate(allSegmentations);
- segmentationPredicate->AddPredicate(NodePredicateNot::New(NodePredicateProperty::New("helper object")));
-
- return segmentationPredicate;
-}
diff --git a/Modules/SemanticRelations/src/mitkRelationStorage.cpp b/Modules/SemanticRelations/src/mitkRelationStorage.cpp
deleted file mode 100644
index e8c49818aa..0000000000
--- a/Modules/SemanticRelations/src/mitkRelationStorage.cpp
+++ /dev/null
@@ -1,1567 +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 "mitkRelationStorage.h"
-
-// semantic relations module
-#include "mitkDICOMHelper.h"
-
-// multi label module
-#include <mitkLabelSetImage.h>
-
-// mitk core
-#include <mitkIPersistenceService.h>
-#include <mitkVectorProperty.h>
-
-// c++
-#include <algorithm>
-#include <iostream>
-
-namespace
-{
- std::vector<mitk::SemanticTypes::CaseID> GetCaseIDs()
- {
- PERSISTENCE_GET_SERVICE_MACRO
- if (nullptr == persistenceService)
- {
- MITK_DEBUG << "Persistence service could not be loaded";
- return std::vector<mitk::SemanticTypes::CaseID>();
- }
- // the property list is valid for a certain scenario and contains all the case IDs of the radiological user's MITK session
- std::string listIdentifier = "caseIDs";
- mitk::PropertyList::Pointer propertyList = persistenceService->GetPropertyList(listIdentifier);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << listIdentifier << " for the current MITK workbench / session.";
- return std::vector<mitk::SemanticTypes::CaseID>();
- }
- // retrieve a vector property that contains all case IDs
- mitk::VectorProperty<std::string>* caseIDsVectorProperty = dynamic_cast<mitk::VectorProperty<std::string>*>(propertyList->GetProperty(listIdentifier));
- if (nullptr == caseIDsVectorProperty)
- {
- MITK_DEBUG << "Could not find the property " << listIdentifier << " for the " << listIdentifier << " property list.";
- return std::vector<mitk::SemanticTypes::CaseID>();
- }
-
- return caseIDsVectorProperty->GetValue();
- }
-
- bool CaseIDExists(const mitk::SemanticTypes::CaseID& caseID)
- {
- auto allCaseIDs = GetCaseIDs();
- auto existingCase = std::find(allCaseIDs.begin(), allCaseIDs.end(), caseID);
- if (existingCase == allCaseIDs.end())
- {
- return false;
- }
-
- return true;
- }
-
- mitk::PropertyList::Pointer GetStorageData(const mitk::SemanticTypes::CaseID& caseID)
- {
- // access the storage
- PERSISTENCE_GET_SERVICE_MACRO
- if (nullptr == persistenceService)
- {
- MITK_DEBUG << "Persistence service could not be loaded";
- return nullptr;
- }
-
- // The persistence service may create a new property list with the given ID, if no property list is found.
- // Since we don't want to return a new property list but rather inform the user that the given case
- // is not a valid, stored case, we will return nullptr in that case.
- if (CaseIDExists(caseID))
- {
- // the property list is valid for a whole case and contains all the properties for the current case
- return persistenceService->GetPropertyList(const_cast<mitk::SemanticTypes::CaseID&>(caseID));
- }
-
- return nullptr;
- }
-
- mitk::SemanticTypes::Lesion GenerateLesion(const mitk::SemanticTypes::CaseID& caseID, const mitk::SemanticTypes::ID& lesionID)
- {
- mitk::PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return mitk::SemanticTypes::Lesion();
- }
-
- mitk::VectorProperty<std::string>* lesionDataProperty = dynamic_cast<mitk::VectorProperty<std::string>*>(propertyList->GetProperty(lesionID));
- if (nullptr == lesionDataProperty)
- {
- MITK_DEBUG << "Lesion " << lesionID << " not found. Lesion can not be retrieved.";
- return mitk::SemanticTypes::Lesion();
- }
-
- std::vector<std::string> lesionData = lesionDataProperty->GetValue();
- // a lesion date has to have exactly two values (the name of the lesion and the UID of the lesion class)
- if (lesionData.size() != 2)
- {
- MITK_DEBUG << "Incorrect lesion data storage. Not two (2) strings of the lesion name and the lesion UID are stored.";
- return mitk::SemanticTypes::Lesion();
- }
-
- // the lesion class ID is stored as the second property
- std::string lesionClassID = lesionData[1];
- mitk::StringProperty* lesionClassProperty = dynamic_cast<mitk::StringProperty*>(propertyList->GetProperty(lesionClassID));
- if (nullptr != lesionClassProperty)
- {
- mitk::SemanticTypes::LesionClass generatedLesionClass;
- generatedLesionClass.UID = lesionClassID;
- generatedLesionClass.classType = lesionClassProperty->GetValue();
-
- mitk::SemanticTypes::Lesion generatedLesion;
- generatedLesion.UID = lesionID;
- generatedLesion.name = lesionData[0];
- generatedLesion.lesionClass = generatedLesionClass;
-
- return generatedLesion;
- }
-
- MITK_DEBUG << "Incorrect lesion class storage. Lesion " << lesionID << " can not be retrieved.";
- return mitk::SemanticTypes::Lesion();
- }
-
- mitk::SemanticTypes::ControlPoint GenerateControlpoint(const mitk::SemanticTypes::CaseID& caseID, const mitk::SemanticTypes::ID& controlPointUID)
- {
- mitk::PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return mitk::SemanticTypes::ControlPoint();
- }
-
- // retrieve a vector property that contains the integer values of the date of a control point (0. year 1. month 2. day)
- mitk::VectorProperty<int>* controlPointVectorProperty = dynamic_cast<mitk::VectorProperty<int>*>(propertyList->GetProperty(controlPointUID));
- if (nullptr == controlPointVectorProperty)
- {
- MITK_DEBUG << "Could not find the control point " << controlPointUID << " in the storage.";
- return mitk::SemanticTypes::ControlPoint();
- }
-
- std::vector<int> controlPointVectorPropertyValue = controlPointVectorProperty->GetValue();
- // a control point has to have exactly three integer values (year, month and day)
- if (controlPointVectorPropertyValue.size() != 3)
- {
- MITK_DEBUG << "Incorrect control point storage. Not three (3) values of the date are stored.";
- return mitk::SemanticTypes::ControlPoint();
- }
-
- // set the values of the control point
- mitk::SemanticTypes::ControlPoint generatedControlPoint;
- generatedControlPoint.UID = controlPointUID;
- generatedControlPoint.date = boost::gregorian::date(controlPointVectorPropertyValue[0],
- controlPointVectorPropertyValue[1],
- controlPointVectorPropertyValue[2]);
-
- return generatedControlPoint;
- }
-}
-
-mitk::SemanticTypes::LesionVector mitk::RelationStorage::GetAllLesionsOfCase(const SemanticTypes::CaseID& caseID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::LesionVector();
- }
- // retrieve a vector property that contains the valid lesion-IDs for the current case
- VectorProperty<std::string>* lesionsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("lesions"));
- if (nullptr == lesionsVectorProperty)
- {
- MITK_DEBUG << "Could not find any lesion in the storage.";
- return SemanticTypes::LesionVector();
- }
-
- std::vector<std::string> lesionsVectorPropertyValue = lesionsVectorProperty->GetValue();
- SemanticTypes::LesionVector allLesionsOfCase;
- for (const auto& lesionID : lesionsVectorPropertyValue)
- {
- SemanticTypes::Lesion generatedLesion = GenerateLesion(caseID, lesionID);
- if (!generatedLesion.UID.empty())
- {
- allLesionsOfCase.push_back(generatedLesion);
- }
- }
-
- return allLesionsOfCase;
-}
-
-mitk::SemanticTypes::Lesion mitk::RelationStorage::GetLesionOfSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::Lesion();
- }
-
- // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID)
- VectorProperty<std::string>* segmentationVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(segmentationID));
- if (nullptr == segmentationVectorProperty)
- {
- MITK_DEBUG << "Could not find the segmentation " << segmentationID << " in the storage.";
- return SemanticTypes::Lesion();
- }
-
- std::vector<std::string> segmentationVectorPropertyValue = segmentationVectorProperty->GetValue();
- // the lesion ID of a segmentation is the second value in the vector
- if (segmentationVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect segmentation storage. Not two (2) IDs stored.";
- return SemanticTypes::Lesion();
- }
-
- std::string lesionID = segmentationVectorPropertyValue[1];
- if (lesionID.empty())
- {
- // segmentation does not refer to any lesion; return empty lesion
- return SemanticTypes::Lesion();
- }
-
- return GenerateLesion(caseID, lesionID);
-}
-
-mitk::SemanticTypes::ControlPointVector mitk::RelationStorage::GetAllControlPointsOfCase(const SemanticTypes::CaseID& caseID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::ControlPointVector();
- }
-
- // retrieve a vector property that contains the valid control point-IDs for the current case
- VectorProperty<std::string>* controlPointsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("controlpoints"));
- if (nullptr == controlPointsVectorProperty)
- {
- MITK_DEBUG << "Could not find any control points in the storage.";
- return SemanticTypes::ControlPointVector();
- }
-
- std::vector<std::string> controlPointsVectorPropertyValue = controlPointsVectorProperty->GetValue();
- SemanticTypes::ControlPointVector allControlPointsOfCase;
- for (const auto& controlPointUID : controlPointsVectorPropertyValue)
- {
- SemanticTypes::ControlPoint generatedControlPoint = GenerateControlpoint(caseID, controlPointUID);
- if (!generatedControlPoint.UID.empty())
- {
- allControlPointsOfCase.push_back(generatedControlPoint);
- }
- }
-
- return allControlPointsOfCase;
-}
-
-mitk::SemanticTypes::ControlPoint mitk::RelationStorage::GetControlPointOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::ControlPoint();
- }
- // retrieve a vector property that contains the information type and the referenced ID of a control point (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- MITK_DEBUG << "Could not find the image " << imageID << " in the storage.";
- return SemanticTypes::ControlPoint();
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- SemanticTypes::ControlPoint controlPoint;
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect data storage. Not two (2) values stored.";
- return SemanticTypes::ControlPoint();
- }
-
- // the second value of the image vector is the ID of the referenced control point
- std::string controlPointID = imageVectorPropertyValue[1];
- // retrieve a vector property that contains the integer values of the date of a control point (0. year 1. month 2. day)
- VectorProperty<int>* controlPointVectorProperty = dynamic_cast<VectorProperty<int>*>(propertyList->GetProperty(controlPointID));
- if (nullptr == controlPointVectorProperty)
- {
- MITK_DEBUG << "Could not find the control point " << controlPointID << " in the storage.";
- return SemanticTypes::ControlPoint();
- }
-
- std::vector<int> controlPointVectorPropertyValue = controlPointVectorProperty->GetValue();
- // a control point has to have exactly three integer values (year, month and day)
- if (controlPointVectorPropertyValue.size() != 3)
- {
- MITK_DEBUG << "Incorrect control point storage. Not three (3) values of the date are stored.";
- return SemanticTypes::ControlPoint();
- }
-
- // set the values of the control point
- controlPoint.UID = controlPointID;
- controlPoint.date = boost::gregorian::date(controlPointVectorPropertyValue[0],
- controlPointVectorPropertyValue[1],
- controlPointVectorPropertyValue[2]);
-
- return controlPoint;
-}
-
-mitk::SemanticTypes::ExaminationPeriodVector mitk::RelationStorage::GetAllExaminationPeriodsOfCase(const SemanticTypes::CaseID& caseID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::ExaminationPeriodVector();
- }
-
- // retrieve a vector property that contains the valid examination period UIDs for the current case
- VectorProperty<std::string>::Pointer examinationPeriodsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("examinationperiods"));
- if (nullptr == examinationPeriodsVectorProperty)
- {
- MITK_DEBUG << "Could not find any examination periods in the storage.";
- return SemanticTypes::ExaminationPeriodVector();
- }
-
- std::vector<std::string> examinationPeriodsVectorPropertyValue = examinationPeriodsVectorProperty->GetValue();
- SemanticTypes::ExaminationPeriodVector allExaminationPeriods;
- for (const auto& examinationPeriodID : examinationPeriodsVectorPropertyValue)
- {
- // retrieve a vector property that contains the represented control point-IDs
- VectorProperty<std::string>::Pointer examinationPeriodVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(examinationPeriodID));
- if (nullptr == examinationPeriodVectorProperty)
- {
- MITK_DEBUG << "Could not find the examination period " << examinationPeriodID << " in the storage.";
- continue;
- }
-
- std::vector<std::string> examinationPeriodVectorPropertyValue = examinationPeriodVectorProperty->GetValue();
- // an examination period has an arbitrary number of vector values (name and control point UIDs) (at least one for the name)
- if (examinationPeriodVectorPropertyValue.empty())
- {
- MITK_DEBUG << "Incorrect examination period storage. At least one (1) value for the examination period name has to be stored.";
- continue;
- }
- else
- {
- // set the values of the name and the control points
- SemanticTypes::ExaminationPeriod generatedExaminationPeriod;
- generatedExaminationPeriod.UID = examinationPeriodID;
- generatedExaminationPeriod.name = examinationPeriodVectorPropertyValue[0];
- for (size_t i = 1; i < examinationPeriodVectorPropertyValue.size(); ++i)
- {
- generatedExaminationPeriod.controlPointUIDs.push_back(examinationPeriodVectorPropertyValue[i]);
- }
-
- allExaminationPeriods.push_back(generatedExaminationPeriod);
- }
- }
- return allExaminationPeriods;
-}
-
-mitk::SemanticTypes::InformationTypeVector mitk::RelationStorage::GetAllInformationTypesOfCase(const SemanticTypes::CaseID& caseID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::InformationTypeVector();
- }
- // retrieve a vector property that contains the valid information types of the current case
- VectorProperty<std::string>* informationTypesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("informationtypes"));
- if (nullptr == informationTypesVectorProperty)
- {
- MITK_DEBUG << "Could not find any information types in the storage.";
- return SemanticTypes::InformationTypeVector();
- }
-
- return informationTypesVectorProperty->GetValue();
-}
-
-mitk::SemanticTypes::InformationType mitk::RelationStorage::GetInformationTypeOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::InformationType();
- }
- // retrieve a vector property that contains the information type and the referenced ID of an image (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- MITK_DEBUG << "Could not find the image " << imageID << " in the storage.";
- return SemanticTypes::InformationType();
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect data storage. Not two (2) values stored.";
- return SemanticTypes::InformationType();
- }
-
- // the first value of the image vector is the information type
- return imageVectorPropertyValue[0];
-}
-
-mitk::SemanticTypes::IDVector mitk::RelationStorage::GetAllImageIDsOfCase(const SemanticTypes::CaseID& caseID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::IDVector();
- }
- // retrieve a vector property that contains the valid image-IDs of the current case
- VectorProperty<std::string>* imagesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("images"));
- if (nullptr == imagesVectorProperty)
- {
- MITK_DEBUG << "Could not find any image in the storage.";
- return SemanticTypes::IDVector();
- }
-
- return imagesVectorProperty->GetValue();
-}
-
-mitk::SemanticTypes::IDVector mitk::RelationStorage::GetAllImageIDsOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::IDVector();
- }
- // retrieve a vector property that contains the valid image-IDs of the current case
- VectorProperty<std::string>* imagesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("images"));
- if (nullptr == imagesVectorProperty)
- {
- MITK_DEBUG << "Could not find any image in the storage.";
- return SemanticTypes::IDVector();
- }
-
- mitk::SemanticTypes::IDVector allImageIDsOfControlPoint;
- std::vector<std::string> imagesVectorPropertyValue = imagesVectorProperty->GetValue();
- for (const auto& imageID : imagesVectorPropertyValue)
- {
- // retrieve a vector property that contains the referenced ID of an image (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- continue;
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- continue;
- }
-
- // the second value of the image vector is the ID of the referenced control point
- if (imageVectorPropertyValue[1] == controlPoint.UID)
- {
- allImageIDsOfControlPoint.push_back(imageID);
- }
- }
-
- return allImageIDsOfControlPoint;
-}
-
-mitk::SemanticTypes::IDVector mitk::RelationStorage::GetAllImageIDsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::IDVector();
- }
- // retrieve a vector property that contains the valid image-IDs of the current case
- VectorProperty<std::string>* imagesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("images"));
- if (nullptr == imagesVectorProperty)
- {
- MITK_DEBUG << "Could not find any image in the storage.";
- return SemanticTypes::IDVector();
- }
-
- mitk::SemanticTypes::IDVector allImageIDsOfInformationType;
- std::vector<std::string> imagesVectorPropertyValue = imagesVectorProperty->GetValue();
- for (const auto& imageID : imagesVectorPropertyValue)
- {
- // retrieve a vector property that contains the referenced ID of an image (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- continue;
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- continue;
- }
-
- // the first value of the image vector is the ID of the referenced information type
- if (imageVectorPropertyValue[0] == informationType)
- {
- allImageIDsOfInformationType.push_back(imageID);
- }
- }
-
- return allImageIDsOfInformationType;
-}
-
-mitk::SemanticTypes::IDVector mitk::RelationStorage::GetAllSegmentationIDsOfCase(const SemanticTypes::CaseID& caseID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::IDVector();
- }
- // retrieve a vector property that contains the valid segmentation-IDs for the current case
- VectorProperty<std::string>* segmentationsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("segmentations"));
- if (nullptr == segmentationsVectorProperty)
- {
- MITK_DEBUG << "Could not find any segmentation in the storage.";
- return SemanticTypes::IDVector();
- }
-
- return segmentationsVectorProperty->GetValue();
-}
-
-mitk::SemanticTypes::IDVector mitk::RelationStorage::GetAllSegmentationIDsOfImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::IDVector();
- }
- // retrieve a vector property that contains the valid segmentation-IDs for the current case
- VectorProperty<std::string>* segmentationsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("segmentations"));
- if (nullptr == segmentationsVectorProperty)
- {
- MITK_DEBUG << "Could not find any segmentation in the storage.";
- return SemanticTypes::IDVector();
- }
-
- mitk::SemanticTypes::IDVector allSegmentationIDsOfImage;
- std::vector<std::string> segmentationsVectorPropertyValue = segmentationsVectorProperty->GetValue();
- for (const auto& segmentationID : segmentationsVectorPropertyValue)
- {
- // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID)
- VectorProperty<std::string>* segmentationVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(segmentationID));
- if (nullptr == segmentationVectorProperty)
- {
- continue;
- }
-
- std::vector<std::string> segmentationVectorPropertyValue = segmentationVectorProperty->GetValue();
- // a segmentation has to have exactly two values (the ID of the referenced image and the ID of the referenced lesion)
- if (segmentationVectorPropertyValue.size() != 2)
- {
- continue;
- }
-
- // the first value of the segmentation vector is the ID of the referenced image
- if (segmentationVectorPropertyValue[0] == imageID)
- {
- allSegmentationIDsOfImage.push_back(segmentationID);
- }
- }
-
- return allSegmentationIDsOfImage;
-}
-
-mitk::SemanticTypes::IDVector mitk::RelationStorage::GetAllSegmentationIDsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::IDVector();
- }
- // retrieve a vector property that contains the valid segmentation-IDs for the current case
- VectorProperty<std::string>* segmentationsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("segmentations"));
- if (nullptr == segmentationsVectorProperty)
- {
- MITK_DEBUG << "Could not find any segmentation in the storage.";
- return SemanticTypes::IDVector();
- }
-
- mitk::SemanticTypes::IDVector allSegmentationIDsOfLesion;
- std::vector<std::string> segmentationsVectorPropertyValue = segmentationsVectorProperty->GetValue();
- for (const auto& segmentationID : segmentationsVectorPropertyValue)
- {
- // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID)
- VectorProperty<std::string>* segmentationVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(segmentationID));
- if (nullptr == segmentationVectorProperty)
- {
- continue;
- }
-
- std::vector<std::string> segmentationVectorPropertyValue = segmentationVectorProperty->GetValue();
- // a segmentation has to have exactly two values (the ID of the referenced image and the ID of the referenced lesion)
- if (segmentationVectorPropertyValue.size() != 2)
- {
- continue;
- }
-
- // the second value of the segmentation vector is the ID of the referenced lesion
- if (segmentationVectorPropertyValue[1] == lesion.UID)
- {
- allSegmentationIDsOfLesion.push_back(segmentationID);
- }
- }
-
- return allSegmentationIDsOfLesion;
-}
-
-mitk::SemanticTypes::ID mitk::RelationStorage::GetImageIDOfSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return SemanticTypes::ID();
- }
-
- // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID)
- VectorProperty<std::string>* segmentationVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(segmentationID));
- if (nullptr == segmentationVectorProperty)
- {
- MITK_DEBUG << "Could not find the segmentation " << segmentationID << " in the storage.";
- return SemanticTypes::ID();
- }
-
- std::vector<std::string> segmentationVectorPropertyValue = segmentationVectorProperty->GetValue();
- // the lesion ID of a segmentation is the second value in the vector
- if (segmentationVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect segmentation storage. Not two (2) IDs stored.";
- return SemanticTypes::ID();
- }
-
- return segmentationVectorPropertyValue[0];
-}
-
-std::vector<mitk::SemanticTypes::CaseID> mitk::RelationStorage::GetAllCaseIDs()
-{
- return GetCaseIDs();
-}
-
-bool mitk::RelationStorage::InstanceExists(const SemanticTypes::CaseID& caseID)
-{
- return CaseIDExists(caseID);
-}
-
-void mitk::RelationStorage::AddCase(const SemanticTypes::CaseID& caseID)
-{
- PERSISTENCE_GET_SERVICE_MACRO
- if (nullptr == persistenceService)
- {
- MITK_DEBUG << "Persistence service could not be loaded";
- return;
- }
- // the property list is valid for a certain scenario and contains all the case IDs of the radiological user's MITK session
- std::string listIdentifier = "caseIDs";
- PropertyList::Pointer propertyList = persistenceService->GetPropertyList(listIdentifier);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << listIdentifier << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains all case IDs
- VectorProperty<std::string>::Pointer caseIDsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(listIdentifier));
- std::vector<std::string> caseIDsVectorPropertyValue;
- if (nullptr == caseIDsVectorProperty)
- {
- caseIDsVectorProperty = VectorProperty<std::string>::New();
- }
- else
- {
- caseIDsVectorPropertyValue = caseIDsVectorProperty->GetValue();
- }
-
- auto existingCase = std::find(caseIDsVectorPropertyValue.begin(), caseIDsVectorPropertyValue.end(), caseID);
- if (existingCase != caseIDsVectorPropertyValue.end())
- {
- return;
- }
-
- // add case to the "caseIDs" property list
- caseIDsVectorPropertyValue.push_back(caseID);
- caseIDsVectorProperty->SetValue(caseIDsVectorPropertyValue);
- propertyList->SetProperty(listIdentifier, caseIDsVectorProperty);
-}
-
-void mitk::RelationStorage::AddImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
-
- // retrieve a vector property that contains the valid image-IDs for the current case
- VectorProperty<std::string>::Pointer imagesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("images"));
- std::vector<std::string> imagesVectorPropertyValue;
- if (nullptr == imagesVectorProperty)
- {
- imagesVectorProperty = VectorProperty<std::string>::New();
- }
- else
- {
- imagesVectorPropertyValue = imagesVectorProperty->GetValue();
- }
-
- auto existingImage = std::find(imagesVectorPropertyValue.begin(), imagesVectorPropertyValue.end(), imageID);
- if (existingImage != imagesVectorPropertyValue.end())
- {
- return;
- }
-
- // add image to the "images" property list
- imagesVectorPropertyValue.push_back(imageID);
- imagesVectorProperty->SetValue(imagesVectorPropertyValue);
- propertyList->SetProperty("images", imagesVectorProperty);
-
- // add the image itself
- VectorProperty<std::string>::Pointer imageVectorProperty = VectorProperty<std::string>::New();
- // an image has to have exactly two values (the information type and the ID of the control point)
- std::vector<std::string> imageVectorPropertyValue(2);
- imageVectorProperty->SetValue(imageVectorPropertyValue);
- propertyList->SetProperty(imageID, imageVectorProperty);
-}
-
-void mitk::RelationStorage::RemoveImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
-
- // retrieve a vector property that contains the valid image-IDs for the current case
- VectorProperty<std::string>::Pointer imagesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("images"));
- if (nullptr == imagesVectorProperty)
- {
- MITK_DEBUG << "Could not find any images in the storage.";
- return;
- }
-
- // remove the image reference from the list of all images of the current case
- std::vector<std::string> imagesVectorPropertyValue = imagesVectorProperty->GetValue();
- imagesVectorPropertyValue.erase(std::remove(imagesVectorPropertyValue.begin(), imagesVectorPropertyValue.end(), imageID), imagesVectorPropertyValue.end());
- if (imagesVectorPropertyValue.empty())
- {
- // no more images stored -> remove the images property list
- propertyList->DeleteProperty("images");
- }
- else
- {
- // or store the modified vector value
- imagesVectorProperty->SetValue(imagesVectorPropertyValue);
- }
-
- // remove the image instance itself
- propertyList->DeleteProperty(imageID);
-}
-
-void mitk::RelationStorage::AddSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID, const SemanticTypes::ID& parentID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
-
- // retrieve a vector property that contains the valid segmentation-IDs for the current case
- VectorProperty<std::string>::Pointer segmentationsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("segmentations"));
- std::vector<std::string> segmentationsVectorPropertyValue;
- if (nullptr == segmentationsVectorProperty)
- {
- segmentationsVectorProperty = VectorProperty<std::string>::New();
- }
- else
- {
- segmentationsVectorPropertyValue = segmentationsVectorProperty->GetValue();
- }
-
- auto existingSegmentation = std::find(segmentationsVectorPropertyValue.begin(), segmentationsVectorPropertyValue.end(), segmentationID);
- if (existingSegmentation != segmentationsVectorPropertyValue.end())
- {
- return;
- }
-
- // add segmentation to the "segmentations" property list
- segmentationsVectorPropertyValue.push_back(segmentationID);
- segmentationsVectorProperty->SetValue(segmentationsVectorPropertyValue);
- propertyList->SetProperty("segmentations", segmentationsVectorProperty);
-
- // add the segmentation itself
- VectorProperty<std::string>::Pointer segmentationVectorProperty = VectorProperty<std::string>::New();
- // a segmentation has to have exactly two values (the ID of the referenced image and the ID of the referenced lesion)
- std::vector<std::string> segmentationVectorPropertyValue(2);
- segmentationVectorPropertyValue[0] = parentID;
- segmentationVectorProperty->SetValue(segmentationVectorPropertyValue);
- propertyList->SetProperty(segmentationID, segmentationVectorProperty);
-}
-
-void mitk::RelationStorage::RemoveSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
-
- // retrieve a vector property that contains the valid segmentation-IDs for the current case
- VectorProperty<std::string>::Pointer segmentationsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("segmentations"));
- if (nullptr == segmentationsVectorProperty)
- {
- MITK_DEBUG << "Could not find any segmentation in the storage.";
- return;
- }
-
- // remove the lesion reference from the list of all lesions of the current case
- std::vector<std::string> segmentationsVectorPropertyValue = segmentationsVectorProperty->GetValue();
- segmentationsVectorPropertyValue.erase(std::remove(segmentationsVectorPropertyValue.begin(), segmentationsVectorPropertyValue.end(), segmentationID), segmentationsVectorPropertyValue.end());
- if (segmentationsVectorPropertyValue.empty())
- {
- // no more segmentations stored -> remove the segmentations property list
- propertyList->DeleteProperty("segmentations");
- }
- else
- {
- // or store the modified vector value
- segmentationsVectorProperty->SetValue(segmentationsVectorPropertyValue);
- }
-
- // remove the lesion instance itself
- propertyList->DeleteProperty(segmentationID);
-}
-
-void mitk::RelationStorage::AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid lesion-IDs for the current case
- VectorProperty<std::string>::Pointer lesionsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("lesions"));
- std::vector<std::string> lesionsVectorPropertyValue;
- if (nullptr == lesionsVectorProperty)
- {
- lesionsVectorProperty = VectorProperty<std::string>::New();
- }
- else
- {
- lesionsVectorPropertyValue = lesionsVectorProperty->GetValue();
- }
-
- const auto& existingIndex = std::find(lesionsVectorPropertyValue.begin(), lesionsVectorPropertyValue.end(), lesion.UID);
- if (existingIndex != lesionsVectorPropertyValue.end())
- {
- return;
- }
-
- // add the new lesion id from the given lesion to the vector of all current lesion IDs
- lesionsVectorPropertyValue.push_back(lesion.UID);
- // overwrite the current vector property with the new, extended string vector
- lesionsVectorProperty->SetValue(lesionsVectorPropertyValue);
- propertyList->SetProperty("lesions", lesionsVectorProperty);
-
- // add the lesion with the lesion UID as the key and the lesion information as value
- std::vector<std::string> lesionData;
- lesionData.push_back(lesion.name);
- lesionData.push_back(lesion.lesionClass.UID);
- VectorProperty<std::string>::Pointer newLesionVectorProperty = VectorProperty<std::string>::New();
- newLesionVectorProperty->SetValue(lesionData);
- propertyList->SetProperty(lesion.UID, newLesionVectorProperty);
-
- // add the lesion class with the lesion class UID as key and the class type as value
- std::string lesionClassType = lesion.lesionClass.classType;
- propertyList->SetStringProperty(lesion.lesionClass.UID.c_str(), lesionClassType.c_str());
-}
-
-void mitk::RelationStorage::OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid lesion-IDs for the current case
- VectorProperty<std::string>* lesionVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("lesions"));
- if (nullptr == lesionVectorProperty)
- {
- MITK_DEBUG << "Could not find any lesion in the storage.";
- return;
- }
-
- std::vector<std::string> lesionVectorPropertyValue = lesionVectorProperty->GetValue();
- const auto existingLesion = std::find(lesionVectorPropertyValue.begin(), lesionVectorPropertyValue.end(), lesion.UID);
- if (existingLesion != lesionVectorPropertyValue.end())
- {
- // overwrite the referenced lesion class UID with the new, given lesion class data
- std::vector<std::string> lesionData;
- lesionData.push_back(lesion.name);
- lesionData.push_back(lesion.lesionClass.UID);
- VectorProperty<std::string>::Pointer newLesionVectorProperty = VectorProperty<std::string>::New();
- newLesionVectorProperty->SetValue(lesionData);
- propertyList->SetProperty(lesion.UID, newLesionVectorProperty);
-
- // overwrite the lesion class with the lesion class UID as key and the new, given class type as value
- std::string lesionClassType = lesion.lesionClass.classType;
- propertyList->SetStringProperty(lesion.lesionClass.UID.c_str(), lesionClassType.c_str());
- }
- else
- {
- MITK_DEBUG << "Could not find lesion " << lesion.UID << " in the storage. Cannot overwrite the lesion.";
- }
-}
-
-void mitk::RelationStorage::LinkSegmentationToLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID, const SemanticTypes::Lesion& lesion)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid lesion-IDs for the current case
- VectorProperty<std::string>* lesionVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("lesions"));
- if (nullptr == lesionVectorProperty)
- {
- MITK_DEBUG << "Could not find any lesion in the storage.";
- return;
- }
-
- std::vector<std::string> lesionVectorPropertyValue = lesionVectorProperty->GetValue();
- const auto existingLesion = std::find(lesionVectorPropertyValue.begin(), lesionVectorPropertyValue.end(), lesion.UID);
- if (existingLesion != lesionVectorPropertyValue.end())
- {
- // set / overwrite the lesion reference of the given segmentation
- // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID)
- VectorProperty<std::string>* segmentationVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(segmentationID));
- if (nullptr == segmentationVectorProperty)
- {
- MITK_DEBUG << "Could not find the segmentation " << segmentationID << " in the storage. Cannot link segmentation to lesion.";
- return;
- }
-
- std::vector<std::string> segmentationVectorPropertyValue = segmentationVectorProperty->GetValue();
- if (segmentationVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect segmentation storage. Not two (2) IDs stored.";
- return;
- }
-
- // the lesion ID of a segmentation is the second value in the vector
- segmentationVectorPropertyValue[1] = lesion.UID;
- segmentationVectorProperty->SetValue(segmentationVectorPropertyValue);
- return;
- }
-
- MITK_DEBUG << "Could not find lesion " << lesion.UID << " in the storage. Cannot link segmentation to lesion.";
-}
-
-void mitk::RelationStorage::UnlinkSegmentationFromLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the referenced ID of a segmentation (0. image ID 1. lesion ID)
- VectorProperty<std::string>* segmentationVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(segmentationID));
- if (nullptr == segmentationVectorProperty)
- {
- MITK_DEBUG << "Could not find the segmentation " << segmentationID << " in the storage. Cannot unlink lesion from segmentation.";
- return;
- }
-
- std::vector<std::string> segmentationVectorPropertyValue = segmentationVectorProperty->GetValue();
- // a segmentation has to have exactly two values (the ID of the linked image and the ID of the lesion)
- if (segmentationVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect data storage. Not two (2) values stored.";
- return;
- }
-
- // the second value of the segmentation vector is the ID of the referenced lesion
- // set the lesion reference to an empty string for removal
- segmentationVectorPropertyValue[1] = "";
- segmentationVectorProperty->SetValue(segmentationVectorPropertyValue);
-}
-
-void mitk::RelationStorage::RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid lesions of the current case
- VectorProperty<std::string>* lesionVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("lesions"));
- if (nullptr == lesionVectorProperty)
- {
- MITK_DEBUG << "Could not find any lesion in the storage.";
- return;
- }
-
- // remove the lesion reference from the list of all lesions of the current case
- std::vector<std::string> lesionsVectorPropertyValue = lesionVectorProperty->GetValue();
- lesionsVectorPropertyValue.erase(std::remove(lesionsVectorPropertyValue.begin(), lesionsVectorPropertyValue.end(), lesion.UID), lesionsVectorPropertyValue.end());
- if (lesionsVectorPropertyValue.empty())
- {
- // no more lesions stored -> remove the lesions property list
- propertyList->DeleteProperty("lesions");
- }
- else
- {
- // or store the modified vector value
- lesionVectorProperty->SetValue(lesionsVectorPropertyValue);
- }
-
- // remove the lesion instance itself
- // the lesion data is stored under the lesion ID
- VectorProperty<std::string>* lesionDataProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(lesion.UID));
- if (nullptr == lesionDataProperty)
- {
- MITK_DEBUG << "Lesion " << lesion.UID << " not found (already removed?). Cannot remove the lesion.";
- return;
- }
-
- std::vector<std::string> lesionData = lesionDataProperty->GetValue();
- // a lesion date has to have exactly two values (the name of the lesion and the UID of the lesion class)
- if (lesionData.size() != 2)
- {
- MITK_DEBUG << "Incorrect lesion data storage. Not two (2) strings of the lesion UID and the lesion name are stored.";
- }
- else
- {
- std::string lesionClassID = lesionData[1];
- RemoveLesionClass(caseID, lesionClassID);
- }
- propertyList->DeleteProperty(lesion.UID);
-}
-
-void mitk::RelationStorage::RemoveLesionClass(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& lesionClassID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
-
- // retrieve a vector property that contains the lesion class
- StringProperty* lesionClassProperty = dynamic_cast<StringProperty*>(propertyList->GetProperty(lesionClassID));
- if (nullptr == lesionClassProperty)
- {
- MITK_DEBUG << "Lesion class " << lesionClassID << " not found (already removed?). Cannot remove the lesion class.";
- return;
- }
-
- // retrieve a vector property that contains the valid lesions of the current case
- VectorProperty<std::string>* lesionVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("lesions"));
- if (nullptr == lesionVectorProperty)
- {
- return;
- }
-
- // check if the lesion class ID is referenced by any other lesion
- std::vector<std::string> lesionsVectorPropertyValue = lesionVectorProperty->GetValue();
- const auto existingLesionClass = std::find_if(lesionsVectorPropertyValue.begin(), lesionsVectorPropertyValue.end(),
- [&propertyList, &lesionClassID](const std::string& lesionID)
- {
- VectorProperty<std::string>* lesionDataProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(lesionID));
- if (nullptr == lesionDataProperty)
- {
- return false;
- }
-
- std::vector<std::string> lesionData = lesionDataProperty->GetValue();
- // a lesion date has to have exactly two values (the name of the lesion and the UID of the lesion class)
- if (lesionData.size() != 2)
- {
- return false;
- }
-
- return lesionData[1] == lesionClassID;
- });
-
- if (existingLesionClass == lesionsVectorPropertyValue.end())
- {
- // lesion class ID not referenced; remove lesion class
- propertyList->DeleteProperty(lesionClassID);
- }
-}
-
-void mitk::RelationStorage::AddControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid controlPoint UIDs for the current case
- VectorProperty<std::string>::Pointer controlPointsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("controlpoints"));
- std::vector<std::string> controlPointsVectorPropertyValue;
- if (nullptr == controlPointsVectorProperty)
- {
- controlPointsVectorProperty = VectorProperty<std::string>::New();
- }
- else
- {
- controlPointsVectorPropertyValue = controlPointsVectorProperty->GetValue();
- }
-
- const auto existingControlPoint = std::find(controlPointsVectorPropertyValue.begin(), controlPointsVectorPropertyValue.end(), controlPoint.UID);
- if (existingControlPoint != controlPointsVectorPropertyValue.end())
- {
- return;
- }
-
- // add the new control point UID from the given control point to the vector of all current control point UIDs
- controlPointsVectorPropertyValue.push_back(controlPoint.UID);
- // overwrite the current vector property with the new, extended string vector
- controlPointsVectorProperty->SetValue(controlPointsVectorPropertyValue);
- propertyList->SetProperty("controlpoints", controlPointsVectorProperty);
-
- // store the control point values (the three integer values of a date)
- std::vector<int> controlPointDate;
- controlPointDate.push_back(controlPoint.date.year());
- controlPointDate.push_back(controlPoint.date.month());
- controlPointDate.push_back(controlPoint.date.day());
-
- VectorProperty<int>::Pointer newControlPointVectorProperty = VectorProperty<int>::New();
- newControlPointVectorProperty->SetValue(controlPointDate);
- propertyList->SetProperty(controlPoint.UID, newControlPointVectorProperty);
-}
-
-void mitk::RelationStorage::LinkImageToControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID, const SemanticTypes::ControlPoint& controlPoint)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid controlPoint UIDs for the current case
- VectorProperty<std::string>* controlPointsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("controlpoints"));
- if (nullptr == controlPointsVectorProperty)
- {
- MITK_DEBUG << "Could not find any control point in the storage.";
- return;
- }
-
- std::vector<std::string> controlPointsVectorPropertyValue = controlPointsVectorProperty->GetValue();
- const auto existingControlPoint = std::find(controlPointsVectorPropertyValue.begin(), controlPointsVectorPropertyValue.end(), controlPoint.UID);
- if (existingControlPoint != controlPointsVectorPropertyValue.end())
- {
- // set / overwrite the control point reference of the given data
- // retrieve a vector property that contains the referenced ID of a image (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- MITK_DEBUG << "Could not find the image " << imageID << " in the storage. Cannot link data to control point.";
- return;
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect data storage. Not two (2) values stored.";
- return;
- }
-
- // the second value of the image vector is the ID of the referenced control point
- imageVectorPropertyValue[1] = controlPoint.UID;
- imageVectorProperty->SetValue(imageVectorPropertyValue);
- return;
- }
-
- MITK_DEBUG << "Could not find control point " << controlPoint.UID << " in the storage. Cannot link data to control point.";
-}
-
-void mitk::RelationStorage::UnlinkImageFromControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the referenced ID of a date (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- MITK_DEBUG << "Could not find the date " << imageID << " in the storage. Cannot unlink control point from date.";
- return;
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect data storage. Not two (2) values stored.";
- return;
- }
-
- // the second value of the image vector is the ID of the referenced control point
- // set the control point reference to an empty string for removal
- imageVectorPropertyValue[1] = "";
- imageVectorProperty->SetValue(imageVectorPropertyValue);
-}
-
-void mitk::RelationStorage::RemoveControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid controlPoint UIDs for the current case
- VectorProperty<std::string>* controlPointsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("controlpoints"));
- if (nullptr == controlPointsVectorProperty)
- {
- MITK_DEBUG << "Could not find any control point in the storage.";
- return;
- }
-
- // remove the control point reference from the list of all control points of the current case
- std::vector<std::string> controlPointsVectorPropertyValue = controlPointsVectorProperty->GetValue();
- controlPointsVectorPropertyValue.erase(std::remove(controlPointsVectorPropertyValue.begin(), controlPointsVectorPropertyValue.end(), controlPoint.UID), controlPointsVectorPropertyValue.end());
- if (controlPointsVectorPropertyValue.empty())
- {
- // no more control points stored -> remove the control point property list
- propertyList->DeleteProperty("controlpoints");
- }
- else
- {
- // or store the modified vector value
- controlPointsVectorProperty->SetValue(controlPointsVectorPropertyValue);
- }
-
- // remove the control point instance itself
- propertyList->DeleteProperty(controlPoint.UID);
-}
-
-void mitk::RelationStorage::AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid examination period UIDs for the current case
- VectorProperty<std::string>::Pointer examinationPeriodsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("examinationperiods"));
- std::vector<std::string> examinationPeriodsVectorPropertyValue;
- if (nullptr == examinationPeriodsVectorProperty)
- {
- examinationPeriodsVectorProperty = VectorProperty<std::string>::New();
- }
- else
- {
- examinationPeriodsVectorPropertyValue = examinationPeriodsVectorProperty->GetValue();
- }
-
- const auto& existingIndex = std::find(examinationPeriodsVectorPropertyValue.begin(), examinationPeriodsVectorPropertyValue.end(), examinationPeriod.UID);
- if (existingIndex != examinationPeriodsVectorPropertyValue.end())
- {
- return;
- }
-
- // add the new examination period id from the given examination period to the vector of all current examination period UIDs
- examinationPeriodsVectorPropertyValue.push_back(examinationPeriod.UID);
- // overwrite the current vector property with the new, extended string vector
- examinationPeriodsVectorProperty->SetValue(examinationPeriodsVectorPropertyValue);
- propertyList->SetProperty("examinationperiods", examinationPeriodsVectorProperty);
-
- // add the examination period with the UID as the key and the name as as the vector value
- std::vector<std::string> examinationPeriodData;
- examinationPeriodData.push_back(examinationPeriod.name);
- VectorProperty<std::string>::Pointer newExaminationPeriodVectorProperty = VectorProperty<std::string>::New();
- newExaminationPeriodVectorProperty->SetValue(examinationPeriodData);
- propertyList->SetProperty(examinationPeriod.UID, newExaminationPeriodVectorProperty);
-}
-
-void mitk::RelationStorage::RenameExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the data of the given examination period
- VectorProperty<std::string>* examinationPeriodDataVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(examinationPeriod.UID));
- if (nullptr == examinationPeriodDataVectorProperty)
- {
- MITK_DEBUG << "Could not find examination period " << examinationPeriod.UID << " in the storage. Cannot rename the examination period.";
- return;
- }
-
- std::vector<std::string> examinationPeriodDataVectorPropertyValue = examinationPeriodDataVectorProperty->GetValue();
- // an examination period has an arbitrary number of vector values (name and control point UIDs) (at least one for the name)
- if (examinationPeriodDataVectorPropertyValue.size() < 1)
- {
- MITK_DEBUG << "Incorrect examination period storage. At least one (1) name has to be stored.";
- return;
- }
- else
- {
- // set the first vector value - the name
- examinationPeriodDataVectorPropertyValue[0] = examinationPeriod.name;
- // store the modified vector value
- examinationPeriodDataVectorProperty->SetValue(examinationPeriodDataVectorPropertyValue);
- }
-}
-
-void mitk::RelationStorage::AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
-
- // retrieve a vector property that contains the represented control point UIDs of the given examination period
- VectorProperty<std::string>* controlPointUIDsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(examinationPeriod.UID));
- if (nullptr == controlPointUIDsVectorProperty)
- {
- MITK_DEBUG << "Could not find the examination period " << examinationPeriod.UID << " in the storage. Cannot add the control point to the examination period.";
- return;
- }
-
- std::vector<std::string> controlPointUIDsVectorPropertyValue = controlPointUIDsVectorProperty->GetValue();
- // store the control point UID
- controlPointUIDsVectorPropertyValue.push_back(controlPoint.UID);
- // sort the vector according to the date of the control points referenced by the UIDs
- auto lambda = [&caseID](const SemanticTypes::ID& leftControlPointUID, const SemanticTypes::ID& rightControlPointUID)
- {
- const auto& leftControlPoint = GenerateControlpoint(caseID, leftControlPointUID);
- const auto& rightControlPoint = GenerateControlpoint(caseID, rightControlPointUID);
-
- return leftControlPoint.date <= rightControlPoint.date;
- };
-
- std::sort(controlPointUIDsVectorPropertyValue.begin(), controlPointUIDsVectorPropertyValue.end(), lambda);
- // store the modified and sorted control point UID vector of this examination period
- controlPointUIDsVectorProperty->SetValue(controlPointUIDsVectorPropertyValue);
-}
-
-void mitk::RelationStorage::RemoveControlPointFromExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
-
- // retrieve a vector property that contains the represented control point UIDs of the given examination period
- VectorProperty<std::string>* controlPointUIDsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(examinationPeriod.UID));
- if (nullptr == controlPointUIDsVectorProperty)
- {
- MITK_DEBUG << "Could not find examination period " << examinationPeriod.UID << " in the storage. Cannot add the control point to the examination period.";
- return;
- }
-
- std::vector<std::string> controlPointUIDsVectorPropertyValue = controlPointUIDsVectorProperty->GetValue();
- // an examination period has an arbitrary number of vector values (name and control point UIDs) (at least one for the name)
- if (controlPointUIDsVectorPropertyValue.size() < 2)
- {
- MITK_DEBUG << "Incorrect examination period storage. At least one (1) control point ID has to be stored.";
- return;
- }
- else
- {
- controlPointUIDsVectorPropertyValue.erase(std::remove(controlPointUIDsVectorPropertyValue.begin(), controlPointUIDsVectorPropertyValue.end(), controlPoint.UID), controlPointUIDsVectorPropertyValue.end());
- if (controlPointUIDsVectorPropertyValue.size() < 2)
- {
- RemoveExaminationPeriod(caseID, examinationPeriod);
- }
- else
- {
- // store the modified vector value
- controlPointUIDsVectorProperty->SetValue(controlPointUIDsVectorPropertyValue);
- }
- }
-}
-
-void mitk::RelationStorage::RemoveExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid examination period UIDs for the current case
- VectorProperty<std::string>::Pointer examinationPeriodsVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("examinationperiods"));
- if (nullptr == examinationPeriodsVectorProperty)
- {
- MITK_DEBUG << "Could not find any examination periods in the storage.";
- return;
- }
-
- std::vector<std::string> examinationPeriodsVectorPropertyValue = examinationPeriodsVectorProperty->GetValue();
- examinationPeriodsVectorPropertyValue.erase(std::remove(examinationPeriodsVectorPropertyValue.begin(), examinationPeriodsVectorPropertyValue.end(), examinationPeriod.UID), examinationPeriodsVectorPropertyValue.end());
- if (examinationPeriodsVectorPropertyValue.empty())
- {
- // no more examination periods stored -> remove the examination period property list
- propertyList->DeleteProperty("examinationperiods");
- }
- else
- {
- // or store the modified vector value
- examinationPeriodsVectorProperty->SetValue(examinationPeriodsVectorPropertyValue);
- }
-
- // remove the examination period instance itself
- propertyList->DeleteProperty(examinationPeriod.UID);
-}
-
-void mitk::RelationStorage::AddInformationTypeToImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID, const SemanticTypes::InformationType& informationType)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid information types of the current case
- VectorProperty<std::string>::Pointer informationTypesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("informationtypes"));
- std::vector<std::string> informationTypesVectorPropertyValue;
- if (nullptr == informationTypesVectorProperty)
- {
- informationTypesVectorProperty = VectorProperty<std::string>::New();
- }
- else
- {
- informationTypesVectorPropertyValue = informationTypesVectorProperty->GetValue();
- }
-
- const auto existingInformationType = std::find(informationTypesVectorPropertyValue.begin(), informationTypesVectorPropertyValue.end(), informationType);
- if (existingInformationType == informationTypesVectorPropertyValue.end())
- {
- // at first: add the information type to the storage
- informationTypesVectorPropertyValue.push_back(informationType);
- informationTypesVectorProperty->SetValue(informationTypesVectorPropertyValue);
- propertyList->SetProperty("informationtypes", informationTypesVectorProperty);
- }
-
- // set / overwrite the information type of the given data
- // retrieve a vector property that contains the referenced ID of an image (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- MITK_DEBUG << "Could not find the image " << imageID << " in the storage. Cannot add information type to image.";
- return;
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect data storage. Not two (2) values stored.";
- return;
- }
-
- // the first value of the image vector is the information type
- imageVectorPropertyValue[0] = informationType;
- imageVectorProperty->SetValue(imageVectorPropertyValue);
-}
-
-void mitk::RelationStorage::RemoveInformationTypeFromImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& imageID)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the referenced ID of an image (0. information type 1. control point ID)
- VectorProperty<std::string>* imageVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty(imageID));
- if (nullptr == imageVectorProperty)
- {
- MITK_DEBUG << "Could not find the image " << imageID << " in the storage. Cannot remove information type from image.";
- return;
- }
-
- std::vector<std::string> imageVectorPropertyValue = imageVectorProperty->GetValue();
- // an image has to have exactly two values (the information type and the ID of the control point)
- if (imageVectorPropertyValue.size() != 2)
- {
- MITK_DEBUG << "Incorrect data storage. Not two (2) values stored.";
- return;
- }
-
- // the first value of the image vector is the information type
- // set the information type to an empty string for removal
- imageVectorPropertyValue[0] = "";
- imageVectorProperty->SetValue(imageVectorPropertyValue);
-}
-
-void mitk::RelationStorage::RemoveInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType)
-{
- PropertyList::Pointer propertyList = GetStorageData(caseID);
- if (nullptr == propertyList)
- {
- MITK_DEBUG << "Could not find the property list " << caseID << " for the current MITK workbench / session.";
- return;
- }
- // retrieve a vector property that contains the valid information types of the current case
- VectorProperty<std::string>* informationTypesVectorProperty = dynamic_cast<VectorProperty<std::string>*>(propertyList->GetProperty("informationtypes"));
- if (nullptr == informationTypesVectorProperty)
- {
- MITK_DEBUG << "Could not find any information type in the storage.";
- return;
- }
-
- std::vector<std::string> informationTypesVectorPropertyValue = informationTypesVectorProperty->GetValue();
- informationTypesVectorPropertyValue.erase(std::remove(informationTypesVectorPropertyValue.begin(), informationTypesVectorPropertyValue.end(), informationType), informationTypesVectorPropertyValue.end());
- if (informationTypesVectorPropertyValue.empty())
- {
- // no more information types stored -> remove the information types property list
- propertyList->DeleteProperty("informationtypes");
- }
- else
- {
- // or store the modified vector value
- informationTypesVectorProperty->SetValue(informationTypesVectorPropertyValue);
- }
-}
diff --git a/Modules/SemanticRelations/src/mitkSemanticRelationsDataStorageAccess.cpp b/Modules/SemanticRelations/src/mitkSemanticRelationsDataStorageAccess.cpp
deleted file mode 100644
index 5994a9a4d7..0000000000
--- a/Modules/SemanticRelations/src/mitkSemanticRelationsDataStorageAccess.cpp
+++ /dev/null
@@ -1,348 +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 "mitkSemanticRelationsDataStorageAccess.h"
-
-// semantic relations module
-#include "mitkControlPointManager.h"
-#include "mitkDICOMHelper.h"
-#include "mitkNodePredicates.h"
-#include "mitkRelationStorage.h"
-#include "mitkSemanticRelationException.h"
-#include "mitkSemanticRelationsInference.h"
-
-// c++
-#include <iterator>
-#include <algorithm>
-
-mitk::SemanticRelationsDataStorageAccess::SemanticRelationsDataStorageAccess(DataStorage* dataStorage)
- : m_DataStorage(dataStorage)
-{
- // nothing here
-}
-
-/************************************************************************/
-/* functions to get instances / attributes */
-/************************************************************************/
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSegmentationsOfCase(const SemanticTypes::CaseID& caseID) const
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data storage.";
- }
-
- SemanticTypes::IDVector allSegmentationIDsOfCase = RelationStorage::GetAllSegmentationIDsOfCase(caseID);
- DataNodeVector allSegmentationsOfCase;
- // get all segmentation nodes of the current data storage
- // only those nodes are respected, that are currently held in the data storage
- DataStorage::SetOfObjects::ConstPointer segmentationNodes = dataStorage->GetSubset(NodePredicates::GetSegmentationPredicate());
- for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it)
- {
- DataNode* segmentationNode = it->Value();
-
- SemanticTypes::CaseID currentCaseID;
- SemanticTypes::ID segmentationID;
- try
- {
- // find the corresponding segmentation node for the given segmentation ID
- currentCaseID = GetCaseIDFromDataNode(segmentationNode);
- segmentationID = GetIDFromDataNode(segmentationNode);
- }
- catch (SemanticRelationException&)
- {
- // found a segmentation node that is not stored in the semantic relations
- // this segmentation node does not have any DICOM information --> exception thrown
- // continue with the next segmentation to compare IDs
- continue;
- }
-
- if (caseID == currentCaseID && (std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), segmentationID) != allSegmentationIDsOfCase.end()))
- {
- // found current image node in the storage, add it to the return vector
- allSegmentationsOfCase.push_back(segmentationNode);
- }
- }
-
- return allSegmentationsOfCase;
-}
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSegmentationsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const
-{
- if (SemanticRelationsInference::InstanceExists(caseID, lesion))
- {
- // lesion exists, retrieve all case segmentations from the storage
- DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfCase(caseID);
-
- // filter all segmentations: check for semantic relation with the given lesion using a lambda function
- auto lambda = [&lesion](DataNode::Pointer segmentation)
- {
- try
- {
- SemanticTypes::Lesion representedLesion = SemanticRelationsInference::GetLesionOfSegmentation(segmentation);
- return lesion.UID != representedLesion.UID;
- }
- catch (const SemanticRelationException&)
- {
- return true;
- }
- };
- allSegmentationsOfLesion.erase(std::remove_if(allSegmentationsOfLesion.begin(), allSegmentationsOfLesion.end(), lambda), allSegmentationsOfLesion.end());
-
- return allSegmentationsOfLesion;
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "Could not find an existing lesion instance for the given caseID " << caseID << " and lesion " << lesion.UID << ".";
- }
-}
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllImagesOfCase(const SemanticTypes::CaseID& caseID) const
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data storage.";
- }
-
- SemanticTypes::IDVector allImageIDsOfCase = RelationStorage::GetAllImageIDsOfCase(caseID);
- DataNodeVector allImagesOfCase;
- // get all image nodes of the current data storage
- // only those nodes are respected, that are currently held in the data storage
- DataStorage::SetOfObjects::ConstPointer imageNodes = dataStorage->GetSubset(NodePredicates::GetImagePredicate());
- for (auto it = imageNodes->Begin(); it != imageNodes->End(); ++it)
- {
- DataNode* imageNode = it->Value();
-
- SemanticTypes::CaseID currentCaseID;
- SemanticTypes::ID imageID;
- try
- {
- // find the corresponding image node for the given segmentation ID
- currentCaseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException&)
- {
- // found an image node that is not stored in the semantic relations
- // this image node does not have any DICOM information --> exception thrown
- // continue with the next image to compare IDs
- continue;
- }
-
- if (caseID == currentCaseID && (std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), imageID) != allImageIDsOfCase.end()))
- {
- // found current image node in the storage, add it to the return vector
- allImagesOfCase.push_back(imageNode);
- }
- }
-
- return allImagesOfCase;
-}
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllImagesByID(const SemanticTypes::IDVector& imageIDs) const
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data storage.";
- }
-
- DataNodeVector allImagesOfCase;
- // get all image nodes of the current data storage
- // only those nodes are respected, that are currently held in the data storage
- DataStorage::SetOfObjects::ConstPointer imageNodes = dataStorage->GetSubset(NodePredicates::GetImagePredicate());
- for (auto it = imageNodes->Begin(); it != imageNodes->End(); ++it)
- {
- DataNode* imageNode = it->Value();
-
- SemanticTypes::CaseID currentCaseID;
- SemanticTypes::ID imageID;
- try
- {
- // find the corresponding image node for the given segmentation ID
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException&)
- {
- // found an image node that is not stored in the semantic relations
- // this image node does not have any DICOM information --> exception thrown
- // continue with the next image to compare IDs
- continue;
- }
-
- if (std::find(imageIDs.begin(), imageIDs.end(), imageID) != imageIDs.end())
- {
- // found current image node in the storage, add it to the return vector
- allImagesOfCase.push_back(imageNode);
- }
- }
-
- return allImagesOfCase;
-}
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllImagesOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion) const
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data storage.";
- }
-
- DataNodeVector allImagesOfLesion;
- // 1. get all segmentations that define the lesion
- // 2. retrieve the parent node (source) of the found segmentation node
- DataNodeVector allSegmentationsOfLesion = GetAllSegmentationsOfLesion(caseID, lesion);
- for (const auto& segmentationNode : allSegmentationsOfLesion)
- {
- // get parent node of the current segmentation node with the node predicate
- DataStorage::SetOfObjects::ConstPointer parentNodes = dataStorage->GetSources(segmentationNode, NodePredicates::GetImagePredicate(), false);
- for (auto it = parentNodes->Begin(); it != parentNodes->End(); ++it)
- {
- DataNode::Pointer dataNode = it->Value();
- allImagesOfLesion.push_back(it->Value());
- }
- }
-
- std::sort(allImagesOfLesion.begin(), allImagesOfLesion.end());
- allImagesOfLesion.erase(std::unique(allImagesOfLesion.begin(), allImagesOfLesion.end()), allImagesOfLesion.end());
- return allImagesOfLesion;
-}
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const
-{
- if (SemanticRelationsInference::InstanceExists(caseID, controlPoint))
- {
- if (SemanticRelationsInference::InstanceExists(caseID, informationType))
- {
- // control point exists, information type exists, retrieve all images from the storage
- DataNodeVector allImagesOfCase = GetAllImagesOfCase(caseID);
- // filter all images to remove the ones with a different control point and information type using a lambda function
- auto lambda = [&controlPoint, &informationType](DataNode::Pointer imageNode)
- {
- return (informationType != SemanticRelationsInference::GetInformationTypeOfImage(imageNode))
- || (controlPoint.date != SemanticRelationsInference::GetControlPointOfImage(imageNode).date);
- };
-
- allImagesOfCase.erase(std::remove_if(allImagesOfCase.begin(), allImagesOfCase.end(), lambda), allImagesOfCase.end());
-
- return allImagesOfCase;
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType << ".";
- }
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "Could not find an existing control point for the given caseID " << caseID << " and control point " << controlPoint.UID << ".";
- }
-}
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificImages(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ExaminationPeriod& examinationPeriod) const
-{
- if (SemanticRelationsInference::InstanceExists(caseID, informationType))
- {
- if (SemanticRelationsInference::InstanceExists(caseID, examinationPeriod))
- {
- // examination period exists, information type exists, retrieve all imageIDs from the storage
- auto allImageIDsOfExaminationPeriod = SemanticRelationsInference::GetAllImageIDsOfExaminationPeriod(caseID, examinationPeriod);
- // filter all images to remove the ones with a different information type using a lambda function
- auto lambda = [&caseID, &informationType](SemanticTypes::ID imageID)
- {
- return (informationType != RelationStorage::GetInformationTypeOfImage(caseID, imageID));
- };
-
- allImageIDsOfExaminationPeriod.erase(std::remove_if(allImageIDsOfExaminationPeriod.begin(), allImageIDsOfExaminationPeriod.end(), lambda), allImageIDsOfExaminationPeriod.end());
-
- auto allImagesOfExaminationPeriod = GetAllImagesByID(allImageIDsOfExaminationPeriod);
- return allImagesOfExaminationPeriod;
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "Could not find an existing examination period for the given caseID " << caseID << " and examination period " << examinationPeriod.name << ".";
- }
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "Could not find an existing information type for the given caseID " << caseID << " and information type " << informationType << ".";
- }
-}
-
-mitk::SemanticRelationsDataStorageAccess::DataNodeVector mitk::SemanticRelationsDataStorageAccess::GetAllSpecificSegmentations(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType) const
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- mitkThrow() << "Not a valid data storage.";
- }
-
- DataNodeVector allSpecificImages;
- try
- {
- allSpecificImages = GetAllSpecificImages(caseID, controlPoint, informationType);
-
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get the specific segmentation.";
- }
-
- DataNodeVector allSpecificSegmentations;
- for (const auto& imageNode : allSpecificImages)
- {
- DataStorage::SetOfObjects::ConstPointer segmentationNodes = dataStorage->GetDerivations(imageNode, NodePredicates::GetSegmentationPredicate(), false);
- for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it)
- {
- allSpecificSegmentations.push_back(it->Value());
- }
- }
-
- return allSpecificSegmentations;
-}
-
-mitk::DataNode::Pointer mitk::SemanticRelationsDataStorageAccess::GetSpecificSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint,
- const SemanticTypes::InformationType& informationType, const SemanticTypes::Lesion& lesion) const
-{
- if (m_DataStorage.IsExpired())
- {
- mitkThrow() << "Not a valid data storage.";
- }
-
- DataNodeVector allSpecificSegmentations;
- try
- {
- allSpecificSegmentations = GetAllSpecificSegmentations(caseID, controlPoint, informationType);
-
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get the specific segmentation.";
- }
-
- for (const auto& segmentationNode : allSpecificSegmentations)
- {
- SemanticTypes::Lesion representedLesion = SemanticRelationsInference::GetLesionOfSegmentation(segmentationNode);
- if (representedLesion.UID == lesion.UID)
- {
- return segmentationNode;
- }
- }
-
- return mitk::DataNode::Pointer();
-}
diff --git a/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp b/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp
deleted file mode 100644
index af3bdfadb3..0000000000
--- a/Modules/SemanticRelations/src/mitkSemanticRelationsInference.cpp
+++ /dev/null
@@ -1,582 +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 "mitkSemanticRelationsInference.h"
-
-// semantic relations module
-#include "mitkControlPointManager.h"
-#include "mitkDICOMHelper.h"
-#include "mitkNodePredicates.h"
-#include "mitkRelationStorage.h"
-#include "mitkSemanticRelationException.h"
-
-/************************************************************************/
-/* functions to get instances / attributes */
-/************************************************************************/
-
-mitk::SemanticTypes::LesionClassVector mitk::SemanticRelationsInference::GetAllLesionClassesOfCase(const SemanticTypes::CaseID& caseID)
-{
- SemanticTypes::LesionVector allLesionsOfCase = RelationStorage::GetAllLesionsOfCase(caseID);
- SemanticTypes::LesionClassVector allLesionClassesOfCase;
-
- for (const auto& lesion : allLesionsOfCase)
- {
- allLesionClassesOfCase.push_back(lesion.lesionClass);
- }
-
- // remove duplicate entries
- auto lessThan = [](const SemanticTypes::LesionClass& lesionClassLeft, const SemanticTypes::LesionClass& lesionClassRight)
- {
- return lesionClassLeft.UID < lesionClassRight.UID;
- };
-
- auto equal = [](const SemanticTypes::LesionClass& lesionClassLeft, const SemanticTypes::LesionClass& lesionClassRight)
- {
- return lesionClassLeft.UID == lesionClassRight.UID;
- };
-
- std::sort(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), lessThan);
- allLesionClassesOfCase.erase(std::unique(allLesionClassesOfCase.begin(), allLesionClassesOfCase.end(), equal), allLesionClassesOfCase.end());
-
- return allLesionClassesOfCase;
-}
-
-mitk::SemanticTypes::Lesion mitk::SemanticRelationsInference::GetLesionOfSegmentation(const DataNode* segmentationNode)
-{
- if (nullptr == segmentationNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node.";
- }
-
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID segmentationID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(segmentationNode);
- segmentationID = GetIDFromDataNode(segmentationNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get the lesion of the given segmentation data node.";
- }
-
- return RelationStorage::GetLesionOfSegmentation(caseID, segmentationID);
-}
-
-mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfImage(const DataNode* imageNode)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID imageID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get all lesions of the given image data node.";
- }
-
- SemanticTypes::LesionVector allLesionsOfImage;
- // 1. get all segmentations that are connected to the given image
- // 2. get the lesion of each segmentation
- // 3. guarantee uniqueness of lesions
- SemanticTypes::IDVector allSegmentationIDsOfImage = RelationStorage::GetAllSegmentationIDsOfImage(caseID, imageID);
- for (const auto& segmentationID : allSegmentationIDsOfImage)
- {
- // get represented lesion of the current segmentation
- SemanticTypes::Lesion representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID);
- if (!representedLesion.UID.empty())
- {
- allLesionsOfImage.push_back(representedLesion);
- }
- }
-
- // remove duplicate entries
- auto lessThan = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight)
- {
- return lesionLeft.UID < lesionRight.UID;
- };
-
- auto equal = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight)
- {
- return lesionLeft.UID == lesionRight.UID;
- };
-
- std::sort(allLesionsOfImage.begin(), allLesionsOfImage.end(), lessThan);
- allLesionsOfImage.erase(std::unique(allLesionsOfImage.begin(), allLesionsOfImage.end(), equal), allLesionsOfImage.end());
-
- return allLesionsOfImage;
-}
-
-mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID);
-
- // filter the lesions: use only those, where the associated data is connected to image data that refers to the given control point using a lambda function
- auto lambda = [&caseID, &controlPoint](const SemanticTypes::Lesion& lesion)
- {
- return !SpecificImageExists(caseID, lesion, controlPoint);
- };
-
- allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end());
-
- return allLesions;
-}
-
-mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllLesionsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType)
-{
- SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID);
-
- // filter the lesions: use only those, where the associated data is connected to image data that refers to the given information type using a lambda function
- auto lambda = [&caseID, &informationType](const SemanticTypes::Lesion& lesion)
- {
- return !SpecificImageExists(caseID, lesion, informationType);
- };
-
- allLesions.erase(std::remove_if(allLesions.begin(), allLesions.end(), lambda), allLesions.end());
-
- return allLesions;
-}
-
-mitk::SemanticTypes::LesionVector mitk::SemanticRelationsInference::GetAllSpecificLesions(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::InformationType& informationType)
-{
- auto allLesionsOfControlPoint = GetAllLesionsOfControlPoint(caseID, controlPoint);
- auto allLesionsOfInformationType = GetAllLesionsOfInformationType(caseID, informationType);
- SemanticTypes::LesionVector allLesionsIntersection;
-
- auto lessThan = [](const SemanticTypes::Lesion& lesionLeft, const SemanticTypes::Lesion& lesionRight)
- {
- return lesionLeft.UID < lesionRight.UID;
- };
-
- std::sort(allLesionsOfControlPoint.begin(), allLesionsOfControlPoint.end(), lessThan);
- std::sort(allLesionsOfInformationType.begin(), allLesionsOfInformationType.end(), lessThan);
- SemanticTypes::IDVector allImageIDsIntersection;
- // set_intersection removes duplicated nodes
- std::set_intersection(allLesionsOfControlPoint.begin(), allLesionsOfControlPoint.end(),
- allLesionsOfInformationType.begin(), allLesionsOfInformationType.end(),
- std::back_inserter(allLesionsIntersection), lessThan);
-
- return allLesionsIntersection;
-}
-
-bool mitk::SemanticRelationsInference::IsRepresentingALesion(const DataNode* segmentationNode)
-{
- SemanticTypes::Lesion representedLesion;
- try
- {
- representedLesion = GetLesionOfSegmentation(segmentationNode);
- }
- catch (const SemanticRelationException&)
- {
- return false;
- }
-
- return !representedLesion.UID.empty();
-}
-
-bool mitk::SemanticRelationsInference::IsRepresentingALesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::ID& segmentationID)
-{
- SemanticTypes::Lesion representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID);
- return !representedLesion.UID.empty();
-}
-
-bool mitk::SemanticRelationsInference::IsLesionPresent(const SemanticTypes::Lesion& lesion, const DataNode* dataNode)
-{
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID dataNodeID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(dataNode);
- dataNodeID = GetIDFromDataNode(dataNode);
- }
- catch (const SemanticRelationException&)
- {
- return false;
- }
-
- if (NodePredicates::GetImagePredicate()->CheckNode(dataNode))
- {
- return IsLesionPresentOnImage(caseID, lesion, dataNodeID);
- }
-
- if (NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode))
- {
- return IsLesionPresentOnSegmentation(caseID, lesion, dataNodeID);
- }
-
- return false;
-}
-
-bool mitk::SemanticRelationsInference::IsLesionPresentOnImage(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& imageID)
-{
- SemanticTypes::IDVector allImageIDsOfLesion;
- try
- {
- allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get all image IDs of the given lesion to determine the lesion presence.";
- }
-
- for (const auto& imageIDOfLesion : allImageIDsOfLesion)
- {
- if (imageIDOfLesion == imageID)
- {
- return true;
- }
- }
-
- return false;
-}
-
-bool mitk::SemanticRelationsInference::IsLesionPresentOnSegmentation(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ID& segmentationID)
-{
- const auto representedLesion = RelationStorage::GetLesionOfSegmentation(caseID, segmentationID);
- return lesion.UID == representedLesion.UID;
-}
-
-bool mitk::SemanticRelationsInference::IsLesionPresentAtControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::IDVector allImageIDsOfLesion;
- try
- {
- allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get all image IDs of the given lesion to determine the lesion presence.";
- }
-
- for (const auto& imageIDOfLesion : allImageIDsOfLesion)
- {
- auto imageControlPoint = RelationStorage::GetControlPointOfImage(caseID, imageIDOfLesion);
- if (imageControlPoint.date == controlPoint.date)
- {
- return true;
- }
- }
-
- return false;
-}
-
-bool mitk::SemanticRelationsInference::InstanceExists(const DataNode* dataNode)
-{
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID dataNodeID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(dataNode);
- dataNodeID = GetIDFromDataNode(dataNode);
- }
- catch (const SemanticRelationException&)
- {
- return false;
- }
-
- if (NodePredicates::GetImagePredicate()->CheckNode(dataNode))
- {
- SemanticTypes::IDVector allImageIDsOfCase = RelationStorage::GetAllImageIDsOfCase(caseID);
- return std::find(allImageIDsOfCase.begin(), allImageIDsOfCase.end(), dataNodeID) != allImageIDsOfCase.end();
- }
-
- if (NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode))
- {
- SemanticTypes::IDVector allSegmentationIDsOfCase = RelationStorage::GetAllSegmentationIDsOfCase(caseID);
- return std::find(allSegmentationIDsOfCase.begin(), allSegmentationIDsOfCase.end(), dataNodeID) != allSegmentationIDsOfCase.end();
- }
-
- return false;
-}
-
-bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- SemanticTypes::LesionVector allLesions = RelationStorage::GetAllLesionsOfCase(caseID);
-
- // filter all lesions: check for equality with the given lesion using a lambda function
- auto lambda = [&lesion](const SemanticTypes::Lesion& currentLesion)
- {
- return currentLesion.UID == lesion.UID;
- };
-
- const auto existingLesion = std::find_if(allLesions.begin(), allLesions.end(), lambda);
-
- return existingLesion != allLesions.end();
-}
-
-mitk::SemanticTypes::IDVector mitk::SemanticRelationsInference::GetAllImageIDsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- if (!InstanceExists(caseID, lesion))
- {
- mitkThrowException(SemanticRelationException) << "Could not find an existing lesion instance for the given caseID " << caseID << " and lesion " << lesion.UID << ".";
- }
-
- SemanticTypes::IDVector allImageIDsOfLesion;
- // 1. get all segmentations that define the lesion
- // 2. get the parentID (imageID) of each segmentation
- // 3. guarantee uniqueness of image IDs
- SemanticTypes::IDVector allSegmentationIDsOfLesion = RelationStorage::GetAllSegmentationIDsOfLesion(caseID, lesion);
- for (const auto& segmentationID : allSegmentationIDsOfLesion)
- {
- // get parent ID of the current segmentation ID
- SemanticTypes::ID imageID = RelationStorage::GetImageIDOfSegmentation(caseID, segmentationID);
- if(!imageID.empty())
- {
- allImageIDsOfLesion.push_back(imageID);
- }
- }
-
- std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end());
- allImageIDsOfLesion.erase(std::unique(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end()), allImageIDsOfLesion.end());
-
- return allImageIDsOfLesion;
-}
-
-mitk::SemanticTypes::IDVector mitk::SemanticRelationsInference::GetAllImageIDsOfExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- if (!InstanceExists(caseID, examinationPeriod))
- {
- mitkThrowException(SemanticRelationException) << "Could not find an existing examination period for the given caseID " << caseID << " and examination period " << examinationPeriod.name << ".";
- }
-
- SemanticTypes::IDVector allImageIDsOfExaminationPeriod;
- // 1. get all control point UIDs of the examination period
- // 2. get all images of each control points to find all images of the examination period
- SemanticTypes::ControlPoint controlPoint;
- for (const auto& controlPointUID : examinationPeriod.controlPointUIDs)
- {
- controlPoint = GetControlPointByUID(caseID, controlPointUID);
- auto allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint);
- allImageIDsOfExaminationPeriod.insert(allImageIDsOfExaminationPeriod.end(), allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end());
- }
-
- return allImageIDsOfExaminationPeriod;
-}
-
-mitk::SemanticTypes::ControlPoint mitk::SemanticRelationsInference::GetControlPointOfImage(const DataNode* imageNode)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid data node.";
- }
-
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID imageID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get the control point of the given image data node.";
- }
-
- return RelationStorage::GetControlPointOfImage(caseID, imageID);
-}
-
-mitk::SemanticTypes::ControlPointVector mitk::SemanticRelationsInference::GetAllControlPointsOfLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
-
- // filter the control points: use only those, where the associated image data has a segmentation that refers to the given lesion using a lambda function
- auto lambda = [&caseID, &lesion](const SemanticTypes::ControlPoint& controlPoint)
- {
- return !SpecificImageExists(caseID, lesion, controlPoint);
- };
-
- allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end());
-
- return allControlPoints;
-}
-
-mitk::SemanticTypes::ControlPointVector mitk::SemanticRelationsInference::GetAllControlPointsOfInformationType(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType)
-{
- SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
-
- // filter the control points: use only those, where the associated image data refers to the given information type using a lambda function
- auto lambda = [&caseID, &informationType](const SemanticTypes::ControlPoint& controlPoint)
- {
- return !SpecificImageExists(caseID, informationType, controlPoint);
- };
-
- allControlPoints.erase(std::remove_if(allControlPoints.begin(), allControlPoints.end(), lambda), allControlPoints.end());
-
- return allControlPoints;
-}
-
-bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
-
- // filter all control points: check for equality with the given control point using a lambda function
- auto lambda = [&controlPoint](const SemanticTypes::ControlPoint& currentControlPoint) { return currentControlPoint.UID == controlPoint.UID; };
- const auto existingControlPoint = std::find_if(allControlPoints.begin(), allControlPoints.end(), lambda);
-
- if (existingControlPoint != allControlPoints.end())
- {
- return true;
- }
- else
- {
- return false;
- }
-}
-
-bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- SemanticTypes::ExaminationPeriodVector allExaminationPeriods = RelationStorage::GetAllExaminationPeriodsOfCase(caseID);
-
- // filter all examination periods: check for equality with the given examination period using a lambda function
- auto lambda = [&examinationPeriod](const SemanticTypes::ExaminationPeriod& currentExaminationPeriod) { return currentExaminationPeriod.UID == examinationPeriod.UID; };
- const auto existingExaminationPeriod = std::find_if(allExaminationPeriods.begin(), allExaminationPeriods.end(), lambda);
-
- if (existingExaminationPeriod != allExaminationPeriods.end())
- {
- return true;
- }
- else
- {
- return false;
- }
-}
-
-mitk::SemanticTypes::InformationType mitk::SemanticRelationsInference::GetInformationTypeOfImage(const DataNode* imageNode)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID imageID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot get the information type of the given image data node.";
- }
-
- return RelationStorage::GetInformationTypeOfImage(caseID, imageID);
-}
-
-mitk::SemanticTypes::InformationTypeVector mitk::SemanticRelationsInference::GetAllInformationTypesOfControlPoint(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::InformationTypeVector allInformationTypes = RelationStorage::GetAllInformationTypesOfCase(caseID);
-
- // filter the information types: use only those, where the associated data refers to the given control point using a lambda function
- auto lambda = [&caseID, &controlPoint](const SemanticTypes::InformationType& informationType)
- {
- return !SpecificImageExists(caseID, informationType, controlPoint);
- };
-
- allInformationTypes.erase(std::remove_if(allInformationTypes.begin(), allInformationTypes.end(), lambda), allInformationTypes.end());
-
- return allInformationTypes;
-}
-
-bool mitk::SemanticRelationsInference::InstanceExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType)
-{
- SemanticTypes::InformationTypeVector allInformationTypes = RelationStorage::GetAllInformationTypesOfCase(caseID);
-
- // filter all information types: check for equality with the given information type using a lambda function
- auto lambda = [&informationType](const SemanticTypes::InformationType& currentInformationType) { return currentInformationType == informationType; };
- const auto existingInformationType = std::find_if(allInformationTypes.begin(), allInformationTypes.end(), lambda);
-
- if (existingInformationType != allInformationTypes.end())
- {
- return true;
- }
- else
- {
- return false;
- }
-}
-
-bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::InformationType& informationType)
-{
- SemanticTypes::IDVector allImageIDsOfLesion;
- try
- {
- allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion);
- }
- catch (const SemanticRelationException&)
- {
- return false;
- }
-
- SemanticTypes::IDVector allImageIDsOfInformationType = RelationStorage::GetAllImageIDsOfInformationType(caseID, informationType);
-
- std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end());
- std::sort(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end());
- SemanticTypes::IDVector allImageIDsIntersection;
- // set_intersection removes duplicated nodes, since 'GetAllImageIDsOfInformationType' only contains at most one of each node
- std::set_intersection(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end(),
- allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end(),
- std::back_inserter(allImageIDsIntersection));
-
- // if the vector of intersecting image IDs is empty, the information type does not contain the lesion
- return !allImageIDsIntersection.empty();
-}
-
-bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::IDVector allImageIDsOfLesion;
- try
- {
- allImageIDsOfLesion = GetAllImageIDsOfLesion(caseID, lesion);
- }
- catch (const SemanticRelationException&)
- {
- return false;
- }
-
- SemanticTypes::IDVector allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint);
-
- std::sort(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end());
- std::sort(allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end());
- SemanticTypes::IDVector allImageIDsIntersection;
- // set_intersection removes duplicated nodes, since 'GetAllImageIDsOfControlPoint' only contains at most one of each node
- std::set_intersection(allImageIDsOfLesion.begin(), allImageIDsOfLesion.end(),
- allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end(),
- std::back_inserter(allImageIDsIntersection));
-
- // if the vector of intersecting image IDs is empty, the control point does not contain the lesion
- return !allImageIDsIntersection.empty();
-}
-
-bool mitk::SemanticRelationsInference::SpecificImageExists(const SemanticTypes::CaseID& caseID, const SemanticTypes::InformationType& informationType, const SemanticTypes::ControlPoint& controlPoint)
-{
- SemanticTypes::IDVector allImageIDsOfInformationType = RelationStorage::GetAllImageIDsOfInformationType(caseID, informationType);
- SemanticTypes::IDVector allImageIDsOfControlPoint = RelationStorage::GetAllImageIDsOfControlPoint(caseID, controlPoint);
-
- std::sort(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end());
- std::sort(allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end());
- SemanticTypes::IDVector allImageIDsIntersection;
- // set_intersection removes duplicated nodes
- std::set_intersection(allImageIDsOfInformationType.begin(), allImageIDsOfInformationType.end(),
- allImageIDsOfControlPoint.begin(), allImageIDsOfControlPoint.end(),
- std::back_inserter(allImageIDsIntersection));
-
- // if the vector of intersecting image IDs is empty no image exists for the given information type and control point
- return !allImageIDsIntersection.empty();
-}
diff --git a/Modules/SemanticRelations/src/mitkSemanticRelationsIntegration.cpp b/Modules/SemanticRelations/src/mitkSemanticRelationsIntegration.cpp
deleted file mode 100644
index 935bc10202..0000000000
--- a/Modules/SemanticRelations/src/mitkSemanticRelationsIntegration.cpp
+++ /dev/null
@@ -1,606 +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 "mitkSemanticRelationsIntegration.h"
-
-// semantic relations module
-#include "mitkControlPointManager.h"
-#include "mitkDICOMHelper.h"
-#include "mitkNodePredicates.h"
-#include "mitkRelationStorage.h"
-#include "mitkSemanticRelationException.h"
-#include "mitkSemanticRelationsInference.h"
-#include "mitkUIDGeneratorBoost.h"
-
-// multi label module
-#include <mitkLabelSetImage.h>
-
-// c++
-#include <iterator>
-#include <algorithm>
-
-std::vector<mitk::ISemanticRelationsObserver*> mitk::SemanticRelationsIntegration::m_ObserverVector;
-
-void mitk::SemanticRelationsIntegration::AddObserver(ISemanticRelationsObserver* observer)
-{
- std::vector<ISemanticRelationsObserver*>::iterator existingObserver = std::find(m_ObserverVector.begin(), m_ObserverVector.end(), observer);
- if (existingObserver != m_ObserverVector.end())
- {
- // no need to add the already existing observer
- return;
- }
-
- m_ObserverVector.push_back(observer);
-}
-
-void mitk::SemanticRelationsIntegration::RemoveObserver(ISemanticRelationsObserver* observer)
-{
- m_ObserverVector.erase(std::remove(m_ObserverVector.begin(), m_ObserverVector.end(), observer), m_ObserverVector.end());
-}
-
-/************************************************************************/
-/* functions to add / remove instances / attributes */
-/************************************************************************/
-
-void mitk::SemanticRelationsIntegration::AddImage(const DataNode* imageNode)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID;
- SemanticTypes::ID imageID;
- SemanticTypes::InformationType informationType;
- SemanticTypes::ControlPoint controlPoint;
- try // retrieve information
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
-
- informationType = GetDICOMModalityFromDataNode(imageNode);
- controlPoint = GenerateControlPoint(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot add the given image data node.";
- }
-
- try // add and set information
- {
- RelationStorage::AddCase(caseID);
- RelationStorage::AddImage(caseID, imageID);
-
- AddInformationTypeToImage(imageNode, informationType);
- SetControlPointOfImage(imageNode, controlPoint);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot add the given image data node.";
- }
-}
-
-void mitk::SemanticRelationsIntegration::RemoveImage(const DataNode* imageNode)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID;
- SemanticTypes::ID imageID;
- try // retrieve information
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot remove the given image data node.";
- }
-
- try
- {
- RemoveInformationTypeFromImage(imageNode);
- UnlinkImageFromControlPoint(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot remove the given image data node.";
- }
-
- RelationStorage::RemoveImage(caseID, imageID);
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::AddLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- if (SemanticRelationsInference::InstanceExists(caseID, lesion))
- {
- mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to add already exists for the given case.";
- }
-
- RelationStorage::AddLesion(caseID, lesion);
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::OverwriteLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- if (SemanticRelationsInference::InstanceExists(caseID, lesion))
- {
- RelationStorage::OverwriteLesion(caseID, lesion);
- NotifyObserver(caseID);
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to overwrite does not exist for the given case.";
- }
-}
-
-void mitk::SemanticRelationsIntegration::AddLesionAndLinkSegmentation(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion)
-{
- if (nullptr == segmentationNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node.";
- }
-
- SemanticTypes::CaseID caseID;
- try
- {
- caseID = GetCaseIDFromDataNode(segmentationNode);
- AddLesion(caseID, lesion);
- LinkSegmentationToLesion(segmentationNode, lesion);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot add given lesion and link the given segmentation data node.";
- }
-
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::RemoveLesion(const SemanticTypes::CaseID& caseID, const SemanticTypes::Lesion& lesion)
-{
- if (SemanticRelationsInference::InstanceExists(caseID, lesion))
- {
- SemanticTypes::IDVector allSegmentationIDsOfLesion = RelationStorage::GetAllSegmentationIDsOfLesion(caseID, lesion);
- if (allSegmentationIDsOfLesion.empty())
- {
- // no more segmentations are linked to the specific lesion
- // the lesion can be removed from the storage
- RelationStorage::RemoveLesion(caseID, lesion);
- NotifyObserver(caseID);
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to remove is still referred to by a segmentation node. Lesion will not be removed.";
- }
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to remove does not exist for the given case.";
- }
-}
-
-void mitk::SemanticRelationsIntegration::AddSegmentation(const DataNode* segmentationNode, const DataNode* parentNode)
-{
- if (nullptr == segmentationNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node.";
- }
-
- if (nullptr == parentNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid parent data node.";
- }
-
- SemanticTypes::CaseID caseID;
- SemanticTypes::ID segmentationNodeID;
- SemanticTypes::ID parentNodeID;
- try
- {
- caseID = GetCaseIDFromDataNode(segmentationNode);
- segmentationNodeID = GetIDFromDataNode(segmentationNode);
- parentNodeID = GetIDFromDataNode(parentNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot add the given segmentation data node.";
- }
-
- RelationStorage::AddSegmentation(caseID, segmentationNodeID, parentNodeID);
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::LinkSegmentationToLesion(const DataNode* segmentationNode, const SemanticTypes::Lesion& lesion)
-{
- if (nullptr == segmentationNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node.";
- }
-
- SemanticTypes::CaseID caseID;
- SemanticTypes::ID segmentationID;
- try
- {
- caseID = GetCaseIDFromDataNode(segmentationNode);
- segmentationID = GetIDFromDataNode(segmentationNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot link the given segmentation data node to the given lesion.";
- }
-
- if (SemanticRelationsInference::InstanceExists(caseID, lesion))
- {
- RelationStorage::LinkSegmentationToLesion(caseID, segmentationID, lesion);
- NotifyObserver(caseID);
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "The lesion " << lesion.UID << " to link does not exist for the given case.";
- }
-}
-
-void mitk::SemanticRelationsIntegration::UnlinkSegmentationFromLesion(const DataNode* segmentationNode)
-{
- if (nullptr == segmentationNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node.";
- }
-
- SemanticTypes::CaseID caseID;
- SemanticTypes::ID segmentationID;
- try
- {
- caseID = GetCaseIDFromDataNode(segmentationNode);
- segmentationID = GetIDFromDataNode(segmentationNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot unlink the given segmentation data node from its lesion.";
- }
-
- RelationStorage::UnlinkSegmentationFromLesion(caseID, segmentationID);
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::RemoveSegmentation(const DataNode* segmentationNode)
-{
- if (nullptr == segmentationNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid segmentation data node.";
- }
-
- SemanticTypes::CaseID caseID;
- SemanticTypes::ID segmentationNodeID;
- try
- {
- caseID = GetCaseIDFromDataNode(segmentationNode);
- segmentationNodeID = GetIDFromDataNode(segmentationNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot remove the given segmentation data node.";
- }
-
- try
- {
- UnlinkSegmentationFromLesion(segmentationNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot remove the given segmentation data node.";
- }
-
- RelationStorage::RemoveSegmentation(caseID, segmentationNodeID);
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::SetControlPointOfImage(const DataNode* imageNode, const SemanticTypes::ControlPoint& controlPoint)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID;
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot set the given control point for the given image data node.";
- }
-
- SemanticTypes::ControlPointVector allControlPoints = RelationStorage::GetAllControlPointsOfCase(caseID);
- // need to check if an already existing control point fits/contains the user control point
- SemanticTypes::ControlPoint existingControlPoint = FindExistingControlPoint(caseID, controlPoint);
- try
- {
- if (!existingControlPoint.UID.empty())
- {
- // found an already existing control point
- LinkImageToControlPoint(imageNode, existingControlPoint, false);
- }
- else
- {
- // find closest control point to add the new control point to the correct examination period
- SemanticTypes::ControlPoint closestControlPoint = FindClosestControlPoint(caseID, controlPoint);
- SemanticTypes::ExaminationPeriod examinationPeriod = FindContainingExaminationPeriod(caseID, closestControlPoint);
- if (examinationPeriod.UID.empty())
- {
- // no closest control point (exceed threshold) or no examination period found
- // create a new examination period for this control point and add it to the storage
- examinationPeriod.UID = UIDGeneratorBoost::GenerateUID();
- examinationPeriod.name = "New examination period";
- AddExaminationPeriod(caseID, examinationPeriod);
- }
-
- // added a new control point
- AddControlPointAndLinkImage(imageNode, controlPoint, false);
- // add the control point to the (newly created or found / close) examination period
- AddControlPointToExaminationPeriod(caseID, controlPoint, examinationPeriod);
- }
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot set the given control point for the given image data node.";
- }
-
- ClearControlPoints(caseID);
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::AddControlPointAndLinkImage(const DataNode* imageNode, const SemanticTypes::ControlPoint& controlPoint, bool checkConsistence)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID;
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot add the given control point and link the given image data node.";
- }
-
- if (SemanticRelationsInference::InstanceExists(caseID, controlPoint))
- {
- mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to add already exists for the given case. \n Use 'LinkImageToControlPoint' instead.";
- }
-
- RelationStorage::AddControlPoint(caseID, controlPoint);
-
- try
- {
- LinkImageToControlPoint(imageNode, controlPoint, checkConsistence);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot add the given control point and link the given image data node.";
- }
-}
-
-void mitk::SemanticRelationsIntegration::LinkImageToControlPoint(const DataNode* imageNode, const SemanticTypes::ControlPoint& controlPoint, bool /*checkConsistence*/)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID;
- SemanticTypes::ID imageID;
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot link the image data node to the given control point.";
- }
-
- if (SemanticRelationsInference::InstanceExists(caseID, controlPoint))
- {
- RelationStorage::LinkImageToControlPoint(caseID, imageID, controlPoint);
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to link does not exist for the given case.";
- }
-}
-
-void mitk::SemanticRelationsIntegration::UnlinkImageFromControlPoint(const DataNode* imageNode)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID imageID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot unlink the given image data node from its control point.";
- }
-
- RelationStorage::UnlinkImageFromControlPoint(caseID, imageID);
- ClearControlPoints(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::AddExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- if (SemanticRelationsInference::InstanceExists(caseID, examinationPeriod))
- {
- mitkThrowException(SemanticRelationException) << "The examination period " << examinationPeriod.UID << " to add already exists for the given case.";
- }
- else
- {
- RelationStorage::AddExaminationPeriod(caseID, examinationPeriod);
- }
-}
-
-void mitk::SemanticRelationsIntegration::RenameExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- if (SemanticRelationsInference::InstanceExists(caseID, examinationPeriod))
- {
- RelationStorage::RenameExaminationPeriod(caseID, examinationPeriod);
- NotifyObserver(caseID);
- }
- else
- {
- mitkThrowException(SemanticRelationException) << "The examination period " << examinationPeriod.UID << " to overwrite does not exist for the given case.";
- }
-}
-
-void mitk::SemanticRelationsIntegration::AddControlPointToExaminationPeriod(const SemanticTypes::CaseID& caseID, const SemanticTypes::ControlPoint& controlPoint, const SemanticTypes::ExaminationPeriod& examinationPeriod)
-{
- if (!SemanticRelationsInference::InstanceExists(caseID, controlPoint))
- {
- mitkThrowException(SemanticRelationException) << "The control point " << controlPoint.UID << " to add does not exist for the given case.";
- }
-
- if (!SemanticRelationsInference::InstanceExists(caseID, examinationPeriod))
- {
- mitkThrowException(SemanticRelationException) << "The examination period " << examinationPeriod.UID << " does not exist for the given case. \n Use 'AddExaminationPeriod' before.";
- }
-
- RelationStorage::AddControlPointToExaminationPeriod(caseID, controlPoint, examinationPeriod);
-}
-
-void mitk::SemanticRelationsIntegration::SetInformationType(const DataNode* imageNode, const SemanticTypes::InformationType& informationType)
-{
- SemanticTypes::CaseID caseID;
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
-
- RemoveInformationTypeFromImage(imageNode);
- AddInformationTypeToImage(imageNode, informationType);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot set the given information type for the given image data node.";
- }
-
- NotifyObserver(caseID);
-}
-
-void mitk::SemanticRelationsIntegration::AddInformationTypeToImage(const DataNode* imageNode, const SemanticTypes::InformationType& informationType)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID imageID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot add the given information type to the given image data node.";
- }
-
- RelationStorage::AddInformationTypeToImage(caseID, imageID, informationType);
-}
-
-void mitk::SemanticRelationsIntegration::RemoveInformationTypeFromImage(const DataNode* imageNode)
-{
- if (nullptr == imageNode)
- {
- mitkThrowException(SemanticRelationException) << "Not a valid image data node.";
- }
-
- SemanticTypes::CaseID caseID = "";
- SemanticTypes::ID imageID = "";
- try
- {
- caseID = GetCaseIDFromDataNode(imageNode);
- imageID = GetIDFromDataNode(imageNode);
- }
- catch (SemanticRelationException& e)
- {
- mitkReThrow(e) << "Cannot remove the information type from the given image data node.";
- }
-
- SemanticTypes::InformationType originalInformationType = RelationStorage::GetInformationTypeOfImage(caseID, imageID);
- RelationStorage::RemoveInformationTypeFromImage(caseID, imageID);
-
- // check for further references to the removed information type
- SemanticTypes::IDVector allImageIDsVectorValue = RelationStorage::GetAllImageIDsOfCase(caseID);
- for (const auto& otherImageID : allImageIDsVectorValue)
- {
- SemanticTypes::InformationType otherInformationType = RelationStorage::GetInformationTypeOfImage(caseID, otherImageID);
- if (otherInformationType == originalInformationType)
- {
- // found the information type in another image -> cannot remove the information type from the case
- return;
- }
- }
-
- // given information type was not referred by any other image of the case -> the information type can be removed from the case
- RelationStorage::RemoveInformationType(caseID, originalInformationType);
-}
-
-/************************************************************************/
-/* private functions */
-/************************************************************************/
-void mitk::SemanticRelationsIntegration::NotifyObserver(const SemanticTypes::CaseID& caseID) const
-{
- for (auto& observer : m_ObserverVector)
- {
- observer->Update(caseID);
- }
-}
-
-void mitk::SemanticRelationsIntegration::ClearControlPoints(const SemanticTypes::CaseID& caseID)
-{
- SemanticTypes::ControlPointVector allControlPointsOfCase = RelationStorage::GetAllControlPointsOfCase(caseID);
-
- SemanticTypes::IDVector allImageIDsVectorValue = RelationStorage::GetAllImageIDsOfCase(caseID);
- SemanticTypes::ControlPointVector referencedControlPoints;
- for (const auto& imageID : allImageIDsVectorValue)
- {
- SemanticTypes::ControlPoint controlPointOfImage = RelationStorage::GetControlPointOfImage(caseID, imageID);
- referencedControlPoints.push_back(controlPointOfImage);
- }
-
- std::sort(allControlPointsOfCase.begin(), allControlPointsOfCase.end());
- std::sort(referencedControlPoints.begin(), referencedControlPoints.end());
-
- SemanticTypes::ControlPointVector nonReferencedControlPoints;
- std::set_difference(allControlPointsOfCase.begin(), allControlPointsOfCase.end(),
- referencedControlPoints.begin(), referencedControlPoints.end(),
- std::inserter(nonReferencedControlPoints, nonReferencedControlPoints.begin()));
-
- for (const auto& controlPoint : nonReferencedControlPoints)
- {
- const SemanticTypes::ExaminationPeriod& examinationPeriod = FindContainingExaminationPeriod(caseID, controlPoint);
- RelationStorage::RemoveControlPointFromExaminationPeriod(caseID, controlPoint, examinationPeriod);
- RelationStorage::RemoveControlPoint(caseID, controlPoint);
- }
-}
diff --git a/Modules/SemanticRelations/src/mitkUIDGeneratorBoost.cpp b/Modules/SemanticRelations/src/mitkUIDGeneratorBoost.cpp
deleted file mode 100644
index 394113e499..0000000000
--- a/Modules/SemanticRelations/src/mitkUIDGeneratorBoost.cpp
+++ /dev/null
@@ -1,24 +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.
-
-============================================================================*/
-
-// semantic relation module
-#include "mitkUIDGeneratorBoost.h"
-
-#include <boost/uuid/uuid.hpp>
-#include <boost/uuid/uuid_generators.hpp>
-#include <boost/uuid/uuid_io.hpp>
-
-std::string mitk::UIDGeneratorBoost::GenerateUID()
-{
- boost::uuids::uuid uuid = boost::uuids::random_generator()();
- return boost::uuids::to_string(uuid);
-}
diff --git a/Modules/SemanticRelationsUI/CMakeLists.txt b/Modules/SemanticRelationsUI/CMakeLists.txt
deleted file mode 100644
index 8bda1aaa31..0000000000
--- a/Modules/SemanticRelationsUI/CMakeLists.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-MITK_CREATE_MODULE(
- DEPENDS MitkQtWidgets MitkSemanticRelations
- PACKAGE_DEPENDS Qt6|Core
-)
diff --git a/Modules/SemanticRelationsUI/files.cmake b/Modules/SemanticRelationsUI/files.cmake
deleted file mode 100644
index a10162f616..0000000000
--- a/Modules/SemanticRelationsUI/files.cmake
+++ /dev/null
@@ -1,36 +0,0 @@
-file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*")
-
-set(CPP_FILES
- mitkModuleActivator.cpp
- QmitkAbstractSemanticRelationsStorageInspector.cpp
- QmitkAbstractSemanticRelationsStorageModel.cpp
- QmitkControlPointDialog.cpp
- QmitkLesionTextDialog.cpp
- QmitkLesionTreeItem.cpp
- QmitkLesionTreeModel.cpp
- QmitkPatientTableHeaderView.cpp
- QmitkPatientTableInspector.cpp
- QmitkPatientTableModel.cpp
- QmitkSemanticRelationsUIHelper.cpp
- QmitkStatisticsCalculator.cpp
- QmitkStatisticsTreeModel.cpp
- QmitkTableItemThumbnailDelegate.cpp
-)
-
-set(MOC_H_FILES
- include/QmitkAbstractSemanticRelationsStorageInspector.h
- include/QmitkAbstractSemanticRelationsStorageModel.h
- include/QmitkControlPointDialog.h
- include/QmitkLesionTextDialog.h
- include/QmitkLesionTreeModel.h
- include/QmitkPatientTableHeaderView.h
- include/QmitkPatientTableInspector.h
- include/QmitkPatientTableModel.h
- include/QmitkStatisticsCalculator.h
- include/QmitkStatisticsTreeModel.h
- include/QmitkTableItemThumbnailDelegate.h
-)
-
-set(UI_FILES
- src/QmitkPatientTableInspector.ui
-)
diff --git a/Modules/SemanticRelationsUI/include/QmitkAbstractSemanticRelationsStorageInspector.h b/Modules/SemanticRelationsUI/include/QmitkAbstractSemanticRelationsStorageInspector.h
deleted file mode 100644
index 91603012dc..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkAbstractSemanticRelationsStorageInspector.h
+++ /dev/null
@@ -1,57 +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 QmitkAbstractSemanticRelationsStorageInspector_h
-#define QmitkAbstractSemanticRelationsStorageInspector_h
-
-// semantic relations UI module
-#include "MitkSemanticRelationsUIExports.h"
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-// qt widgets module
-#include "QmitkAbstractDataStorageInspector.h"
-
-/*
-* @brief The QmitkAbstractSemanticRelationsStorageInspector is a QmitkAbstractDataStorageInspector that can be used to
-* show the currently available data of an (abstract) semantic relations storage model.
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkAbstractSemanticRelationsStorageInspector : public QmitkAbstractDataStorageInspector
-{
- Q_OBJECT
-
-public:
-
- ~QmitkAbstractSemanticRelationsStorageInspector() override;
-
- /**
- * @brief Extends the abstract base class to allow setting the current case ID which is needed to access the
- * semantic relations storage. The function sets the case ID in the storage model.
- *
- * @param caseID A case ID as string
- */
- virtual void SetCaseID(const mitk::SemanticTypes::CaseID& caseID) = 0;
- /**
- * @brief Extends the abstract base class to allow setting the current lesion.
- * The function sets the lesion in the storage model.
- *
- *@param lesion The selected lesion
- */
- virtual void SetLesion(const mitk::SemanticTypes::Lesion& lesion) = 0;
-
-protected:
-
- QmitkAbstractSemanticRelationsStorageInspector(QWidget* parent = nullptr);
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkAbstractSemanticRelationsStorageModel.h b/Modules/SemanticRelationsUI/include/QmitkAbstractSemanticRelationsStorageModel.h
deleted file mode 100644
index e427abe2a9..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkAbstractSemanticRelationsStorageModel.h
+++ /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.
-
-============================================================================*/
-
-#ifndef QmitkAbstractSemanticRelationsStorageModel_h
-#define QmitkAbstractSemanticRelationsStorageModel_h
-
-// mitk semantic relations UI
-#include "MitkSemanticRelationsUIExports.h"
-
-// semantic relations module
-#include <mitkISemanticRelationsObserver.h>
-#include <mitkSemanticRelationsDataStorageAccess.h>
-#include <mitkSemanticRelationsIntegration.h>
-#include <mitkSemanticTypes.h>
-
-// qt widgets module
-#include "QmitkAbstractDataStorageModel.h"
-
-/*
-* @brief The QmitkAbstractSemanticRelationsStorageModel is a subclass of 'QmitkAbstractDataStorageModel' and provides additional
-* functionality to set and store a semantic relations instance, the current case ID and the current lesion.
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkAbstractSemanticRelationsStorageModel : public QmitkAbstractDataStorageModel, public mitk::ISemanticRelationsObserver
-{
- Q_OBJECT
-
-public:
-
- QmitkAbstractSemanticRelationsStorageModel(QObject* parent = nullptr);
- ~QmitkAbstractSemanticRelationsStorageModel() override;
-
- /*
- * @brief Update this model with the data from the semantic relations,
- * if the case ID is equal to the currently selected case ID of the table model.
- *
- * Overridden from 'ISemanticRelationsObserver'.
- * In order for the Update-function to be called, this model has to be added as an observer of SemanticRelation
- * (e.g. m_SemanticRelations->AddObserver(m_SemanticRelationsStorageModel);)
- *
- * @par caseID The current case ID to identify the currently active patient / case.
- */
- void Update(const mitk::SemanticTypes::CaseID& caseID) override;
-
- /**
- * @brief Set the current case ID which is needed to access the semantic relations storage.
- *
- * @param caseID A case ID as string
- */
- void SetCaseID(const mitk::SemanticTypes::CaseID& caseID);
-
- const mitk::SemanticTypes::CaseID& GetCaseID() const { return m_CaseID; }
- /**
- * @brief Set the current lesion which can be used to show on which images the lesion is visible.
- *
- * @param lesion The selected lesion
- */
- void SetLesion(const mitk::SemanticTypes::Lesion& lesion);
-
- const mitk::SemanticTypes::Lesion& GetLesion() const { return m_Lesion; }
- /**
- * @brief Set the current data node selection which can be used to show which lesions
- * are visible on the node selection.
- *
- * @param dataNodeSelection The selected data nodes
- */
- void SetDataNodeSelection(const QList<mitk::DataNode::Pointer>& dataNodeSelection);
-
- const QList<mitk::DataNode::Pointer>& GetSelectedDataNodes() const { return m_SelectedDataNodes; };
- /*
- * @brief Update the semantic relations storage model with the current data from the semantic relations model
- * and the current case ID.
- */
- void UpdateModelData();
-
-Q_SIGNALS:
- void ModelUpdated();
-
-protected:
-
- /**
- * @brief Create a new 'SemanticRelationsDataStorageAccess' instance with the new data storage and
- * update the model data.
- * This functions is called inside the 'SetDataStorage'-function from the parent class.
- */
- void DataStorageChanged() override;
-
- /**
- * @brief This function is called if the model data is updated. It can be used by subclasses to define
- * the way the data of a specific model is generated. It typically consists of access to the
- * semantic relations storage to retrieve certain information.
- */
- virtual void SetData() = 0;
-
- std::unique_ptr<mitk::SemanticRelationsDataStorageAccess> m_SemanticRelationsDataStorageAccess;
- std::unique_ptr<mitk::SemanticRelationsIntegration> m_SemanticRelationsIntegration;
-
- mitk::SemanticTypes::CaseID m_CaseID;
- QList<mitk::DataNode::Pointer> m_SelectedDataNodes;
- mitk::SemanticTypes::Lesion m_Lesion;
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkControlPointDialog.h b/Modules/SemanticRelationsUI/include/QmitkControlPointDialog.h
deleted file mode 100644
index 9bb1b46640..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkControlPointDialog.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 QmitkControlPointDialog_h
-#define QmitkControlPointDialog_h
-
-#include <MitkSemanticRelationsUIExports.h>
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-#include <QDateEdit>
-#include <QDialog>
-
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkControlPointDialog : public QDialog
-{
- Q_OBJECT
-
-public:
-
- QmitkControlPointDialog(QWidget *parent = nullptr);
-
- void SetCurrentDate(mitk::SemanticTypes::ControlPoint currentControlPoint);
- QDate GetCurrentDate() const;
-
-private:
-
- QDateEdit* m_DateEdit;
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkLesionTextDialog.h b/Modules/SemanticRelationsUI/include/QmitkLesionTextDialog.h
deleted file mode 100644
index 01b4b18ee3..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkLesionTextDialog.h
+++ /dev/null
@@ -1,43 +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 QmitkLesionTextDialog_h
-#define QmitkLesionTextDialog_h
-
-#include <MitkSemanticRelationsUIExports.h>
-
-// semantic relations module
-#include "mitkSemanticTypes.h"
-
-#include <QLineEdit>
-#include <QDialog>
-
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkLesionTextDialog : public QDialog
-{
- Q_OBJECT
-
-public:
-
- QmitkLesionTextDialog(QWidget *parent = nullptr);
-
- void SetLineEditText(const std::string& lineEditText);
- QString GetLineEditText() const;
-
- QLineEdit* GetLineEdit() const;
-
-private:
-
- QLineEdit* m_LineEdit;
-
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkLesionTreeItem.h b/Modules/SemanticRelationsUI/include/QmitkLesionTreeItem.h
deleted file mode 100644
index 0787b7501a..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkLesionTreeItem.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 QmitkLesionTreeItem_h
-#define QmitkLesionTreeItem_h
-
-// mitk semantic relations UI
-#include "mitkLesionData.h"
-
-// mitk semantic relations
-#include <mitkSemanticTypes.h>
-
-// qt
-#include <QVariant>
-
-// c++
-#include <memory>
-#include <vector>
-
-/*
-* @brief This class is used by custom tree models to create their tree items.
-* It provides functions to traverse and modify the tree.
-* Additionally it holds some 'LesionData' that is used to display lesion properties inside a tree view.
-*/
-class QmitkLesionTreeItem : public std::enable_shared_from_this<QmitkLesionTreeItem>
-{
-public:
-
- using ChildPointer = std::shared_ptr<QmitkLesionTreeItem>;
- using ChildConstPointer = std::shared_ptr<const QmitkLesionTreeItem>;
- using ParentPointer = std::weak_ptr<QmitkLesionTreeItem>;
-
- QmitkLesionTreeItem(mitk::LesionData lesionData = mitk::LesionData());
-
- /**
- * @brief Return the child of this item at a specific position.
- *
- * @param row Determines the position of a child item to return.
- *
- * @return The child of this item at a specific position.
- */
- ChildPointer GetChildInRow(int row) const { return m_Children.at(row); };
- /**
- * @brief Return the parent item.
- *
- * @return The parent item as std::weak_ptr.
- */
- ParentPointer GetParent() const { return m_ParentItem; };
- /**
- * @brief Set the parent item of this item.
- *
- * @param parent The new parent item of this item.
- */
- void SetParent(ParentPointer parent);
- /**
- * @brief Return the item data, which contains ...
- *
- * see <code>mitk::LesionItemData</code>
- */
- mitk::LesionData& GetData() { return m_ItemData; };
- /**
- * @brief Get the row of this item relative to its parent item using 'GetRowOfChild'.
- *
- * @return The row of this item relative to its parent item.
- */
- int GetRow() const;
- /**
- * @brief Get the row of the given child item relative to this item.
- *
- * @param child The child item whose row is to be determined.
- *
- * @return The row of the child item.
- */
- int GetRowOfChild(ChildConstPointer child) const;
- /**
- * @brief Return the number of child items.
- *
- * @return Number of child items.
- */
- size_t ChildCount() const { return m_Children.size(); };
- /**
- * @brief Add a new child to the list of children of this item if it is not already a child item.
- *
- * @param child The child item to add to this item.
- */
- void AddChild(ChildPointer child);
- /**
- * @brief Remove a child from the list of children of this item.
- *
- * @param child The child item to remove from this item.
- */
- void RemoveChild(ChildPointer child);
- /**
- * @brief Set the item data of this item.
- *
- * @param lesionData LesionData that provides information about this item.
- */
- void SetData(const mitk::LesionData& lesionData);
-
-private:
-
- ParentPointer m_ParentItem;
- std::vector<ChildPointer> m_Children;
- mitk::LesionData m_ItemData;
-
-};
-
-Q_DECLARE_METATYPE(QmitkLesionTreeItem)
-Q_DECLARE_METATYPE(QmitkLesionTreeItem*)
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkLesionTreeModel.h b/Modules/SemanticRelationsUI/include/QmitkLesionTreeModel.h
deleted file mode 100644
index 23fc04ca86..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkLesionTreeModel.h
+++ /dev/null
@@ -1,106 +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 QmitkLesionTreeModel_h
-#define QmitkLesionTreeModel_h
-
-// mitk semantic relations UI
-#include "MitkSemanticRelationsUIExports.h"
-#include "QmitkAbstractSemanticRelationsStorageModel.h"
-#include "QmitkLesionTreeItem.h"
-
-/*
-* @brief The 'QmitkLesionTreeModel' is a subclass of 'QmitkAbstractSemanticRelationsStorageModel' and provides
-* functionality to serve as a tree model.
-* The tree model creates a new top-level tree item for each lesion that is stored inside the semantic relations storage.
-* Each lesion tree item contains lesion data that can be display inside a tree view. The lesion data
-* consists of a lesion with with its UID, name and lesion class. The name or UID is used for the top-level tree items.
-* Additionally the lesion data contains two vectors which define the lesion presence (bool) and the lesion volume (double)
-* for each control-point - information type pair. The lesion presence will be used inside this model for the tree items.
-* The volume is used inside another tree model.
-*
-* The model holds the last segmentation that is added to the data storage to support the process of defining a new lesion
-* (and linking it with the latest segmentation) (see 'NodeAdded').
-* Furthermore the model is able to accept a 'QList' of currently selected data nodes and to use it to change the background
-* color of each lesion tree item that is connected to this data node(s). This helps to see which lesion is already found and
-* defined for a given (set of) data node(s).
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkLesionTreeModel : public QmitkAbstractSemanticRelationsStorageModel
-{
- Q_OBJECT
-
-public:
-
- /**
- * @brief Initialize the root item of the model. The root item does not have a parent item.
- */
- QmitkLesionTreeModel(QObject* parent = nullptr);
-
- //////////////////////////////////////////////////////////////////////////
- // overridden virtual functions from QAbstractItemModel
- //////////////////////////////////////////////////////////////////////////
- QModelIndex index(int row, int column, const QModelIndex& itemIndex = QModelIndex()) const override;
- QModelIndex parent(const QModelIndex& itemIndex) const override;
-
- int rowCount(const QModelIndex& itemIndex = QModelIndex()) const override;
- int columnCount(const QModelIndex& itemIndex = QModelIndex()) const override;
-
- QVariant data(const QModelIndex& index, int role = Qt::DisplayRole) const override;
-
- QVariant headerData(int section, Qt::Orientation orientation, int role = Qt::DisplayRole) const override;
- //////////////////////////////////////////////////////////////////////////
- // end override
- //////////////////////////////////////////////////////////////////////////
-
- const mitk::DataNode* GetLastSegmentation() const;
-
-protected:
-
- // the following functions have to be overridden but are not implemented in this model
- void NodePredicateChanged() override { }
- void NodeAdded(const mitk::DataNode*) override;
- void NodeChanged(const mitk::DataNode*) override { }
- void NodeRemoved(const mitk::DataNode*) override { }
- /**
- * @brief Overridden from 'QmitkAbstractSemanticRelationsStorageModel': This function retrieves all control points
- * of the current case and stores them to define the header of the tree.
- * Furthermore all lesions are retrieved and the lesion data is stored and show in the tree view.
- */
- void SetData() override;
-
-private:
-
- void SetLesionData();
- void AddLesion(const mitk::SemanticTypes::Lesion& lesion);
- void SetSelectedDataNodesPresence();
- /**
- * @brief The function uses the ID of the lesion to see if a data node presence was already set.
- * If not, the given bool value is used and stored inside a member variable. If the lesion presence
- * was already set, it will be overwritten.
- * The function is used by the 'SetSelectedDataNodesPresence' function.
- *
- * @param lesion The lesion whose data node presence should be set
- * @param dataNodePresence The bool value that defines the data node presence of the given lesion
- */
- void SetDataNodePresenceOfLesion(const mitk::SemanticTypes::Lesion* lesion, bool dataNodePresence);
-
- QmitkLesionTreeItem* GetItemByIndex(const QModelIndex& index) const;
-
- std::map<mitk::SemanticTypes::ID, bool> m_DataNodePresence;
- const mitk::DataNode* m_LastSegmentation;
-
- std::shared_ptr<QmitkLesionTreeItem> m_RootItem;
- mitk::SemanticTypes::ControlPointVector m_ControlPoints;
- mitk::SemanticTypes::LesionVector m_CurrentLesions;
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkPatientInfoWidget.h b/Modules/SemanticRelationsUI/include/QmitkPatientInfoWidget.h
deleted file mode 100644
index 482c3d6d38..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkPatientInfoWidget.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 QmitkPatientInfoWidget_h
-#define QmitkPatientInfoWidget_h
-
-// semantic relations UI module
-#include "MitkSemanticRelationsUIExports.h"
-#include <ui_QmitkPatientInfoWidgetControls.h>
-
-// qt
-#include <QWidget>
-
-// mitk core
-#include <mitkDataNode.h>
-
-/*
-* @brief The QmitkPatientInfoWidget is a widget that shows some DICOM information about a specific patient (data node).
-*
-* CURRENTLY NOT USED
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkPatientInfoWidget : public QWidget
-{
- Q_OBJECT
-
-public:
-
- QmitkPatientInfoWidget(QWidget* parent = nullptr);
- ~QmitkPatientInfoWidget();
-
- void SetPatientInfo(const mitk::DataNode* dataNode);
-
-private:
-
- void QmitkPatientInfoWidget::Init();
-
- Ui::QmitkPatientInfoWidgetControls m_Controls;
-
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkPatientTableHeaderView.h b/Modules/SemanticRelationsUI/include/QmitkPatientTableHeaderView.h
deleted file mode 100644
index 393caac921..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkPatientTableHeaderView.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 QmitkPatientTableHeaderView_h
-#define QmitkPatientTableHeaderView_h
-
-// semantic relations ui module
-#include "MitkSemanticRelationsUIExports.h"
-
-// qt
-#include <QStandardItemModel>
-#include <QHeaderView>
-#include <QPointer>
-
-/*
-* @brief
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkPatientTableHeaderView : public QHeaderView
-{
- Q_OBJECT
-
-public:
-
- QmitkPatientTableHeaderView(QWidget* parent = nullptr);
- ~QmitkPatientTableHeaderView() override;
-
- enum HeaderDataModelRoles
- {
- HorizontalHeaderDataRole = Qt::UserRole
- };
-
- /**
- * @brief Set the model of the table view of this header view.
- * This model returns a standard item model for the 'HorizontalHeaderDataRole'-role.
- * The header model has been previously filled with header data.
- * This function is overwritten from QHeaderView.
- */
- void setModel(QAbstractItemModel* model) override;
-
-protected:
-
- /**
- * @brief Paint each header using 'PaintHeader'.
- * This function is overwritten from QHeaderView.
- */
- void paintSection(QPainter* painter, const QRect& rect, int logicalIndex) const override;
- /**
- * @brief Get the section size by retrieving the text content.
- * The section size is dependent on the child and parent headers.
- * This function is overwritten from QHeaderView.
- */
- QSize sectionSizeFromContents(int logicalIndex) const override;
-
-private:
-
- int PaintHeader(QPainter* painter, const QModelIndex& currentIndex, int logicalIndex, const QRect& sectionRect, int top) const;
- QSize HeaderSize(const QModelIndex& index) const;
- int CurrentHeaderLeft(const QModelIndex& currentIndex, const QModelIndex& headerIndex, int sectionIndex, int left) const;
- int CurrentHeaderWidth(const QModelIndex& currentIndex, const QModelIndex& headerIndex, int sectionIndex) const;
-
- QModelIndexList ParentIndexList(QModelIndex index) const;
- QModelIndex HeaderIndex(int sectionIndex) const;
- QModelIndex FindHeader(const QModelIndex& currentIndex, int sectionIndex, int& currentHeaderIndex) const;
- QModelIndexList ListHeader(const QModelIndex& currentIndex) const;
-
- QStandardItemModel* m_HeaderModel;
-
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkPatientTableInspector.h b/Modules/SemanticRelationsUI/include/QmitkPatientTableInspector.h
deleted file mode 100644
index 9ffc9ad505..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkPatientTableInspector.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 QmitkPatientTableInspector_h
-#define QmitkPatientTableInspector_h
-
-// semantic relations UI module
-#include "MitkSemanticRelationsUIExports.h"
-#include "QmitkAbstractSemanticRelationsStorageInspector.h"
-#include "QmitkPatientTableModel.h"
-#include "QmitkTableItemThumbnailDelegate.h"
-
-#include "ui_QmitkPatientTableInspector.h"
-
-// qt widgets module
-#include <QmitkEnums.h>
-
-// qt
-#include <QMenu>
-
-/*
-* @brief The QmitkPatientTableInspector is a QmitkAbstractSemanticRelationsStorageInspector that shows the currently
-* available data of the semantic relations storage model in a control-point - information type matrix.
-*
-* The QmitkPatientTableInspector uses the QmitkSemanticRelationsStorageModel, a QmitkAbstractDataStorageModel that
-* presents the semantic relations data as a table, showing a QPixmap as thumbnail for the data nodes.
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkPatientTableInspector : public QmitkAbstractSemanticRelationsStorageInspector
-{
- Q_OBJECT
-
-public:
-
- QmitkPatientTableInspector(QWidget* parent = nullptr);
-
- QAbstractItemView* GetView() override;
- const QAbstractItemView* GetView() const override;
-
- void SetSelectionMode(SelectionMode mode) override;
- SelectionMode GetSelectionMode() const override;
-
- void SetCaseID(const mitk::SemanticTypes::CaseID& caseID) override;
- void SetLesion(const mitk::SemanticTypes::Lesion& lesion) override;
-
- QItemSelectionModel* GetSelectionModel();
-
-Q_SIGNALS:
-
- void DataNodeDoubleClicked(const mitk::DataNode*);
- void OnContextMenuRequested(const QPoint&);
- void OnNodeRemoved(const mitk::DataNode*);
-
-private Q_SLOTS:
-
- void OnModelUpdated();
- void OnNodeButtonClicked(const QString&);
- void OnDataNodeSelectionChanged(const QList<mitk::DataNode::Pointer>&);
- void OnItemDoubleClicked(const QModelIndex&);
-
-protected:
-
- void Initialize() override;
-
-private:
-
- void SetUpConnections();
-
- void keyPressEvent(QKeyEvent* e) override;
-
- Ui::QmitkPatientTableInspector m_Controls;
- QmitkPatientTableModel* m_StorageModel;
- QmitkTableItemThumbnailDelegate* m_ItemDelegate;
-
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkPatientTableModel.h b/Modules/SemanticRelationsUI/include/QmitkPatientTableModel.h
deleted file mode 100644
index c19f2f41ef..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkPatientTableModel.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 QmitkPatientTableModel_h
-#define QmitkPatientTableModel_h
-
-// semantic relations UI module
-#include "QmitkAbstractSemanticRelationsStorageModel.h"
-
-// semantic relations module
-#include <mitkSemanticTypes.h>
-#include <mitkSemanticRelationsDataStorageAccess.h>
-
-// mitk core
-#include <mitkDataNode.h>
-
-// qt
-#include <QPixmap>
-#include <QStandardItemModel>
-
-/**
-* @brief The QmitkPatientTableModel is a subclass of the QmitkAbstractSemanticRelationsStorageModel and holds the semantic relations data of the currently selected case.
-*
-* The QmitkPatientTableModel uses the 'data' function to return either the data node of a table cell or the thumbnail of the underlying image.
-* The horizontal header of the table shows the control points of the current case and the vertical header of the table shows the information types of the current case.
-* Using the 'GetFilteredData'-function of the SemanticRelations-class the model is able to retrieve the correct data node for each table entry.
-*
-* Additionally the model creates and holds the QPixmaps of the known data nodes in order to return a thumbnail, if needed.
-*/
-class QmitkPatientTableModel : public QmitkAbstractSemanticRelationsStorageModel
-{
- Q_OBJECT
-
-public:
-
- QmitkPatientTableModel(QObject* parent = nullptr);
- ~QmitkPatientTableModel() override;
-
- //////////////////////////////////////////////////////////////////////////
- // overridden functions from QAbstractItemModel
- //////////////////////////////////////////////////////////////////////////
- QModelIndex index(int row, int column, const QModelIndex& parent = QModelIndex()) const override;
- QModelIndex parent(const QModelIndex& child) const override;
-
- int rowCount(const QModelIndex& parent = QModelIndex()) const override;
- int columnCount(const QModelIndex& parent = QModelIndex()) const override;
-
- QVariant data(const QModelIndex& index, int role = Qt::DisplayRole) const override;
-
- QVariant headerData(int section, Qt::Orientation orientation, int role = Qt::DisplayRole) const override;
- Qt::ItemFlags flags(const QModelIndex& index) const override;
- //////////////////////////////////////////////////////////////////////////
- /// end override
- /////////////////////////////////////////////////////////////////////////
-
- void SetNodeType(const std::string& nodeType);
-
-protected:
-
- // the following functions have to be overridden...
- void NodePredicateChanged() override;
- // but are not implemented in this model
- void NodeAdded(const mitk::DataNode*) override { }
- void NodeChanged(const mitk::DataNode*) override { }
- void NodeRemoved(const mitk::DataNode*) override { }
- /**
- * @brief Overridden from 'QmitkAbstractSemanticRelationsStorageModel': This function retrieves all control points
- * and information types of the current case and stores them to define the header of the table.
- * Furthermore all images are retrieved and the pixmap of the images are generated and stored.
- */
- void SetData() override;
-
-private:
-
- void SetHeaderModel();
- void SetPixmaps();
- void SetLesionPresences();
-
- /**
- * @brief The function uses the ID of the node to see if a pixmap was already set. If not, the given pixmap
- * is used and stored inside a member variable. If the pixmap was already set, it will be overwritten.
- * Using 'nullptr' as a pixmap will erase the entry for the given data node.
- *
- * @param dataNode The data node whose pixmap should be set
- * @param pixmapFromImage The pixmap that shows an image of the content of the data node
- */
- void SetPixmapOfNode(const mitk::DataNode* dataNode, QPixmap* pixmapFromImage);
- /**
- * @brief The function uses the ID of the node to see if a lesion presence was already set. If not, the given
- * bool value is used and stored inside a member variable. If the lesion presence was already set, it
- * will be overwritten.
- * The function is used by the 'SetLesionPresences' function.
- *
- * @param dataNode The data node whose lesion presence should be set
- * @param lesionPresence The bool value that defines the lesion presence of the given data node
- */
- void SetLesionPresenceOfNode(const mitk::DataNode* dataNode, bool lesionPresence);
- /**
- * @brief Returns the data node that is associated with the given table entry (index).
- *
- * The function uses the SemanticRelations-class and the current control point data and information type data to
- * filter the nodes of the current case.
- * The index is used to access the correct row in the table (information type) and the correct column in the table (control point).
- *
- * @par index The QModelIndex of the table entry
- */
- mitk::DataNode* GetCurrentDataNode(const QModelIndex &index) const;
-
- std::map<mitk::DataNode::ConstPointer, QPixmap> m_PixmapMap;
- std::map<mitk::DataNode::ConstPointer, bool> m_LesionPresence;
-
- mitk::SemanticTypes::ExaminationPeriodVector m_ExaminationPeriods;
- mitk::SemanticTypes::InformationTypeVector m_InformationTypes;
- mitk::SemanticRelationsDataStorageAccess::DataNodeVector m_CurrentDataNodes;
- std::string m_SelectedNodeType;
-
- QStandardItemModel* m_HeaderModel;
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkSemanticRelationsUIHelper.h b/Modules/SemanticRelationsUI/include/QmitkSemanticRelationsUIHelper.h
deleted file mode 100644
index 0aed38c9fe..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkSemanticRelationsUIHelper.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 QmitkSemanticRelationsUIHelper_h
-#define QmitkSemanticRelationsUIHelper_h
-
-// semantic relations ui module
-#include "MitkSemanticRelationsUIExports.h"
-
-// mitk core
-#include <mitkDataNode.h>
-
-// qt
-#include <QPixmap>
-
-/**
-* @brief Provides a helper function to generate a pixmap from a given image node.
-*/
-namespace QmitkSemanticRelationsUIHelper
-{
- /*
- * @brief Generates a QPixmap of a DICOM image.
- *
- * The center sagittal image slice is extracted and used as the thumbnail image.
- *
- * @par dataNode The data node that holds the image data.
- */
- MITKSEMANTICRELATIONSUI_EXPORT QPixmap GetPixmapFromImageNode(const mitk::DataNode* dataNode);
-
-} // namespace QmitkSemanticRelationsUIHelper
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkStatisticsCalculator.h b/Modules/SemanticRelationsUI/include/QmitkStatisticsCalculator.h
deleted file mode 100644
index 9f9fef5b98..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkStatisticsCalculator.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 QmitkStatisticsCalculator_h
-#define QmitkStatisticsCalculator_h
-
-// mitk semantic relations UI
-#include "MitkSemanticRelationsUIExports.h"
-
-// mitk semantic relations module
-#include <mitkLesionData.h>
-#include <mitkSemanticTypes.h>
-
-// mitk core
-#include <mitkDataStorage.h>
-#include <mitkWeakPointer.h>
-
-// mitk image statistics ui module
-#include <QmitkImageStatisticsCalculationJob.h>
-
-/*
-* @brief This class provides functions to compute the lesion volume of a given lesion.
-* A lesion can be defined by a specific segmentation at each control-point - information type pair.
-* This segmentation and its parent image will be used inside the private 'GetSegmentationMaskVolume' function.
-* This function in turn uses the image statistics module (the 'ImageStatisticsContainerManager') to retrieve
-* the specific statistics values from a statistics node. However, if the statistics are not found,
-* a new 'QmitkImageStatisticsCalculationJob' is started. If the job is finished and the statistics are calculated,
-* a new statistics node is added to the data storage (or an existing statistics data node is updated).
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkStatisticsCalculator : public QObject
-{
- Q_OBJECT
-
-public:
-
- QmitkStatisticsCalculator();
- ~QmitkStatisticsCalculator() override;
-
- void SetDataStorage(mitk::DataStorage* dataStorage) { m_DataStorage = dataStorage; }
- /**
- * @brief Compute and store lesion volume for all available control points and information types.
- *
- * @param lesionData The lesion data that holds the lesion and will hold the additional lesion data.
- * @param caseID The current case ID.
- */
- void ComputeLesionVolume(mitk::LesionData& lesionData, const mitk::SemanticTypes::CaseID& caseID);
-
-private:
-
- /**
- * @brief
- *
- *
- */
- double GetSegmentationMaskVolume(mitk::DataNode::Pointer imageNode, mitk::DataNode::Pointer segmentationNode);
-
- void OnStatisticsCalculationEnds();
-
- QmitkImageStatisticsCalculationJob* m_CalculationJob;
- mitk::WeakPointer<mitk::DataStorage> m_DataStorage;
- mitk::DataNode::Pointer m_ImageNode;
- mitk::DataNode::Pointer m_SegmentationNode;
- double m_MaskVolume;
-
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkStatisticsTreeModel.h b/Modules/SemanticRelationsUI/include/QmitkStatisticsTreeModel.h
deleted file mode 100644
index 1b50084082..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkStatisticsTreeModel.h
+++ /dev/null
@@ -1,94 +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 QmitkStatisticsTreeModel_h
-#define QmitkStatisticsTreeModel_h
-
-// mitk semantic relations UI
-#include "MitkSemanticRelationsUIExports.h"
-#include "QmitkAbstractSemanticRelationsStorageModel.h"
-#include "QmitkLesionTreeItem.h"
-#include "QmitkStatisticsCalculator.h"
-
-/*
-* @brief The 'QmitkStatisticsTreeModel' is a subclass of 'QmitkAbstractSemanticRelationsStorageModel' and provides
-* functionality to serve as a tree model.
-* The tree model creates a new top-level tree item for each lesion that is stored inside the semantic relations storage.
-* The top-level lesion tree items hold child items for each information type.
-* Each lesion tree item contains lesion data that can be display inside a tree view. The lesion data
-* consists of a lesion with with its UID, name and lesion class. The name or UID is used for the top-level tree items.
-* Additionally the lesion data contains two vectors which define the lesion presence (bool) and the lesion volume (double)
-* for each control-point - information type pair. The lesion volume will be used inside this model for the child items.
-* The presence is used inside another tree model.
-*
-* The model uses the 'QmitkStatisticsCalculator' to start the lesion volume calculation for each lesion.
-* This calculator is able to find an existing lesion volume or to trigger the computation of the required statistics.
-* If the required statistics are newly computed and added as a statistics container to the data storage,
-* this model will be notified about this event (see 'NodeAdded', 'NodeChanged' and 'NodeRemoved') and will update
-* its lesion tree items.
-*/
-class MITKSEMANTICRELATIONSUI_EXPORT QmitkStatisticsTreeModel : public QmitkAbstractSemanticRelationsStorageModel
-{
- Q_OBJECT
-
-public:
-
- /**
- * @brief Initialize the root item of the model. The root item does not have a parent item.
- */
- QmitkStatisticsTreeModel(QObject* parent = nullptr);
-
- //////////////////////////////////////////////////////////////////////////
- // overridden virtual functions from QAbstractItemModel
- //////////////////////////////////////////////////////////////////////////
- QModelIndex index(int row, int column, const QModelIndex& itemIndex = QModelIndex()) const override;
- QModelIndex parent(const QModelIndex& itemIndex) const override;
-
- int rowCount(const QModelIndex& itemIndex = QModelIndex()) const override;
- int columnCount(const QModelIndex& itemIndex = QModelIndex()) const override;
-
- QVariant data(const QModelIndex& index, int role = Qt::DisplayRole) const override;
- QVariant headerData(int section, Qt::Orientation orientation, int role = Qt::DisplayRole) const override;
- //////////////////////////////////////////////////////////////////////////
- // end override
- //////////////////////////////////////////////////////////////////////////
-
-protected:
-
- void DataStorageChanged() override;
- void NodePredicateChanged() override { }
- void NodeAdded(const mitk::DataNode*) override;
- void NodeChanged(const mitk::DataNode*) override;
- void NodeRemoved(const mitk::DataNode*) override;
- /**
- * @brief Overridden from 'QmitkAbstractSemanticRelationsStorageModel': This function retrieves all control points
- * of the current case and stores them to define the header of the tree.
- * Furthermore all lesions are retrieved and the lesion data is stored and show in the tree view.
- */
- void SetData() override;
-
-private:
-
- void SetLesionData();
- void AddLesion(const mitk::SemanticTypes::Lesion& lesion);
-
- QmitkLesionTreeItem* GetItemByIndex(const QModelIndex& index) const;
-
- std::unique_ptr<QmitkStatisticsCalculator> m_StatisticsCalculator;
-
- std::shared_ptr<QmitkLesionTreeItem> m_RootItem;
- mitk::SemanticTypes::ControlPointVector m_ControlPoints;
- mitk::SemanticTypes::InformationTypeVector m_InformationTypes;
- mitk::SemanticTypes::LesionVector m_CurrentLesions;
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/QmitkTableItemThumbnailDelegate.h b/Modules/SemanticRelationsUI/include/QmitkTableItemThumbnailDelegate.h
deleted file mode 100644
index d46d68d5da..0000000000
--- a/Modules/SemanticRelationsUI/include/QmitkTableItemThumbnailDelegate.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 QmitkTableItemThumbnailDelegate_h
-#define QmitkTableItemThumbnailDelegate_h
-
-#include <QStyledItemDelegate>
-
-/*
-* @brief The QmitkTableItemThumbnailDelegate is a subclass of the QmitkAbstractSemanticRelationsStorageModel
-*/
-class QmitkTableItemThumbnailDelegate : public QStyledItemDelegate
-{
- Q_OBJECT
-
-public:
-
- QmitkTableItemThumbnailDelegate(QObject* parent = nullptr);
-
- void paint(QPainter* painter, const QStyleOptionViewItem& option, const QModelIndex& index) const override;
-};
-
-#endif
diff --git a/Modules/SemanticRelationsUI/include/mitkModuleActivator.h b/Modules/SemanticRelationsUI/include/mitkModuleActivator.h
deleted file mode 100644
index e9ab999834..0000000000
--- a/Modules/SemanticRelationsUI/include/mitkModuleActivator.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 mitkModuleActivator_h
-#define mitkModuleActivator_h
-
-// Micro Services
-#include <usModuleActivator.h>
-#include <usModuleEvent.h>
-#include <usServiceRegistration.h>
-#include <usServiceTracker.h>
-
-#include <memory>
-
-// qt widgets module
-#include "mitkIDataStorageInspectorProvider.h"
-
-namespace mitk
-{
- /*
- * This is the module activator for the "SemanticRelationsUI" module.
- */
- class SemanticRelationsUIActivator : public us::ModuleActivator
- {
- public:
- void Load(us::ModuleContext* context) override;
- void Unload(us::ModuleContext* context) override;
-
- private:
- std::unique_ptr<mitk::IDataStorageInspectorProvider> m_PatientTableInspector;
- };
-}
-#endif
diff --git a/Modules/SemanticRelationsUI/src/QmitkAbstractSemanticRelationsStorageInspector.cpp b/Modules/SemanticRelationsUI/src/QmitkAbstractSemanticRelationsStorageInspector.cpp
deleted file mode 100644
index 0bd50689da..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkAbstractSemanticRelationsStorageInspector.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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkAbstractSemanticRelationsStorageInspector.h"
-
-QmitkAbstractSemanticRelationsStorageInspector::QmitkAbstractSemanticRelationsStorageInspector(QWidget* parent /*= nullptr*/)
- : QmitkAbstractDataStorageInspector(parent)
-{
- // nothing here
-}
-
-QmitkAbstractSemanticRelationsStorageInspector::~QmitkAbstractSemanticRelationsStorageInspector()
-{
- // nothing here
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkAbstractSemanticRelationsStorageModel.cpp b/Modules/SemanticRelationsUI/src/QmitkAbstractSemanticRelationsStorageModel.cpp
deleted file mode 100644
index b0f0254cd6..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkAbstractSemanticRelationsStorageModel.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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkAbstractSemanticRelationsStorageModel.h"
-
-#include "QmitkCustomVariants.h"
-
-QmitkAbstractSemanticRelationsStorageModel::QmitkAbstractSemanticRelationsStorageModel(QObject* parent /*= nullptr*/)
- : QmitkAbstractDataStorageModel(parent)
- , m_SemanticRelationsDataStorageAccess(nullptr)
-{
- m_SemanticRelationsIntegration = std::make_unique<mitk::SemanticRelationsIntegration>();
- m_SemanticRelationsIntegration->AddObserver(this);
-}
-
-QmitkAbstractSemanticRelationsStorageModel::~QmitkAbstractSemanticRelationsStorageModel()
-{
- if (nullptr != m_SemanticRelationsIntegration)
- {
- m_SemanticRelationsIntegration->RemoveObserver(this);
- }
-}
-
-void QmitkAbstractSemanticRelationsStorageModel::Update(const mitk::SemanticTypes::CaseID& caseID)
-{
- // if the case ID of updated instance is equal to the currently active caseID
- if (caseID == m_CaseID)
- {
- UpdateModelData();
- }
-}
-
-void QmitkAbstractSemanticRelationsStorageModel::SetCaseID(const mitk::SemanticTypes::CaseID& caseID)
-{
- m_CaseID = caseID;
- UpdateModelData();
-}
-
-void QmitkAbstractSemanticRelationsStorageModel::SetLesion(const mitk::SemanticTypes::Lesion& lesion)
-{
- m_Lesion = lesion;
- UpdateModelData();
-}
-
-void QmitkAbstractSemanticRelationsStorageModel::SetDataNodeSelection(const QList<mitk::DataNode::Pointer>& dataNodeSelection)
-{
- m_SelectedDataNodes = dataNodeSelection;
- UpdateModelData();
-}
-
-void QmitkAbstractSemanticRelationsStorageModel::UpdateModelData()
-{
- if (nullptr == m_SemanticRelationsDataStorageAccess)
- {
- return;
- }
-
- // update the model, so that the table will be filled with the new patient information
- beginResetModel();
-
- SetData();
-
- endResetModel();
- emit ModelUpdated();
-}
-
-void QmitkAbstractSemanticRelationsStorageModel::DataStorageChanged()
-{
- m_SemanticRelationsDataStorageAccess = std::make_unique<mitk::SemanticRelationsDataStorageAccess>(m_DataStorage.Lock());
- UpdateModelData();
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkControlPointDialog.cpp b/Modules/SemanticRelationsUI/src/QmitkControlPointDialog.cpp
deleted file mode 100644
index c6400ad1d3..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkControlPointDialog.cpp
+++ /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.
-
-============================================================================*/
-
-#include "QmitkControlPointDialog.h"
-
-#include <QAbstractItemModel>
-#include <QStringListModel>
-#include <QLabel>
-#include <QLayout>
-#include <qpushbutton.h>
-
-QmitkControlPointDialog::QmitkControlPointDialog(QWidget* parent)
- : QDialog(parent)
-{
- QBoxLayout* verticalLayout = new QVBoxLayout(this);
- verticalLayout->setContentsMargins(QMargins(5, 5, 5, 5));
- verticalLayout->setSpacing(5);
-
- QLabel* dateLabel = new QLabel(tr("Set date"), this);
- verticalLayout->addWidget(dateLabel);
-
- m_DateEdit = new QDateEdit(this);
- m_DateEdit->setDisplayFormat("yyyy-MM-dd");
- m_DateEdit->setFocus();
- verticalLayout->addWidget(m_DateEdit);
-
- QPushButton* acceptButton = new QPushButton(tr("Ok"), this);
- QPushButton* cancelButton = new QPushButton(tr("Cancel"), this);
- acceptButton->setDefault(true);
-
- connect(acceptButton, &QPushButton::clicked, this, &QmitkControlPointDialog::accept);
- connect(cancelButton, &QPushButton::clicked, this, &QmitkControlPointDialog::reject);
-
- QBoxLayout* horizontalLayout = new QHBoxLayout();
- horizontalLayout->setSpacing(5);
- horizontalLayout->addStretch();
- horizontalLayout->addWidget(acceptButton);
- horizontalLayout->addWidget(cancelButton);
- verticalLayout->addLayout(horizontalLayout);
-
- setMinimumSize(250, 100);
-}
-
-void QmitkControlPointDialog::SetCurrentDate(mitk::SemanticTypes::ControlPoint currentControlPoint)
-{
- m_DateEdit->setDate(QDate(currentControlPoint.date.year(), currentControlPoint.date.month(), currentControlPoint.date.day()));
-}
-
-QDate QmitkControlPointDialog::GetCurrentDate() const
-{
- return m_DateEdit->date();
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkLesionTextDialog.cpp b/Modules/SemanticRelationsUI/src/QmitkLesionTextDialog.cpp
deleted file mode 100644
index 1def6eaf60..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkLesionTextDialog.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 "QmitkLesionTextDialog.h"
-
-#include <QLabel>
-#include <QLayout>
-#include <qpushbutton.h>
-
-QmitkLesionTextDialog::QmitkLesionTextDialog(QWidget* parent)
- : QDialog(parent)
-{
- QBoxLayout* verticalLayout = new QVBoxLayout(this);
- verticalLayout->setContentsMargins(QMargins(5, 5, 5, 5));
- verticalLayout->setSpacing(5);
-
- QLabel* dialogLabel = new QLabel(tr("Set lesion information"), this);
- verticalLayout->addWidget(dialogLabel);
-
- m_LineEdit = new QLineEdit(this);
- m_LineEdit->setFocus();
- verticalLayout->addWidget(m_LineEdit);
-
- QPushButton* acceptButton = new QPushButton(tr("Ok"), this);
- QPushButton* cancelButton = new QPushButton(tr("Cancel"), this);
- acceptButton->setDefault(true);
-
- connect(acceptButton, &QPushButton::clicked, this, &QmitkLesionTextDialog::accept);
- connect(cancelButton, &QPushButton::clicked, this, &QmitkLesionTextDialog::reject);
-
- QBoxLayout* horizontalLayout = new QHBoxLayout();
- horizontalLayout->setSpacing(5);
- horizontalLayout->addStretch();
- horizontalLayout->addWidget(acceptButton);
- horizontalLayout->addWidget(cancelButton);
- verticalLayout->addLayout(horizontalLayout);
-
- setMinimumSize(250, 100);
-}
-
-void QmitkLesionTextDialog::SetLineEditText(const std::string& lineEditText)
-{
- m_LineEdit->setText(QString::fromStdString(lineEditText));
-}
-
-QString QmitkLesionTextDialog::GetLineEditText() const
-{
- return m_LineEdit->text();
-}
-
-QLineEdit* QmitkLesionTextDialog::GetLineEdit() const
-{
- return m_LineEdit;
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkLesionTreeItem.cpp b/Modules/SemanticRelationsUI/src/QmitkLesionTreeItem.cpp
deleted file mode 100644
index 1546baeb32..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkLesionTreeItem.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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkLesionTreeItem.h"
-
-// qt
-#include <QStringList>
-
-QmitkLesionTreeItem::QmitkLesionTreeItem(mitk::LesionData lesionData/* = mitk::LesionTreeItemData()*/)
-{
- m_ItemData = lesionData;
-}
-
-void QmitkLesionTreeItem::SetParent(ParentPointer parent)
-{
- m_ParentItem = parent;
-}
-
-int QmitkLesionTreeItem::GetRow() const
-{
- if (m_ParentItem.expired())
- {
- return 0;
- }
-
- auto parentItem = m_ParentItem.lock();
- return parentItem->GetRowOfChild(this->shared_from_this());
-}
-
-int QmitkLesionTreeItem::GetRowOfChild(ChildConstPointer child) const
-{
- auto it = std::find(m_Children.begin(), m_Children.end(), child);
- if (it == m_Children.end())
- {
- return -1;
- }
- else
- {
- return std::distance(m_Children.begin(), it);
- }
-}
-
-void QmitkLesionTreeItem::AddChild(ChildPointer child)
-{
- auto it = std::find(m_Children.begin(), m_Children.end(), child);
- if (it == m_Children.end())
- {
- // child does not already exist; add to vector of children
- m_Children.push_back(child);
- // add parent item
- child->SetParent(this->shared_from_this());
- }
-}
-
-void QmitkLesionTreeItem::RemoveChild(ChildPointer child)
-{
- auto it = std::find(m_Children.begin(), m_Children.end(), child);
- if (it != m_Children.end())
- {
- m_Children.erase(it);
- }
-}
-
-void QmitkLesionTreeItem::SetData(const mitk::LesionData& lesionData)
-{
- m_ItemData = lesionData;
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp b/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp
deleted file mode 100644
index eceb1003be..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp
+++ /dev/null
@@ -1,298 +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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkLesionTreeModel.h"
-
-// semantic relations module
-#include <mitkControlPointManager.h>
-#include <mitkLesionManager.h>
-#include <mitkNodePredicates.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkRelationStorage.h>
-
-// qt
-#include <QColor>
-
-QmitkLesionTreeModel::QmitkLesionTreeModel(QObject* parent/* = nullptr*/)
- : QmitkAbstractSemanticRelationsStorageModel(parent)
- , m_LastSegmentation(nullptr)
- , m_RootItem(std::make_shared<QmitkLesionTreeItem>(mitk::LesionData()))
-{
- // nothing here
-}
-
-//////////////////////////////////////////////////////////////////////////
-// overridden virtual functions from QAbstractItemModel
-//////////////////////////////////////////////////////////////////////////
-QModelIndex QmitkLesionTreeModel::index(int row, int column, const QModelIndex& itemIndex) const
-{
- if (!hasIndex(row, column, itemIndex))
- {
- return QModelIndex();
- }
-
- auto childItem = GetItemByIndex(itemIndex)->GetChildInRow(row);
- if (nullptr == childItem)
- {
- return QModelIndex();
- }
-
- return createIndex(row, column, childItem.get());
-}
-
-QModelIndex QmitkLesionTreeModel::parent(const QModelIndex& itemIndex) const
-{
- if (!itemIndex.isValid())
- {
- return QModelIndex();
- }
-
- auto parentItem = GetItemByIndex(itemIndex)->GetParent();
- if (parentItem.expired())
- {
- return QModelIndex();
- }
-
- auto sharedParent = parentItem.lock();
- if (sharedParent == m_RootItem)
- {
- return QModelIndex();
- }
-
- return createIndex(sharedParent->GetRow(), 0, sharedParent.get());
-}
-
-int QmitkLesionTreeModel::rowCount(const QModelIndex& itemIndex/* = QModelIndex()*/) const
-{
- return GetItemByIndex(itemIndex)->ChildCount();
-}
-
-int QmitkLesionTreeModel::columnCount(const QModelIndex&/* itemIndex = QModelIndex() */) const
-{
- if (0 == m_RootItem->ChildCount())
- {
- // no lesion items stored, no need to display columns
- return 0;
- }
-
- return m_ControlPoints.size() + 1;
-}
-
-QVariant QmitkLesionTreeModel::data(const QModelIndex& index, int role) const
-{
- if (!index.isValid())
- {
- return QVariant();
- }
-
- if (index.column() < 0 || index.column() > static_cast<int>(m_ControlPoints.size()))
- {
- return QVariant();
- }
-
- QmitkLesionTreeItem* currentItem = GetItemByIndex(index);
- if (Qt::DisplayRole == role)
- {
- if (currentItem->GetParent().expired())
- {
- return QVariant();
- }
-
- auto parentItem = currentItem->GetParent().lock();
- // parent exists and is the root item -> 1. item of a lesion entry
- if (m_RootItem == parentItem)
- {
- // display role fills the first columns with the lesion UID / name
- if (0 == index.column())
- {
- std::string itemString = currentItem->GetData().GetLesionName();
- if (itemString.empty())
- {
- itemString = currentItem->GetData().GetLesionUID();
- }
- return QString::fromStdString(itemString);
- }
- else
- {
- // display role fills other columns with the lesion presence info
- const auto lesionPresence = currentItem->GetData().GetLesionPresence();
- if (index.column() - 1 > static_cast<int>(lesionPresence.size()))
- {
- return "N/A";
- }
-
- if (lesionPresence.at(index.column() - 1))
- {
- return QString::fromStdString("present");
- }
-
- return QString::fromStdString("not present");
- }
- }
- }
-
- if (Qt::BackgroundRole == role)
- {
- auto it = m_DataNodePresence.find(currentItem->GetData().GetLesion().UID);
- if (it != m_DataNodePresence.end())
- {
- return it->second ? QVariant(QColor(Qt::darkGreen)) : QVariant(QColor(Qt::transparent));
- }
-
- return QVariant(QColor(Qt::transparent));
- }
-
- if (Qt::UserRole == role)
- {
- return QVariant::fromValue(currentItem);
- }
-
- return QVariant();
-}
-
-QVariant QmitkLesionTreeModel::headerData(int section, Qt::Orientation orientation, int role) const
-{
- if (0 == m_RootItem->ChildCount())
- {
- // no lesion items stored, no need to display the header
- return QVariant();
- }
-
- if (Qt::Horizontal == orientation && Qt::DisplayRole == role)
- {
- if (0 == section)
- {
- return QVariant("Lesion");
- }
-
- if (static_cast<int>(m_ControlPoints.size()) >= section)
- {
- mitk::SemanticTypes::ControlPoint currentControlPoint = m_ControlPoints.at(section-1);
- return QVariant(QString::fromStdString(currentControlPoint.ToString()));
- }
- }
-
- return QVariant();
-}
-
-const mitk::DataNode* QmitkLesionTreeModel::GetLastSegmentation() const
-{
- return m_LastSegmentation;
-}
-
-void QmitkLesionTreeModel::NodeAdded(const mitk::DataNode* dataNode)
-{
- if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode))
- {
- m_LastSegmentation = dataNode;
- }
-}
-
-void QmitkLesionTreeModel::SetData()
-{
- m_RootItem = std::make_shared<QmitkLesionTreeItem>(mitk::LesionData());
-
- // get all control points of current case
- m_ControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(m_CaseID);
- // sort the vector of control points for the timeline
- std::sort(m_ControlPoints.begin(), m_ControlPoints.end());
-
- SetLesionData();
- SetSelectedDataNodesPresence();
-}
-
-void QmitkLesionTreeModel::SetLesionData()
-{
- m_CurrentLesions = mitk::RelationStorage::GetAllLesionsOfCase(m_CaseID);
- for (auto& lesion : m_CurrentLesions)
- {
- AddLesion(lesion);
- }
-}
-
-void QmitkLesionTreeModel::AddLesion(const mitk::SemanticTypes::Lesion& lesion)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- // create new lesion tree item data and modify it according to the control point data
- mitk::LesionData lesionData(lesion);
- mitk::ComputeLesionPresence(lesionData, m_CaseID);
-
- // add the top-level lesion item to the root item
- std::shared_ptr<QmitkLesionTreeItem> newLesionTreeItem = std::make_shared<QmitkLesionTreeItem>(lesionData);
- m_RootItem->AddChild(newLesionTreeItem);
-}
-
-void QmitkLesionTreeModel::SetSelectedDataNodesPresence()
-{
- m_DataNodePresence.clear();
- for (const auto& dataNode : std::as_const(m_SelectedDataNodes))
- {
- if (!mitk::SemanticRelationsInference::InstanceExists(dataNode))
- {
- continue;
- }
-
- for (const auto& lesion : m_CurrentLesions)
- {
- if (!mitk::SemanticRelationsInference::InstanceExists(m_CaseID, lesion))
- {
- continue;
- }
- try
- {
- // set the lesion presence for the current node
- bool dataNodePresence = mitk::SemanticRelationsInference::IsLesionPresent(lesion, dataNode);
- SetDataNodePresenceOfLesion(&lesion, dataNodePresence);
- }
- catch (const mitk::SemanticRelationException&)
- {
- continue;
- }
- }
- }
-}
-
-void QmitkLesionTreeModel::SetDataNodePresenceOfLesion(const mitk::SemanticTypes::Lesion* lesion, bool dataNodePresence)
-{
- std::map<mitk::SemanticTypes::ID, bool>::iterator iter = m_DataNodePresence.find(lesion->UID);
- if (iter != m_DataNodePresence.end())
- {
- // key already existing, overwrite already stored bool value
- iter->second = dataNodePresence;
- }
- else
- {
- m_DataNodePresence.insert(std::make_pair(lesion->UID, dataNodePresence));
- }
-}
-
-QmitkLesionTreeItem* QmitkLesionTreeModel::GetItemByIndex(const QModelIndex& index) const
-{
- if (index.isValid())
- {
- auto item = static_cast<QmitkLesionTreeItem*>(index.internalPointer());
- if (nullptr != item)
- {
- return item;
- }
- }
-
- return m_RootItem.get();
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientInfoWidget.cpp b/Modules/SemanticRelationsUI/src/QmitkPatientInfoWidget.cpp
deleted file mode 100644
index a0e769cd51..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkPatientInfoWidget.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 "QmitkPatientInfoWidget.h"
-
-// semantic relations module
-#include <mitkDICOMHelper.h>
-
-// mitk core
-#include <mitkPropertyNameHelper.h>
-
-QmitkPatientInfoWidget::QmitkPatientInfoWidget(QWidget* parent)
- : QWidget(parent)
-{
- Init();
-}
-
-QmitkPatientInfoWidget::~QmitkPatientInfoWidget()
-{
- // nothing here
-}
-
-void QmitkPatientInfoWidget::Init()
-{
- // Create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi(this);
-}
-
-void QmitkPatientInfoWidget::SetPatientInfo(const mitk::DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- MITK_INFO << "Not a valid data node.";
- return;
- }
-
- mitk::BaseData* baseData = dataNode->GetData();
- if (nullptr == baseData)
- {
- MITK_INFO << "No valid base data.";
- return;
- }
-
- mitk::BaseProperty* acquisitionDate = baseData->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0022).c_str());
- std::string acquisitionDateAsString = "";
- if (nullptr != acquisitionDate)
- {
- acquisitionDateAsString = acquisitionDate->GetValueAsString();
- mitk::DICOMHelper::ReformatDICOMTag(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0022).c_str(), acquisitionDateAsString);
- }
-
- mitk::BaseProperty* acquisitionTime = baseData->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0032).c_str());
- std::string acquisitionTimeAsString = "";
- if (nullptr != acquisitionTime)
- {
- acquisitionTimeAsString = acquisitionTime->GetValueAsString();
- mitk::DICOMHelper::ReformatDICOMTag(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0032).c_str(), acquisitionTimeAsString);
- }
-
- std::string patiensBirthDateAsString = "";
- mitk::BaseProperty* patientBirthDate = baseData->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0010, 0x0030).c_str());
- if (nullptr != patientBirthDate)
- {
- patiensBirthDateAsString = patientBirthDate->GetValueAsString();
- mitk::DICOMHelper::ReformatDICOMTag(mitk::GeneratePropertyNameForDICOMTag(0x0010, 0x0030).c_str(), patiensBirthDateAsString);
- }
-
- mitk::BaseProperty* modality = baseData->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0060).c_str());
- std::string modalityAsString = "";
- if (nullptr != modality)
- {
- modalityAsString = modality->GetValueAsString();
- mitk::DICOMHelper::ReformatDICOMTag(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0060).c_str(), modalityAsString);
- }
-
- mitk::BaseProperty* gender = baseData->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0010, 0x0040).c_str());
- std::string genderAsString = "";
- if (nullptr != gender)
- {
- genderAsString = gender->GetValueAsString();
- mitk::DICOMHelper::ReformatDICOMTag(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0060).c_str(), genderAsString);
- }
-
- m_Controls.dataIDLineEdit->setText(QString::fromStdString(mitk::DICOMHelper::GetIDFromDataNode(dataNode)));
- m_Controls.nameLineEdit->setText(QString::fromStdString(mitk::DICOMHelper::GetCaseIDFromDataNode(dataNode)));
- m_Controls.dateLineEdit->setText(QString::fromStdString(acquisitionDateAsString));
- m_Controls.timeLineEdit->setText(QString::fromStdString(acquisitionTimeAsString));
- m_Controls.scannerLineEdit->setText("");
- m_Controls.modalityLineEdit->setText(QString::fromStdString(modalityAsString));
- m_Controls.birthdateLineEdit->setText(QString::fromStdString(patiensBirthDateAsString));
- m_Controls.genderLineEdit->setText(QString::fromStdString(genderAsString));
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientInfoWidgetControls.ui b/Modules/SemanticRelationsUI/src/QmitkPatientInfoWidgetControls.ui
deleted file mode 100644
index 3ffbe69f32..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkPatientInfoWidgetControls.ui
+++ /dev/null
@@ -1,166 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkPatientInfoWidgetControls</class>
- <widget class="QWidget" name="QmitkPatientInfoWidgetControls">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>350</width>
- <height>300</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="1" column="0" colspan="2">
- <widget class="QLabel" name="patientInfoLabel">
- <property name="font">
- <font>
- <weight>75</weight>
- <italic>false</italic>
- <bold>true</bold>
- </font>
- </property>
- <property name="text">
- <string>Patient data information</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter</set>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="dataIDLabel">
- <property name="text">
- <string>ID*:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QLineEdit" name="dataIDLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QLabel" name="nameLabel">
- <property name="text">
- <string>Name:</string>
- </property>
- </widget>
- </item>
- <item row="3" column="1">
- <widget class="QLineEdit" name="nameLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QLabel" name="dateLabel">
- <property name="text">
- <string>Acq. Date:</string>
- </property>
- </widget>
- </item>
- <item row="4" column="1">
- <widget class="QLineEdit" name="dateLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- <property name="placeholderText">
- <string>YYYY-MM-DD</string>
- </property>
- </widget>
- </item>
- <item row="5" column="0">
- <widget class="QLabel" name="timeLabel">
- <property name="text">
- <string>Time:</string>
- </property>
- </widget>
- </item>
- <item row="5" column="1">
- <widget class="QLineEdit" name="timeLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- <property name="placeholderText">
- <string>hh:mm:ss</string>
- </property>
- </widget>
- </item>
- <item row="6" column="0">
- <widget class="QLabel" name="scannerLabel">
- <property name="text">
- <string>Scanner:</string>
- </property>
- </widget>
- </item>
- <item row="6" column="1">
- <widget class="QLineEdit" name="scannerLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="7" column="0">
- <widget class="QLabel" name="modalityLabel">
- <property name="text">
- <string>Modality:</string>
- </property>
- </widget>
- </item>
- <item row="7" column="1">
- <widget class="QLineEdit" name="modalityLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="8" column="0">
- <widget class="QLabel" name="birthdateLabel">
- <property name="text">
- <string>Birthdate:</string>
- </property>
- </widget>
- </item>
- <item row="8" column="1">
- <widget class="QLineEdit" name="birthdateLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- <property name="placeholderText">
- <string>YYYY-MM-DD</string>
- </property>
- </widget>
- </item>
- <item row="9" column="0">
- <widget class="QLabel" name="genderLabel">
- <property name="text">
- <string>Gender:</string>
- </property>
- </widget>
- </item>
- <item row="9" column="1">
- <widget class="QLineEdit" name="genderLineEdit">
- <property name="readOnly">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="10" column="0" colspan="2">
- <widget class="QLabel" name="mandatoryLabel">
- <property name="text">
- <string>* mandatory field</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientTableHeaderView.cpp b/Modules/SemanticRelationsUI/src/QmitkPatientTableHeaderView.cpp
deleted file mode 100644
index 7a2eb49438..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkPatientTableHeaderView.cpp
+++ /dev/null
@@ -1,240 +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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkPatientTableHeaderView.h"
-
-// qt
-#include <QPainter>
-#include <QSize>
-
-QmitkPatientTableHeaderView::QmitkPatientTableHeaderView(QWidget* parent/* = nullptr*/)
- : QHeaderView(Qt::Horizontal, parent)
- , m_HeaderModel(nullptr)
-{
- // nothing here
-}
-
-QmitkPatientTableHeaderView::~QmitkPatientTableHeaderView()
-{
- // nothing here
-}
-
-void QmitkPatientTableHeaderView::setModel(QAbstractItemModel* model)
-{
- // retrieve the header model from the given table model
- QVariant variant = model->data(QModelIndex(), HorizontalHeaderDataRole);
- if (variant.isValid() && variant.canConvert<QStandardItemModel*>())
- {
- m_HeaderModel = variant.value<QStandardItemModel*>();
- }
-
- QHeaderView::setModel(model);
-}
-
-void QmitkPatientTableHeaderView::paintSection(QPainter* painter, const QRect& rect, int logicalIndex) const
-{
- if (rect.isValid())
- {
- int top = rect.y();
-
- QModelIndex leafIndex = HeaderIndex(logicalIndex);
- QModelIndexList indexes = ParentIndexList(leafIndex);
- for (const auto& index : std::as_const(indexes))
- {
- top = PaintHeader(painter, index, logicalIndex, rect, top);
- }
-
- return;
- }
-
- QHeaderView::paintSection(painter, rect, logicalIndex);
-}
-
-QSize QmitkPatientTableHeaderView::sectionSizeFromContents(int logicalIndex) const
-{
- if (nullptr != m_HeaderModel)
- {
- QModelIndex headerIndex = HeaderIndex(logicalIndex);
- if (headerIndex.isValid())
- {
- QSize headerSize = HeaderSize(headerIndex);
- headerIndex = headerIndex.parent();
- while (headerIndex.isValid())
- {
- QSize currentHeaderSize = HeaderSize(headerIndex);
- headerSize.rheight() += currentHeaderSize.height();
- if (currentHeaderSize.width() > headerSize.width())
- {
- headerSize.rwidth() = currentHeaderSize.width();
- }
-
- headerIndex = headerIndex.parent();
- }
- return headerSize;
- }
- }
-
- return QHeaderView::sectionSizeFromContents(logicalIndex);
-}
-
-int QmitkPatientTableHeaderView::PaintHeader(QPainter* painter, const QModelIndex& currentIndex, int logicalIndex, const QRect& sectionRect, int top) const
-{
- QModelIndex headerIndex = HeaderIndex(logicalIndex);
- int height = HeaderSize(currentIndex).height();
- if (currentIndex == headerIndex)
- {
- height = sectionRect.height() - top;
- }
- int left = CurrentHeaderLeft(currentIndex, headerIndex, logicalIndex, sectionRect.left());
- int width = CurrentHeaderWidth(currentIndex, headerIndex, logicalIndex);
-
- QStyleOptionHeader headerStyleOptions;
- initStyleOption(&headerStyleOptions);
- headerStyleOptions.text = currentIndex.data(Qt::DisplayRole).toString();
- headerStyleOptions.textAlignment = Qt::AlignCenter;
- painter->save();
-
- QRect rect(left, top, width, height);
- headerStyleOptions.rect = rect;
- style()->drawControl(QStyle::CE_Header, &headerStyleOptions, painter, this);
- painter->restore();
-
- return top + height;
-}
-
-QSize QmitkPatientTableHeaderView::HeaderSize(const QModelIndex& index) const
-{
- QFont font = this->font();
- font.setBold(true);
- QFontMetrics fontMetrics(font);
- QSize fontSize = fontMetrics.size(0, index.data(Qt::DisplayRole).toString());
- QSize emptyFontSize = fontMetrics.size(0, "");
-
- return fontSize + emptyFontSize;
-}
-
-int QmitkPatientTableHeaderView::CurrentHeaderLeft(const QModelIndex& currentIndex, const QModelIndex& headerIndex, int sectionIndex, int left) const
-{
- QModelIndexList headerList = ListHeader(currentIndex);
- if (!headerList.empty())
- {
- int index = headerList.indexOf(headerIndex);
- int firstHeaderSectionIndex = sectionIndex - index;
- --index;
- for (; index >= 0; --index)
- {
- left -= sectionSize(firstHeaderSectionIndex + index);
- }
- }
-
- return left;
-}
-
-int QmitkPatientTableHeaderView::CurrentHeaderWidth(const QModelIndex& currentIndex, const QModelIndex& headerIndex, int sectionIndex) const
-{
- QModelIndexList headerList = ListHeader(currentIndex);
- if (headerList.empty())
- {
- return sectionSize(sectionIndex);
- }
-
- int width = 0;
- int index = headerList.indexOf(headerIndex);
- int firstHeaderSectionIndex = sectionIndex - index;
- for (int i = 0; i < headerList.size(); ++i)
- {
- width += sectionSize(firstHeaderSectionIndex + i);
- }
-
- return width;
-}
-
-QModelIndexList QmitkPatientTableHeaderView::ParentIndexList(QModelIndex index) const
-{
- QModelIndexList indexList;
- while (index.isValid())
- {
- indexList.push_front(index);
- index = index.parent();
- }
-
- return indexList;
-}
-
-QModelIndex QmitkPatientTableHeaderView::HeaderIndex(int sectionIndex) const
-{
- if (nullptr != m_HeaderModel)
- {
- int currentHeaderIndex = -1;
- for (int i = 0; i < m_HeaderModel->columnCount(); ++i)
- {
- QModelIndex modelIndex = FindHeader(m_HeaderModel->index(0, i), sectionIndex, currentHeaderIndex);
- if (modelIndex.isValid())
- {
- return modelIndex;
- }
- }
- }
-
- return QModelIndex();
-}
-
-QModelIndex QmitkPatientTableHeaderView::FindHeader(const QModelIndex& currentIndex, int sectionIndex, int& currentHeaderIndex) const
-{
- if (currentIndex.isValid())
- {
- int childCount = currentIndex.model()->columnCount(currentIndex);
- if (childCount > 0)
- {
- for (int i = 0; i < childCount; ++i)
- {
- QModelIndex modelIndex = FindHeader(currentIndex.model()->index(0, i, currentIndex), sectionIndex, currentHeaderIndex);
- if (modelIndex.isValid())
- {
- return modelIndex;
- }
- }
- }
- else
- {
- ++currentHeaderIndex;
- if (currentHeaderIndex == sectionIndex)
- {
- return currentIndex;
- }
- }
- }
-
- return QModelIndex();
-}
-
-QModelIndexList QmitkPatientTableHeaderView::ListHeader(const QModelIndex& currentIndex) const
-{
- QModelIndexList headerList;
- if (currentIndex.isValid())
- {
- int childCount = currentIndex.model()->columnCount(currentIndex);
- if (childCount > 0)
- {
- for (int i = 0; i < childCount; ++i)
- {
- headerList += ListHeader(currentIndex.model()->index(0, i, currentIndex));
- }
- }
- else
- {
- headerList.push_back(currentIndex);
- }
- }
- return headerList;
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientTableInspector.cpp b/Modules/SemanticRelationsUI/src/QmitkPatientTableInspector.cpp
deleted file mode 100644
index 9dc1841155..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkPatientTableInspector.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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkPatientTableInspector.h"
-#include "QmitkPatientTableHeaderView.h"
-
-// mitk qt widgets module
-#include "QmitkCustomVariants.h"
-#include "QmitkEnums.h"
-
-// qt
-#include <QKeyEvent>
-#include <QSignalMapper>
-
-QmitkPatientTableInspector::QmitkPatientTableInspector(QWidget* parent/* =nullptr*/)
- : QmitkAbstractSemanticRelationsStorageInspector(parent)
-{
- m_Controls.setupUi(this);
-
- QmitkPatientTableHeaderView* patientTableHeaderView = new QmitkPatientTableHeaderView(m_Controls.tableView);
- m_Controls.tableView->setHorizontalHeader(patientTableHeaderView);
- m_Controls.tableView->horizontalHeader()->setHighlightSections(false);
- m_Controls.tableView->horizontalHeader()->setSectionResizeMode(QHeaderView::Fixed);
- m_Controls.tableView->verticalHeader()->setHighlightSections(false);
- m_Controls.tableView->verticalHeader()->setSectionResizeMode(QHeaderView::Fixed);
- m_Controls.tableView->setSelectionMode(QAbstractItemView::SingleSelection);
- m_Controls.tableView->setSelectionBehavior(QAbstractItemView::SelectItems);
- m_Controls.tableView->setContextMenuPolicy(Qt::CustomContextMenu);
-
- m_StorageModel = new QmitkPatientTableModel(m_Controls.tableView);
- m_Controls.tableView->setModel(m_StorageModel);
- m_ItemDelegate = new QmitkTableItemThumbnailDelegate(m_Controls.tableView);
- //m_Controls.tableView->setItemDelegate(m_ItemDelegate);
-
- SetUpConnections();
-}
-
-QAbstractItemView* QmitkPatientTableInspector::GetView()
-{
- return m_Controls.tableView;
-}
-
-const QAbstractItemView* QmitkPatientTableInspector::GetView() const
-{
- return m_Controls.tableView;
-}
-
-void QmitkPatientTableInspector::SetSelectionMode(SelectionMode mode)
-{
- m_Controls.tableView->setSelectionMode(mode);
-}
-
-QmitkPatientTableInspector::SelectionMode QmitkPatientTableInspector::GetSelectionMode() const
-{
- return m_Controls.tableView->selectionMode();
-}
-
-void QmitkPatientTableInspector::SetCaseID(const mitk::SemanticTypes::CaseID& caseID)
-{
- m_StorageModel->SetCaseID(caseID);
-}
-
-void QmitkPatientTableInspector::SetLesion(const mitk::SemanticTypes::Lesion& lesion)
-{
- m_StorageModel->SetLesion(lesion);
-}
-
-QItemSelectionModel* QmitkPatientTableInspector::GetSelectionModel()
-{
- return m_Controls.tableView->selectionModel();
-}
-
-void QmitkPatientTableInspector::Initialize()
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- m_StorageModel->SetDataStorage(dataStorage);
- m_StorageModel->SetNodePredicate(m_NodePredicate);
-
- m_Connector->SetView(m_Controls.tableView);
-}
-
-void QmitkPatientTableInspector::OnModelUpdated()
-{
- m_Controls.tableView->resizeRowsToContents();
- m_Controls.tableView->resizeColumnsToContents();
-}
-
-void QmitkPatientTableInspector::OnNodeButtonClicked(const QString& nodeType)
-{
- m_StorageModel->SetNodeType(nodeType.toStdString());
-}
-
-void QmitkPatientTableInspector::OnDataNodeSelectionChanged(const QList<mitk::DataNode::Pointer>& dataNodeSelection)
-{
- if (m_StorageModel->GetLesion().UID.empty())
- {
- return;
- }
-
- // if lesion is set, reset to empty lesion to hide the "lesion presence background highlighting" in the model
- m_StorageModel->SetLesion(mitk::SemanticTypes::Lesion());
- // need to explicitly set the data node selection
- SetCurrentSelection(dataNodeSelection);
-}
-
-void QmitkPatientTableInspector::OnItemDoubleClicked(const QModelIndex& itemIndex)
-{
- if (itemIndex.isValid())
- {
- QVariant qvariantDataNode = m_StorageModel->data(itemIndex, QmitkDataNodeRawPointerRole);
- if (qvariantDataNode.canConvert<mitk::DataNode*>())
- {
- mitk::DataNode* dataNode = qvariantDataNode.value<mitk::DataNode*>();
- emit DataNodeDoubleClicked(dataNode);
- }
- }
-}
-
-void QmitkPatientTableInspector::SetUpConnections()
-{
- connect(m_StorageModel, &QmitkPatientTableModel::ModelUpdated, this, &QmitkPatientTableInspector::OnModelUpdated);
- connect(m_Controls.tableView, &QTableView::customContextMenuRequested, this, &QmitkPatientTableInspector::OnContextMenuRequested);
-
- QSignalMapper* nodeButtonSignalMapper = new QSignalMapper(this);
- nodeButtonSignalMapper->setMapping(m_Controls.imageNodeButton, QString("Image"));
- nodeButtonSignalMapper->setMapping(m_Controls.segmentationNodeButton, QString("Segmentation"));
- connect(nodeButtonSignalMapper, static_cast<void (QSignalMapper::*)(const QString&)>(&QSignalMapper::mappedString), this, &QmitkPatientTableInspector::OnNodeButtonClicked);
- connect(m_Controls.imageNodeButton, &QRadioButton::clicked, nodeButtonSignalMapper, static_cast<void(QSignalMapper::*)()>(&QSignalMapper::map));
- connect(m_Controls.segmentationNodeButton, &QRadioButton::clicked, nodeButtonSignalMapper, static_cast<void(QSignalMapper::*)()>(&QSignalMapper::map));
- m_Controls.imageNodeButton->setChecked(true);
-
- connect(this, &QmitkPatientTableInspector::CurrentSelectionChanged, this, &QmitkPatientTableInspector::OnDataNodeSelectionChanged);
- connect(m_Controls.tableView, &QTableView::doubleClicked, this, &QmitkPatientTableInspector::OnItemDoubleClicked);
-}
-
-void QmitkPatientTableInspector::keyPressEvent(QKeyEvent* e)
-{
- mitk::DataNode* dataNode = nullptr;
- QModelIndex selectedIndex = m_Controls.tableView->currentIndex();
- if (selectedIndex.isValid())
- {
- QVariant qvariantDataNode = m_StorageModel->data(selectedIndex, QmitkDataNodeRawPointerRole);
- if (qvariantDataNode.canConvert<mitk::DataNode*>())
- {
- dataNode = qvariantDataNode.value<mitk::DataNode*>();
- }
- }
-
- if (nullptr == dataNode)
- {
- return;
- }
-
- int key = e->key();
- switch (key)
- {
- case Qt::Key_Delete:
- emit OnNodeRemoved(dataNode);
- break;
- default:
- break;
- }
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientTableInspector.ui b/Modules/SemanticRelationsUI/src/QmitkPatientTableInspector.ui
deleted file mode 100644
index c953d1b58a..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkPatientTableInspector.ui
+++ /dev/null
@@ -1,63 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkPatientTableInspector</class>
- <widget class="QWidget" name="QmitkPatientTableInspector">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>350</width>
- <height>300</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <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 row="0" column="0">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Semantic Relations content:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="2">
- <widget class="QRadioButton" name="segmentationNodeButton">
- <property name="text">
- <string>Show segmentation nodes</string>
- </property>
- <attribute name="buttonGroup">
- <string notr="true">nodeButtonGroup</string>
- </attribute>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QRadioButton" name="imageNodeButton">
- <property name="text">
- <string>Show image nodes</string>
- </property>
- <attribute name="buttonGroup">
- <string notr="true">nodeButtonGroup</string>
- </attribute>
- </widget>
- </item>
- <item row="1" column="0" colspan="3">
- <widget class="QTableView" name="tableView"/>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
- <buttongroups>
- <buttongroup name="nodeButtonGroup"/>
- </buttongroups>
-</ui>
diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientTableModel.cpp b/Modules/SemanticRelationsUI/src/QmitkPatientTableModel.cpp
deleted file mode 100644
index ff9e330c38..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkPatientTableModel.cpp
+++ /dev/null
@@ -1,346 +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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkPatientTableModel.h"
-#include "QmitkPatientTableHeaderView.h"
-#include "QmitkSemanticRelationsUIHelper.h"
-
-// semantic relations module
-#include <mitkControlPointManager.h>
-#include <mitkNodePredicates.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkRelationStorage.h>
-
-#include <QmitkCustomVariants.h>
-#include <QmitkEnums.h>
-
-// qt
-#include <QColor>
-
-// c++
-#include <iostream>
-#include <string>
-
-QmitkPatientTableModel::QmitkPatientTableModel(QObject* parent /*= nullptr*/)
- : QmitkAbstractSemanticRelationsStorageModel(parent)
- , m_SelectedNodeType("Image")
-{
- m_HeaderModel = new QStandardItemModel(this);
-}
-
-QmitkPatientTableModel::~QmitkPatientTableModel()
-{
- // nothing here
-}
-
-QModelIndex QmitkPatientTableModel::index(int row, int column, const QModelIndex& parent/* = QModelIndex()*/) const
-{
- if (hasIndex(row, column, parent))
- {
- return createIndex(row, column);
- }
-
- return QModelIndex();
-}
-
-QModelIndex QmitkPatientTableModel::parent(const QModelIndex& /*child*/) const
-{
- return QModelIndex();
-}
-
-int QmitkPatientTableModel::rowCount(const QModelIndex& parent/* = QModelIndex()*/) const
-{
- if (parent.isValid())
- {
- return 0;
- }
-
- return m_InformationTypes.size();
-}
-
-int QmitkPatientTableModel::columnCount(const QModelIndex& parent/* = QModelIndex()*/) const
-{
- if (parent.isValid())
- {
- return 0;
- }
-
- return m_ExaminationPeriods.size();
-}
-
-QVariant QmitkPatientTableModel::data(const QModelIndex& index, int role/* = Qt::DisplayRole*/) const
-{
- // special role for returning the horizontal header
- if (QmitkPatientTableHeaderView::HorizontalHeaderDataRole == role)
- {
- return QVariant::fromValue<QStandardItemModel*>(m_HeaderModel);
- }
-
- if (!index.isValid())
- {
- return QVariant();
- }
-
- if (index.row() < 0 || index.row() >= static_cast<int>(m_InformationTypes.size())
- || index.column() < 0 || index.column() >= static_cast<int>(m_ExaminationPeriods.size()))
- {
- return QVariant();
- }
-
- mitk::DataNode* dataNode = GetCurrentDataNode(index);
-
- if (Qt::DecorationRole == role)
- {
- auto it = m_PixmapMap.find(dataNode);
- if (it != m_PixmapMap.end())
- {
- return QVariant(it->second);
- }
-
- auto emptyPixmap = QPixmap(120, 120);
- emptyPixmap.fill(Qt::transparent);
- return emptyPixmap;
- }
-
- if (Qt::BackgroundRole == role)
- {
- auto it = m_LesionPresence.find(dataNode);
- if (it != m_LesionPresence.end())
- {
- return it->second ? QVariant(QColor(Qt::darkGreen)) : QVariant(QColor(Qt::transparent));
- }
-
- return QVariant(QColor(Qt::transparent));
- }
-
- if (QmitkDataNodeRole == role)
- {
- return QVariant::fromValue<mitk::DataNode::Pointer>(mitk::DataNode::Pointer(dataNode));
- }
-
- if (QmitkDataNodeRawPointerRole == role)
- {
- return QVariant::fromValue<mitk::DataNode*>(dataNode);
- }
-
- return QVariant();
-}
-
-QVariant QmitkPatientTableModel::headerData(int section, Qt::Orientation orientation, int role) const
-{
- if (Qt::Vertical == orientation && Qt::DisplayRole == role)
- {
- if (static_cast<int>(m_InformationTypes.size()) > section)
- {
- mitk::SemanticTypes::InformationType currentInformationType = m_InformationTypes.at(section);
- return QVariant(QString::fromStdString(currentInformationType));
- }
- }
-
- return QVariant();
-}
-
-Qt::ItemFlags QmitkPatientTableModel::flags(const QModelIndex& index) const
-{
- Qt::ItemFlags flags;
- mitk::DataNode* dataNode = GetCurrentDataNode(index);
- if (nullptr != dataNode)
- {
- flags = Qt::ItemIsEnabled | Qt::ItemIsSelectable;
- }
-
- return flags;
-}
-
-void QmitkPatientTableModel::SetNodeType(const std::string& nodeType)
-{
- m_SelectedNodeType = nodeType;
- UpdateModelData();
-}
-
-void QmitkPatientTableModel::NodePredicateChanged()
-{
- UpdateModelData();
-}
-
-void QmitkPatientTableModel::SetData()
-{
- // get all examination periods of current case
- m_ExaminationPeriods = mitk::RelationStorage::GetAllExaminationPeriodsOfCase(m_CaseID);
-
- // sort all examination periods for the timeline
- mitk::SortAllExaminationPeriods(m_CaseID, m_ExaminationPeriods);
-
- // rename examination periods according to their new order
- std::string examinationPeriodName = "Baseline";
- for (size_t i = 0; i < m_ExaminationPeriods.size(); ++i)
- {
- auto& examinationPeriod = m_ExaminationPeriods.at(i);
- examinationPeriod.name = examinationPeriodName;
- mitk::RelationStorage::RenameExaminationPeriod(m_CaseID, examinationPeriod);
- examinationPeriodName = "Follow-up " + std::to_string(i);
- }
-
- // get all information types points of current case
- m_InformationTypes = mitk::RelationStorage::GetAllInformationTypesOfCase(m_CaseID);
-
- if ("Image" == m_SelectedNodeType)
- {
- m_CurrentDataNodes = m_SemanticRelationsDataStorageAccess->GetAllImagesOfCase(m_CaseID);
- }
- else if ("Segmentation" == m_SelectedNodeType)
- {
- m_CurrentDataNodes = m_SemanticRelationsDataStorageAccess->GetAllSegmentationsOfCase(m_CaseID);
- }
-
- SetHeaderModel();
- SetPixmaps();
- SetLesionPresences();
-}
-
-void QmitkPatientTableModel::SetHeaderModel()
-{
- m_HeaderModel->clear();
- QStandardItem* rootItem = new QStandardItem("Timeline");
- QList<QStandardItem*> standardItems;
-
- for (const auto& examinationPeriod : m_ExaminationPeriods)
- {
- QStandardItem* examinationPeriodItem = new QStandardItem(QString::fromStdString(examinationPeriod.name));
- standardItems.push_back(examinationPeriodItem);
- rootItem->appendColumn(standardItems);
- standardItems.clear();
- }
-
- m_HeaderModel->setItem(0, 0, rootItem);
-}
-
-void QmitkPatientTableModel::SetPixmaps()
-{
- m_PixmapMap.clear();
- for (const auto& dataNode : m_CurrentDataNodes)
- {
- // set the pixmap for the current node
- QPixmap pixmapFromImage = QmitkSemanticRelationsUIHelper::GetPixmapFromImageNode(dataNode);
- SetPixmapOfNode(dataNode, &pixmapFromImage);
- }
-}
-
-void QmitkPatientTableModel::SetPixmapOfNode(const mitk::DataNode* dataNode, QPixmap* pixmapFromImage)
-{
- if (nullptr == dataNode)
- {
- return;
- }
-
- std::map<mitk::DataNode::ConstPointer, QPixmap>::iterator iter = m_PixmapMap.find(dataNode);
- if (iter != m_PixmapMap.end())
- {
- // key already existing
- if (nullptr != pixmapFromImage)
- {
- // overwrite already stored pixmap
- iter->second = pixmapFromImage->scaled(120, 120, Qt::IgnoreAspectRatio);
- }
- else
- {
- // remove key if no pixmap is given
- m_PixmapMap.erase(iter);
- }
- }
- else
- {
- m_PixmapMap.insert(std::make_pair(dataNode, pixmapFromImage->scaled(120, 120, Qt::IgnoreAspectRatio)));
- }
-}
-
-void QmitkPatientTableModel::SetLesionPresences()
-{
- m_LesionPresence.clear();
- if (!mitk::SemanticRelationsInference::InstanceExists(m_CaseID, m_Lesion))
- {
- return;
- }
-
- for (const auto& dataNode : m_CurrentDataNodes)
- {
- if (!mitk::SemanticRelationsInference::InstanceExists(dataNode))
- {
- continue;
- }
-
- // set the lesion presence for the current node
- bool lesionPresence = mitk::SemanticRelationsInference::IsLesionPresent(m_Lesion, dataNode);
- SetLesionPresenceOfNode(dataNode, lesionPresence);
- }
-}
-
-void QmitkPatientTableModel::SetLesionPresenceOfNode(const mitk::DataNode* dataNode, bool lesionPresence)
-{
- std::map<mitk::DataNode::ConstPointer, bool>::iterator iter = m_LesionPresence.find(dataNode);
- if (iter != m_LesionPresence.end())
- {
- // key already existing, overwrite already stored bool value
- iter->second = lesionPresence;
- }
- else
- {
- m_LesionPresence.insert(std::make_pair(dataNode, lesionPresence));
- }
-}
-
-mitk::DataNode* QmitkPatientTableModel::GetCurrentDataNode(const QModelIndex& index) const
-{
- if (!index.isValid())
- {
- return nullptr;
- }
-
- auto examinationPeriod = m_ExaminationPeriods.at(index.column());
- auto currentInformationType = m_InformationTypes.at(index.row());
- auto controlPointsOfExaminationPeriod = examinationPeriod.controlPointUIDs;
- for (const auto& controlPointUID : controlPointsOfExaminationPeriod)
- {
- auto currentControlPoint = mitk::GetControlPointByUID(m_CaseID, controlPointUID);
- try
- {
- std::vector<mitk::DataNode::Pointer> filteredDataNodes;
- if ("Image" == m_SelectedNodeType)
- {
- filteredDataNodes = m_SemanticRelationsDataStorageAccess->GetAllSpecificImages(m_CaseID, currentControlPoint, currentInformationType);
- }
- else if ("Segmentation" == m_SelectedNodeType)
- {
- filteredDataNodes = m_SemanticRelationsDataStorageAccess->GetAllSpecificSegmentations(m_CaseID, currentControlPoint, currentInformationType);
- }
-
- if (filteredDataNodes.empty())
- {
- // try next control point
- continue;
- }
- else
- {
- // found a specific image
- return filteredDataNodes.front();
- }
- }
- catch (const mitk::SemanticRelationException&)
- {
- return nullptr;
- }
- }
- // could not find a specif image
- return nullptr;
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkSemanticRelationsUIHelper.cpp b/Modules/SemanticRelationsUI/src/QmitkSemanticRelationsUIHelper.cpp
deleted file mode 100644
index cce4954a44..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkSemanticRelationsUIHelper.cpp
+++ /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.
-
-============================================================================*/
-
-// semantic relations ui module
-#include <QmitkSemanticRelationsUIHelper.h>
-
-// mitk core
-#include <mitkExtractSliceFilter.h>
-#include <vtkMitkLevelWindowFilter.h>
-#include <mitkPlanarFigure.h>
-#include <mitkPropertyNameHelper.h>
-
-// vtk
-#include <vtkLookupTable.h>
-
-QPixmap QmitkSemanticRelationsUIHelper::GetPixmapFromImageNode(const mitk::DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- return QPixmap();
- }
-
- const mitk::Image* image = static_cast<const mitk::Image*>(dataNode->GetData());
- if (nullptr == image || !image->IsInitialized())
- {
- return QPixmap();
- }
-
- if (image->GetPixelType().GetNumberOfComponents() != 1) // for now only single component are allowed
- {
- return QPixmap();
- }
-
- mitk::PlaneGeometry::Pointer sagittalPlaneGeometry = mitk::PlaneGeometry::New();
- int sliceNumber = image->GetDimension(1) / 2;
- sagittalPlaneGeometry->InitializeStandardPlane(image->GetGeometry(), mitk::AnatomicalPlane::Sagittal, sliceNumber);
-
- mitk::ExtractSliceFilter::Pointer extractSliceFilter = mitk::ExtractSliceFilter::New();
- extractSliceFilter->SetInput(image);
- extractSliceFilter->SetInterpolationMode(mitk::ExtractSliceFilter::RESLICE_CUBIC);
- extractSliceFilter->SetResliceTransformByGeometry(image->GetGeometry());
- extractSliceFilter->SetWorldGeometry(sagittalPlaneGeometry);
- extractSliceFilter->SetOutputDimensionality(2);
- extractSliceFilter->SetVtkOutputRequest(true);
- extractSliceFilter->Update();
-
- /*
- mitk::Vector3D spacing;
- mitk::FillVector3D(spacing,1.0,1.0,1.0);
- slice->GetGeometry()->SetSpacing(spacing);
- // save image slice
- mitk::IOUtil::SaveImage( slice, d->m_Path + fileName + ".png" );
- */
-
- vtkImageData* imageData = extractSliceFilter->GetVtkOutput();
-
- mitk::LevelWindow levelWindow;
- dataNode->GetLevelWindow(levelWindow);
- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
- lookupTable->SetRange(levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound());
- lookupTable->SetSaturationRange(0.0, 0.0);
- lookupTable->SetValueRange(0.0, 1.0);
- lookupTable->SetHueRange(0.0, 0.0);
- lookupTable->SetRampToLinear();
-
- vtkSmartPointer<vtkMitkLevelWindowFilter> levelWindowFilter = vtkSmartPointer<vtkMitkLevelWindowFilter>::New();
- levelWindowFilter->SetLookupTable(lookupTable);
- levelWindowFilter->SetInputData(imageData);
- levelWindowFilter->SetMinOpacity(0.0);
- levelWindowFilter->SetMaxOpacity(1.0);
- int dims[3];
- imageData->GetDimensions(dims);
- double clippingBounds[] = { 0.0, static_cast<double>(dims[0]), 0.0, static_cast<double>(dims[1]) };
- levelWindowFilter->SetClippingBounds(clippingBounds);
- levelWindowFilter->Update();
- imageData = levelWindowFilter->GetOutput();
-
- QImage thumbnailImage(reinterpret_cast<const unsigned char*>(imageData->GetScalarPointer()), dims[0], dims[1], QImage::Format_ARGB32);
-
- thumbnailImage = thumbnailImage.rgbSwapped().mirrored(false, true);
- return QPixmap::fromImage(thumbnailImage);
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkStatisticsCalculator.cpp b/Modules/SemanticRelationsUI/src/QmitkStatisticsCalculator.cpp
deleted file mode 100644
index 01e9882c3b..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkStatisticsCalculator.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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkStatisticsCalculator.h"
-
-// semantic relations module
-#include <mitkNodePredicates.h>
-#include <mitkRelationStorage.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsDataStorageAccess.h>
-#include <mitkSemanticRelationsInference.h>
-
-// mitk image statistics module
-#include <mitkImageStatisticsContainerManager.h>
-#include <mitkImageStatisticsContainerNodeHelper.h>
-#include <mitkStatisticsToImageRelationRule.h>
-#include <mitkStatisticsToMaskRelationRule.h>
-
-QmitkStatisticsCalculator::QmitkStatisticsCalculator()
- : m_CalculationJob(nullptr)
- , m_DataStorage(nullptr)
- , m_MaskVolume(0.0)
-{
- m_CalculationJob = new QmitkImageStatisticsCalculationJob();
-
- connect(m_CalculationJob, &QmitkImageStatisticsCalculationJob::finished, this,
- &QmitkStatisticsCalculator::OnStatisticsCalculationEnds, Qt::QueuedConnection);
-}
-
-QmitkStatisticsCalculator::~QmitkStatisticsCalculator()
-{
- if (!m_CalculationJob->isFinished())
- {
- m_CalculationJob->terminate();
- m_CalculationJob->wait();
- }
- m_CalculationJob->deleteLater();
-}
-
-void QmitkStatisticsCalculator::ComputeLesionVolume(mitk::LesionData& lesionData, const mitk::SemanticTypes::CaseID& caseID)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- std::vector<double> lesionVolume;
- mitk::SemanticTypes::Lesion lesion = lesionData.GetLesion();
- double volume = 0.0;
-
- mitk::SemanticTypes::ControlPointVector controlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- // sort the vector of control points for the timeline
- std::sort(controlPoints.begin(), controlPoints.end());
- mitk::SemanticTypes::InformationTypeVector informationTypes = mitk::RelationStorage::GetAllInformationTypesOfCase(caseID);
- for (const auto& informationType : informationTypes)
- {
- for (const auto& controlPoint : controlPoints)
- {
- mitk::SemanticRelationsDataStorageAccess semanticRelationsDataStorageAccess(dataStorage);
- mitk::DataNode::Pointer specificImage;
- mitk::DataNode::Pointer specificSegmentation;
- try
- {
- specificSegmentation = semanticRelationsDataStorageAccess.GetSpecificSegmentation(caseID, controlPoint, informationType, lesion);
- if (nullptr == specificSegmentation)
- {
- volume = 0.0;
- }
- else
- {
- // get parent node of the specific segmentation node with the node predicate
- auto parentNodes = dataStorage->GetSources(specificSegmentation, mitk::NodePredicates::GetImagePredicate(), false);
- for (auto it = parentNodes->Begin(); it != parentNodes->End(); ++it)
- {
- specificImage = it->Value();
- }
-
- volume = GetSegmentationMaskVolume(specificImage, specificSegmentation);
- }
- }
- catch (mitk::SemanticRelationException&)
- {
- volume = 0.0;
- }
-
- lesionVolume.push_back(volume);
- }
- }
-
- lesionData.SetLesionVolume(lesionVolume);
-}
-
-double QmitkStatisticsCalculator::GetSegmentationMaskVolume(mitk::DataNode::Pointer imageNode, mitk::DataNode::Pointer segmentationNode)
-{
- m_MaskVolume = 0.0;
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return m_MaskVolume;
- }
-
- if (imageNode.IsNull() || segmentationNode.IsNull())
- {
- return m_MaskVolume;
- }
-
- m_ImageNode = imageNode;
- m_SegmentationNode = segmentationNode;
-
- auto image = dynamic_cast<mitk::Image*>(m_ImageNode->GetData());
- auto segmentation = dynamic_cast<mitk::Image*>(m_SegmentationNode->GetData());
- if (nullptr == image || nullptr == segmentation)
- {
- return m_MaskVolume;
- }
-
- // all nodes and images are valid, retrieve statistics
- mitk::ImageStatisticsContainer::ConstPointer imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(dataStorage, image, segmentation).GetPointer();
-
- bool imageStatisticsOlderThanInputs = false;
- if (imageStatistics && (imageStatistics->GetMTime() < image->GetMTime() || (imageStatistics->GetMTime() < segmentation->GetMTime())))
- {
- imageStatisticsOlderThanInputs = true;
- }
- // statistics need to be (re)computed
- if (!imageStatistics || imageStatisticsOlderThanInputs)
- {
- m_CalculationJob->Initialize(image, segmentation, nullptr);
- try
- {
- m_CalculationJob->start();
- return m_MaskVolume;
- }
- catch (const std::exception&)
- {
- return m_MaskVolume;
- }
- }
-
- // use a valid statistics object to get the volume of the image-segmentation pair
- mitk::ImageStatisticsContainer::ImageStatisticsObject statisticsObject;
- try
- {
- statisticsObject = imageStatistics->GetStatisticsForTimeStep(0);
- }
- catch (mitk::Exception&)
- {
- return m_MaskVolume;
- }
- try
- {
- if (statisticsObject.HasStatistic(mitk::ImageStatisticsConstants::VOLUME()))
- {
- auto valueVariant = statisticsObject.GetValueNonConverted(mitk::ImageStatisticsConstants::VOLUME());
- m_MaskVolume = boost::get<double>(valueVariant);
- }
- }
- catch (mitk::Exception&)
- {
- return m_MaskVolume;
- }
-
- return m_MaskVolume;
-}
-
-void QmitkStatisticsCalculator::OnStatisticsCalculationEnds()
-{
- // taken from 'QmitkImageStatisticsView' (see measurementtoolbox plugin)
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- if (m_CalculationJob->GetStatisticsUpdateSuccessFlag())
- {
- auto statistic = m_CalculationJob->GetStatisticsData();
- auto image = m_CalculationJob->GetStatisticsImage();
- mitk::BaseData::ConstPointer mask = nullptr;
- auto imageRule = mitk::StatisticsToImageRelationRule::New();
- imageRule->Connect(statistic, image);
-
- if (m_CalculationJob->GetMaskImage())
- {
- auto maskRule = mitk::StatisticsToMaskRelationRule::New();
- mask = m_CalculationJob->GetMaskImage();
- maskRule->Connect(statistic, mask);
- }
-
- auto imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(dataStorage, image, mask);
-
- // if statistics base data already exist: add to existing node
- if (nullptr != imageStatistics)
- {
- auto allDataNodes = dataStorage->GetAll()->CastToSTLConstContainer();
- for (auto node : allDataNodes)
- {
- auto nodeData = node->GetData();
- if (nullptr != nodeData && nodeData->GetUID() == imageStatistics->GetUID())
- {
- node->SetData(statistic);
- }
- }
- }
- // statistics base data does not exist: add new node
- else
- {
- auto statisticsNodeName = m_ImageNode->GetName();
- if (m_SegmentationNode)
- {
- statisticsNodeName += "_" + m_SegmentationNode->GetName();
- }
- statisticsNodeName += "_statistics";
- auto statisticsNode = mitk::CreateImageStatisticsNode(statistic, statisticsNodeName);
- dataStorage->Add(statisticsNode);
- }
- }
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkStatisticsTreeModel.cpp b/Modules/SemanticRelationsUI/src/QmitkStatisticsTreeModel.cpp
deleted file mode 100644
index 110bff79dc..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkStatisticsTreeModel.cpp
+++ /dev/null
@@ -1,268 +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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkStatisticsTreeModel.h"
-
-// semantic relations module
-#include <mitkControlPointManager.h>
-#include <mitkLesionManager.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkRelationStorage.h>
-
-QmitkStatisticsTreeModel::QmitkStatisticsTreeModel(QObject* parent/* = nullptr*/)
- : QmitkAbstractSemanticRelationsStorageModel(parent)
- , m_RootItem(std::make_shared<QmitkLesionTreeItem>(mitk::LesionData()))
-{
- m_StatisticsCalculator = std::make_unique<QmitkStatisticsCalculator>();
-}
-
-//////////////////////////////////////////////////////////////////////////
-// overridden virtual functions from QAbstractItemModel
-//////////////////////////////////////////////////////////////////////////
-QModelIndex QmitkStatisticsTreeModel::index(int row, int column, const QModelIndex& itemIndex) const
-{
- if (!hasIndex(row, column, itemIndex))
- {
- return QModelIndex();
- }
-
- auto childItem = GetItemByIndex(itemIndex)->GetChildInRow(row);
- if (nullptr == childItem)
- {
- return QModelIndex();
- }
-
- return createIndex(row, column, childItem.get());
-}
-
-QModelIndex QmitkStatisticsTreeModel::parent(const QModelIndex& itemIndex) const
-{
- if (!itemIndex.isValid())
- {
- return QModelIndex();
- }
-
- auto parentItemWeakPtr = GetItemByIndex(itemIndex)->GetParent();
- if (parentItemWeakPtr.expired())
- {
- return QModelIndex();
- }
-
- auto parentItem = parentItemWeakPtr.lock();
- if (parentItem == m_RootItem)
- {
- return QModelIndex();
- }
-
- return createIndex(parentItem->GetRow(), 0, parentItem.get());
-}
-
-int QmitkStatisticsTreeModel::rowCount(const QModelIndex& itemIndex/* = QModelIndex()*/) const
-{
- return GetItemByIndex(itemIndex)->ChildCount();
-}
-
-int QmitkStatisticsTreeModel::columnCount(const QModelIndex&/* itemIndex = QModelIndex() */) const
-{
- if (0 == m_RootItem->ChildCount())
- {
- // no lesion items stored, no need to display columns
- return 0;
- }
-
- return m_ControlPoints.size() + 1;
-}
-
-QVariant QmitkStatisticsTreeModel::data(const QModelIndex& index, int role) const
-{
- if (!index.isValid())
- {
- return QVariant();
- }
-
- if (index.column() < 0 || index.column() > static_cast<int>(m_ControlPoints.size()))
- {
- return QVariant();
- }
-
- QmitkLesionTreeItem* currentItem = GetItemByIndex(index);
- if (Qt::DisplayRole == role)
- {
- if (currentItem->GetParent().expired())
- {
- return QVariant();
- }
-
- auto parentItem = currentItem->GetParent().lock();
- // parent exists and is the root item -> top level item
- if (m_RootItem == parentItem)
- {
- // display role fills the first columns with the lesion UID / name
- if (0 == index.column())
- {
- std::string itemString = currentItem->GetData().GetLesionName();
- if (itemString.empty())
- {
- itemString = currentItem->GetData().GetLesionUID();
- }
- return QString::fromStdString(itemString);
- }
- }
- // parent is not the root item -> volume item
- else
- {
- // display role fills the first columns with the information type
- if (0 == index.column())
- {
- if (index.row() < static_cast<int>(m_InformationTypes.size()))
- {
- return QString::fromStdString(m_InformationTypes.at(index.row()));
- }
- return "N/A";
- }
- else
- {
- // display role fills other columns with the lesion volume info
- const auto lesionVolume = currentItem->GetData().GetLesionVolume();
- if ((index.column() - 1) * index.row() < static_cast<int>(lesionVolume.size()))
- {
- return QVariant(lesionVolume.at(index.row()*m_ControlPoints.size() + (index.column() - 1)));
- }
- return "N/A";
- }
- }
- }
-
- return QVariant();
-}
-
-QVariant QmitkStatisticsTreeModel::headerData(int section, Qt::Orientation orientation, int role) const
-{
- if (0 == m_RootItem->ChildCount())
- {
- // no lesion items stored, no need to display the header
- return QVariant();
- }
-
- if (Qt::Horizontal == orientation && Qt::DisplayRole == role)
- {
- if (0 == section)
- {
- return QVariant("Lesion");
- }
-
- if (static_cast<int>(m_ControlPoints.size()) >= section)
- {
- mitk::SemanticTypes::ControlPoint currentControlPoint = m_ControlPoints.at(section-1);
- return QVariant(QString::fromStdString(currentControlPoint.ToString()));
- }
- }
-
- return QVariant();
-}
-
-void QmitkStatisticsTreeModel::DataStorageChanged()
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNotNull())
- {
- m_SemanticRelationsDataStorageAccess = std::make_unique<mitk::SemanticRelationsDataStorageAccess>(dataStorage);
- m_StatisticsCalculator->SetDataStorage(dataStorage);
- UpdateModelData();
- }
-}
-
-void QmitkStatisticsTreeModel::NodeAdded(const mitk::DataNode*)
-{
- emit beginResetModel();
- UpdateModelData();
- emit endResetModel();
-}
-
-void QmitkStatisticsTreeModel::NodeChanged(const mitk::DataNode*)
-{
- emit beginResetModel();
- UpdateModelData();
- emit endResetModel();
-}
-
-void QmitkStatisticsTreeModel::NodeRemoved(const mitk::DataNode*)
-{
- emit beginResetModel();
- UpdateModelData();
- emit endResetModel();
-}
-
-void QmitkStatisticsTreeModel::SetData()
-{
- m_RootItem = std::make_shared<QmitkLesionTreeItem>(mitk::LesionData());
-
- // get all control points of current case
- m_ControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(m_CaseID);
- // sort the vector of control points for the timeline
- std::sort(m_ControlPoints.begin(), m_ControlPoints.end());
-
- // get all information types points of current case
- m_InformationTypes = mitk::RelationStorage::GetAllInformationTypesOfCase(m_CaseID);
-
- SetLesionData();
-}
-
-void QmitkStatisticsTreeModel::SetLesionData()
-{
- m_CurrentLesions = mitk::RelationStorage::GetAllLesionsOfCase(m_CaseID);
- for (auto& lesion : m_CurrentLesions)
- {
- AddLesion(lesion);
- }
-}
-
-void QmitkStatisticsTreeModel::AddLesion(const mitk::SemanticTypes::Lesion& lesion)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- // create new lesion tree item data and modify it according to the control point data
- mitk::LesionData lesionData(lesion);
- m_StatisticsCalculator->ComputeLesionVolume(lesionData, m_CaseID);
-
- // add the 1. level lesion item to the root item
- std::shared_ptr<QmitkLesionTreeItem> newLesionTreeItem = std::make_shared<QmitkLesionTreeItem>(lesionData);
- m_RootItem->AddChild(newLesionTreeItem);
-
- for (size_t i = 0; i < m_InformationTypes.size(); ++i)
- {
- std::shared_ptr<QmitkLesionTreeItem> volumeItem = std::make_shared<QmitkLesionTreeItem>(lesionData);
- newLesionTreeItem->AddChild(volumeItem);
- }
-}
-
-QmitkLesionTreeItem* QmitkStatisticsTreeModel::GetItemByIndex(const QModelIndex& index) const
-{
- if (index.isValid())
- {
- auto item = static_cast<QmitkLesionTreeItem*>(index.internalPointer());
- if (nullptr != item)
- {
- return item;
- }
- }
-
- return m_RootItem.get();
-}
diff --git a/Modules/SemanticRelationsUI/src/QmitkTableItemThumbnailDelegate.cpp b/Modules/SemanticRelationsUI/src/QmitkTableItemThumbnailDelegate.cpp
deleted file mode 100644
index 14dcc8f776..0000000000
--- a/Modules/SemanticRelationsUI/src/QmitkTableItemThumbnailDelegate.cpp
+++ /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.
-
-============================================================================*/
-
-// semantic relations UI module
-#include "QmitkTableItemThumbnailDelegate.h"
-
-// qt
-#include <QApplication>
-#include <QPainter>
-#include <QStyle>
-
-QmitkTableItemThumbnailDelegate::QmitkTableItemThumbnailDelegate(QObject* parent /*= nullptr*/)
- : QStyledItemDelegate(parent)
-{
- // nothing here
-}
-
-void QmitkTableItemThumbnailDelegate::paint(QPainter* painter, const QStyleOptionViewItem& option, const QModelIndex& index) const
-{
- QPixmap pixmap = index.data(Qt::DecorationRole).value<QPixmap>();
- QPoint point = option.rect.center() - pixmap.rect().center();
- painter->save();
-
- if (option.state & QStyle::State_Selected)
- {
- painter->setBrush(option.palette.highlightedText());
- const QWidget* widget = option.widget;
- QStyle* style = widget ? widget->style() : QApplication::style();
- style->drawControl(QStyle::CE_ItemViewItem, &option, painter, widget);
- }
- painter->drawPixmap(point, pixmap);
- painter->restore();
-}
diff --git a/Modules/SemanticRelationsUI/src/mitkModuleActivator.cpp b/Modules/SemanticRelationsUI/src/mitkModuleActivator.cpp
deleted file mode 100644
index dfd9482aab..0000000000
--- a/Modules/SemanticRelationsUI/src/mitkModuleActivator.cpp
+++ /dev/null
@@ -1,31 +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 "mitkModuleActivator.h"
-
-// semantic relations ui module
-#include "QmitkPatientTableInspector.h"
-
-// qt widgets module
-#include "QmitkDataStorageInspectorProviderBase.h"
-
-void mitk::SemanticRelationsUIActivator::Load(us::ModuleContext* /*context*/)
-{
- m_PatientTableInspector.reset(new QmitkDataStorageInspectorProviderBase<QmitkPatientTableInspector>("org.mitk.QmitkPatientTableInspector",
- "Patient table inspector", "Displays the content of the semantic relations storage in a control-point - modality table."));
- }
-
-void mitk::SemanticRelationsUIActivator::Unload(us::ModuleContext* /*context*/)
-{
-}
-
-US_EXPORT_MODULE_ACTIVATOR(mitk::SemanticRelationsUIActivator)
diff --git a/Modules/TubeGraph/CMakeLists.txt b/Modules/TubeGraph/CMakeLists.txt
deleted file mode 100644
index 13e719c1a9..0000000000
--- a/Modules/TubeGraph/CMakeLists.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-MITK_CREATE_MODULE(
- INCLUDE_DIRS PRIVATE src/Algorithms src/DataStructure src/Interactions src/Rendering src/IO
- DEPENDS MitkSceneSerializationBase
-)
-
-#add_subdirectory(test)
diff --git a/Modules/TubeGraph/files.cmake b/Modules/TubeGraph/files.cmake
deleted file mode 100644
index 8cd0a31a02..0000000000
--- a/Modules/TubeGraph/files.cmake
+++ /dev/null
@@ -1,21 +0,0 @@
-file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*")
-
-set(CPP_FILES
- DataStructure/mitkCircularProfileTubeElement.cpp
- DataStructure/mitkTubeGraph.cpp
- DataStructure/mitkTubeGraphEdge.cpp
- DataStructure/mitkTubeGraphVertex.cpp
- Interactions/mitkTubeGraphDataInteractor.cpp
- Interactions/mitkTubeGraphPicker.cpp
- IO/mitkTubeGraphDefinitions.cpp
- IO/mitkTubeGraphIO.cpp
- IO/mitkTubeGraphModuleActivator.cpp
- IO/mitkTubeGraphObjectFactory.cpp
- Rendering/mitkTubeGraphProperty.cpp
- Rendering/mitkTubeGraphVtkMapper3D.cpp
-)
-
-set(RESOURCE_FILES
- Interactions/TubeGraphConfig.xml
- Interactions/TubeGraphInteraction.xml
-)
diff --git a/Modules/TubeGraph/include/mitkCircularProfileTubeElement.h b/Modules/TubeGraph/include/mitkCircularProfileTubeElement.h
deleted file mode 100644
index 33a8d8f961..0000000000
--- a/Modules/TubeGraph/include/mitkCircularProfileTubeElement.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 mitkCircularProfileTubeElement_h
-#define mitkCircularProfileTubeElement_h
-
-#include <MitkTubeGraphExports.h>
-
-#include "mitkTubeElement.h"
-
-namespace mitk
-{
- /**
- * \brief Class for elements which describes tubular structur with a circular cross section.
- */
- class MITKTUBEGRAPH_EXPORT CircularProfileTubeElement : virtual public TubeElement
- {
- public:
- CircularProfileTubeElement();
- CircularProfileTubeElement(float x, float y, float z, float d = 0.0f);
- CircularProfileTubeElement(const Point3D, float d = 0.0f);
- ~CircularProfileTubeElement() override;
-
- /**
- * Set the 3D position of the element.
- */
- void SetCoordinates(Point3D coordinates) override;
-
- /**
- * Returns the 3D position of the element.
- */
- const Point3D &GetCoordinates() const override;
-
- /**
- * Set the diameter of the circle.
- */
- void SetDiameter(float d);
-
- /**
- * Returns the diameter of the circle.
- */
- float GetDiameter() const;
-
- /**
- * Comparison operation between this object and the given object.
- * @param right The object to compare with.
- * @return true, if the object is the same;false, if not.
- */
- bool operator==(const TubeElement &right) const override;
-
- private:
- Point3D m_coordinates;
- float m_diameter;
-
- }; // class
-
-} // namespace
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeElement.h b/Modules/TubeGraph/include/mitkTubeElement.h
deleted file mode 100644
index 6290cb40f5..0000000000
--- a/Modules/TubeGraph/include/mitkTubeElement.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 mitkTubeElement_h
-#define mitkTubeElement_h
-
-#include <MitkTubeGraphExports.h>
-
-#include <mitkPoint.h>
-
-namespace mitk
-{
- /**
- * \brief Abstract class for elements which describes tubular structur.
- */
- class MITKTUBEGRAPH_EXPORT TubeElement
- {
- public:
- virtual ~TubeElement(){};
-
- /**
- * Set the 3D position of the element.
- */
- virtual void SetCoordinates(Point3D coordinates) = 0;
-
- /**
- * Returns the 3D position of the element.
- */
- virtual const Point3D &GetCoordinates() const = 0;
-
- /**
- * Comparison operation between this object and the given object.
- * @param right The object to compare with.
- * @return true, if the object is the same;false, if not.
- */
- virtual bool operator==(const TubeElement &right) const = 0;
-
- }; // class
-
-} // namespace
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraph.h b/Modules/TubeGraph/include/mitkTubeGraph.h
deleted file mode 100644
index 10aa38ce70..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraph.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.
-
-============================================================================*/
-
-#ifndef mitkTubeGraph_h
-#define mitkTubeGraph_h
-
-#include <MitkTubeGraphExports.h>
-
-#include "mitkTubeGraphEdge.h"
-#include "mitkTubeGraphVertex.h"
-#include "mitkUndirectedGraph.h"
-
-#ifdef _MSC_VER
-# pragma warning(push)
-# pragma warning(disable: 4172) // boost/graph/named_function_params.hpp(240): returning address of local variable or temporary
-#endif
-
-#include <boost/graph/undirected_dfs.hpp>
-#include <boost/graph/visitors.hpp>
-#include <boost/property_map/property_map.hpp>
-
-#include <boost/graph/breadth_first_search.hpp>
-#include <boost/pending/property.hpp>
-
-#ifdef _MSC_VER
-# pragma warning(pop)
-#endif
-
-namespace mitk
-{
- /**
- * \brief Base Class for Tube Graphs
- */
- class MITKTUBEGRAPH_EXPORT TubeGraph : public UndirectedGraph<TubeGraphVertex, TubeGraphEdge>
- {
- public:
- /**
- * Defines the type of the id of a single tube. It is allways the source and target descriptor: [uint, uint]
- */
- typedef std::pair<VertexDescriptorType, VertexDescriptorType> TubeDescriptorType;
-
- typedef boost::adjacency_list<boost::vecS,
- boost::vecS,
- boost::directedS // directed graph
- >
- DirectedGraphType;
-
- /**
- * Represents a tube id which may not occur. This may be used
- * for error states or for indicating that something went wrong.
- */
- static const TubeDescriptorType ErrorId;
-
- //--- Macros ---//
- mitkClassMacro(TubeGraph, Superclass);
- itkNewMacro(Self);
-
- /**
- * Search only the shortest path between two tubes.
- */
- std::vector<TubeDescriptorType> SearchShortestPath(
- const TubeDescriptorType &startTube, const TubeDescriptorType &endTube /*, std::vector<unsigned long> barrier*/);
-
- /**
- * Search every path between two tubes.
- */
- std::vector<TubeDescriptorType> SearchAllPathBetweenVertices(
- const TubeDescriptorType &startTube, const TubeDescriptorType &endTube /*, std::vector<unsigned long> barrier*/);
- std::vector<TubeDescriptorType> SearchPathToPeriphery(
- const TubeDescriptorType &startTube /*, std::vector<unsigned long> barrier*/);
-
- /**
- * Find thickest tube in the graph. This means the tube which has the element with the largest diameter.
- */
- TubeDescriptorType GetThickestTube();
-
- /**
- * Get this undirected graph as a directed graph. For this convertation you need a start point.
- */
- DirectedGraphType GetDirectedGraph(VertexDescriptorType startVertex);
-
- /**
- * Create a subgraph with all given tubes. The origin graph would not be changed.
- */
- TubeGraph::Pointer CreateSubGraph(std::vector<TubeDescriptorType> subGraphTubes);
-
- /**
- * Remove a part of the graph. All tubes, that means all edges and if necessary also the vertex (no other out-edge)
- * of the tube will be deleted.
- */
- void RemoveSubGraph(std::vector<TubeDescriptorType> deletedTubes);
-
- void SetRootTube(const TubeDescriptorType &root);
- void SetRoot(const VertexDescriptorType &root);
- TubeDescriptorType GetRootTube();
- VertexDescriptorType GetRootVertex();
-
- protected:
- TubeGraph();
- TubeGraph(const TubeGraph &graph);
- ~TubeGraph() override;
-
- TubeGraph &operator=(const TubeGraph &rhs);
-
- private:
- TubeDescriptorType m_RootTube;
- VertexDescriptorType m_Root;
-
- void GetOutEdgesOfAVertex(VertexDescriptorType vertex,
- DirectedGraphType &directedGraph,
- std::vector<TubeDescriptorType> &pathToPeriphery);
- };
-
- /**
- * Defines a own graph visitor for breadth-first-search.
- * This visitor should be create a new directed graph by passing the edges of a undirected graph.
- */
- class DirectedGraphBfsVisitor : public boost::default_bfs_visitor
- {
- public:
- DirectedGraphBfsVisitor(TubeGraph *oldGraph, TubeGraph::DirectedGraphType &newGraph)
- : m_OrignialGraph(oldGraph), m_DirectedGraph(newGraph)
- {
- }
-
- void tree_edge(TubeGraph::EdgeDescriptorType e, const TubeGraph::GraphType &g)
- {
- unsigned int numberSource = boost::source(e, g);
- unsigned int numberTarget = boost::target(e, g);
- boost::graph_traits<TubeGraph::DirectedGraphType>::vertex_descriptor source = numberSource;
- boost::graph_traits<TubeGraph::DirectedGraphType>::vertex_descriptor target = numberTarget;
-
- boost::add_edge(source, target, m_DirectedGraph);
- }
-
- private:
- TubeGraph::Pointer m_OrignialGraph;
- TubeGraph::DirectedGraphType &m_DirectedGraph;
- };
-
-} // namespace mitk
-
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphDataInteractor.h b/Modules/TubeGraph/include/mitkTubeGraphDataInteractor.h
deleted file mode 100644
index 37c09298d5..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphDataInteractor.h
+++ /dev/null
@@ -1,122 +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 mitkTubeGraphDataInteractor_h
-#define mitkTubeGraphDataInteractor_h
-
-#include <MitkTubeGraphExports.h>
-
-#include <mitkBaseRenderer.h>
-#include <mitkDataInteractor.h>
-
-#include "mitkTubeGraph.h"
-#include "mitkTubeGraphProperty.h"
-
-namespace mitk
-{
- // Define events for TubeGraph interaction notifications
- itkEventMacroDeclaration(SelectionChangedTubeGraphEvent, itk::AnyEvent);
-
- /**
- * \brief
- *
- * \ingroup Interaction
- */
- // Inherit from DataInteratcor, this provides functionality of a state machine and configurable inputs.
- class MITKTUBEGRAPH_EXPORT TubeGraphDataInteractor : public DataInteractor
- {
- public:
- mitkClassMacro(TubeGraphDataInteractor, DataInteractor);
- itkNewMacro(Self);
-
- /**
- * Describes, which activation modes are available based on the
- * currently picked tube:
- *
- * \li <b>None</b> means "no tube is active"
- * \li <b>Single</b> means "only the picked tube is active"
- * \li <b>ToRoot</b> means "all tubes from the picked on down to the root of the tube graph are active"
- * \li <b>ToPeriphery</b> means "all tubes included in the subgraph of the currently picked vessel are active"
- * \li <b>Points</b> means "shortes path between two picked tubes are active"
- * \li <b>Multiple</b> means "all picked tubes are active"
- */
- enum ActivationMode
- {
- None = 0,
- Single,
- ToRoot,
- ToPeriphery,
- Points,
- Multiple
- };
-
- enum ActionMode
- {
- AttributationMode = 0,
- AnnotationMode,
- EditMode,
- RootMode,
- InformationMode
- };
-
- void SetActivationMode(const ActivationMode &activationMode);
- ActivationMode GetActivationMode();
-
- void SetActionMode(const ActionMode &actionMode);
- ActionMode GetActionMode();
-
- void ResetPickedTubes();
-
- mitk::Point3D GetLastPickedPosition();
-
- protected:
- TubeGraphDataInteractor();
- ~TubeGraphDataInteractor() override;
-
- /**
- * Here actions strings from the loaded state machine pattern are mapped to functions of
- * the DataInteractor. These functions are called when an action from the state machine pattern is executed.
- */
- void ConnectActionsAndFunctions() override;
-
- /**
- * This function is called when a DataNode has been set/changed.
- */
- void DataNodeChanged() override;
-
- /**
- * Initializes the movement, stores starting position.
- */
- virtual bool CheckOverTube(const InteractionEvent *);
- virtual void SelectTube(StateMachineAction *, InteractionEvent *);
- virtual void DeselectTube(StateMachineAction *, InteractionEvent *);
-
- void SelectTubesByActivationModus();
- void UpdateActivation();
-
- private:
- std::vector<TubeGraph::TubeDescriptorType> GetTubesToRoot();
- std::vector<TubeGraph::TubeDescriptorType> GetTubesBetweenPoints();
- std::vector<TubeGraph::TubeDescriptorType> GetPathToPeriphery();
- std::vector<TubeGraph::TubeDescriptorType> GetPathBetweenTubes(const TubeGraph::TubeDescriptorType &start,
- const TubeGraph::TubeDescriptorType &end);
-
- TubeGraph::Pointer m_TubeGraph;
- TubeGraphProperty::Pointer m_TubeGraphProperty;
- TubeGraph::TubeDescriptorType m_LastPickedTube;
- TubeGraph::TubeDescriptorType m_SecondLastPickedTube;
- ActivationMode m_ActivationMode;
- ActionMode m_ActionMode;
- mitk::TubeElement *m_LastPickedElement = nullptr;
- };
-}
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphDefinitions.h b/Modules/TubeGraph/include/mitkTubeGraphDefinitions.h
deleted file mode 100644
index d5b4a35fef..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphDefinitions.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkTubeGraphDefinitions_h
-#define mitkTubeGraphDefinitions_h
-
-#include <string>
-
-namespace mitk
-{
- /** \brief The XML consts for reading and writing
- */
-
- class TubeGraphDefinitions
- {
- public:
- //============== XML const chars ===================
-
- //==== Header information ====
- static const std::string XML_TUBEGRAPH_FILE;
- static const std::string XML_FILE_VERSION;
- static const std::string VERSION_STRING;
- static const std::string ASCII_FILE;
- static const std::string FILE_NAME;
-
- //==== Geometry details ====
- static const std::string XML_GEOMETRY;
-
- static const std::string XML_MATRIX_XX;
- static const std::string XML_MATRIX_XY;
- static const std::string XML_MATRIX_XZ;
- static const std::string XML_MATRIX_YX;
- static const std::string XML_MATRIX_YY;
- static const std::string XML_MATRIX_YZ;
- static const std::string XML_MATRIX_ZX;
- static const std::string XML_MATRIX_ZY;
- static const std::string XML_MATRIX_ZZ;
-
- static const std::string XML_ORIGIN_X;
- static const std::string XML_ORIGIN_Y;
- static const std::string XML_ORIGIN_Z;
-
- static const std::string XML_SPACING_X;
- static const std::string XML_SPACING_Y;
- static const std::string XML_SPACING_Z;
-
- //==== tube graph structures ====
- static const std::string XML_VERTICES;
- static const std::string XML_EDGES;
- static const std::string XML_LABELGROUPS;
- static const std::string XML_ATTRIBUTIONS;
- static const std::string XML_ANNOTATIONS;
- static const std::string XML_VERTEX;
- static const std::string XML_EDGE;
- static const std::string XML_ELEMENT;
- static const std::string XML_LABELGROUP;
- static const std::string XML_LABEL;
- static const std::string XML_ATTRIBUTION;
- static const std::string XML_ANNOTATION;
-
- //==== vertex properties ====
- static const std::string XML_VERTEX_ID;
-
- //==== edge properties ====
- static const std::string XML_EDGE_ID;
- static const std::string XML_EDGE_SOURCE_ID;
- static const std::string XML_EDGE_TARGET_ID;
-
- //==== element properties ====
-
- static const std::string XML_ELEMENT_X;
- static const std::string XML_ELEMENT_Y;
- static const std::string XML_ELEMENT_Z;
- static const std::string XML_ELEMENT_DIAMETER;
-
- //==== label group properties ====
- static const std::string XML_LABELGROUP_NAME;
-
- //==== label properties ====
- static const std::string XML_LABEL_NAME;
- static const std::string XML_LABEL_VISIBILITY;
- static const std::string XML_LABEL_COLOR_R;
- static const std::string XML_LABEL_COLOR_G;
- static const std::string XML_LABEL_COLOR_B;
-
- //==== tube properties ====
- static const std::string XML_TUBE_ID_1;
- static const std::string XML_TUBE_ID_2;
-
- //==== annotation properties ====
- static const std::string XML_ANNOTATION_NAME;
- static const std::string XML_ANNOTATION_DESCRIPTION;
-
- private:
- TubeGraphDefinitions();
- ~TubeGraphDefinitions();
- };
-
-} // namespace MITK
-
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphEdge.h b/Modules/TubeGraph/include/mitkTubeGraphEdge.h
deleted file mode 100644
index 4debead6b3..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphEdge.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 mitkTubeGraphEdge_h
-#define mitkTubeGraphEdge_h
-
-#include <MitkTubeGraphExports.h>
-
-#include "mitkCircularProfileTubeElement.h"
-#include "mitkTubeElement.h"
-#include "mitkTubeGraphVertex.h"
-
-namespace mitk
-{
- /**
- * \brief Base Class for Tube Graph Edges
- */
- class MITKTUBEGRAPH_EXPORT TubeGraphEdge
- {
- public:
- TubeGraphEdge();
- virtual ~TubeGraphEdge();
-
- /**
- * Set the vector which contains all TubeElements.
- * @param elementVector Vector with all TubeElements
- */
- void SetElementVector(std::vector<TubeElement *> elementVector);
-
- /**
- * Returns the vector which contains all TubeElements.
- * @returns vector with all TubeElements.
- */
- std::vector<TubeElement *> GetElementVector();
-
- /**
- * Returns the number of TubeElements which are contained in this tube.
- * @returns Number of TubeElements.
- */
- unsigned int GetNumberOfElements() const;
-
- /**
- * Adds a new TubeElement at the end of this edge.
- * @param element The new TubeElement.
- */
- void AddTubeElement(TubeElement *element);
-
- /**
- * Adds a new TubeElement at the given position.
- * @param position The position for the TubeElement.
- * @param element The new TubeElement.
- */
- void AddTubeElementAt(unsigned int position, TubeElement *element);
-
- /**
- * Returns the TubeElement at the given position.
- * @param position The position of the Element.
- * @returns The TubeElement at the given position.
- */
- TubeElement *GetTubeElement(unsigned int position);
-
- /**
- * Calculates the length of tube graph edge inc. the source and target vertex..
- *
- * @param source the source vertex of the edge
- * @param target the target vertex of the edge
- * @returns the length of the edge in mm
- */
- float GetEdgeLength(TubeGraphVertex &source, TubeGraphVertex &target);
-
- /**
- * Calculates the average diameter of tube graph edge inc. the source and target vertex.
- *
- * @param source the source vertex of the edge
- * @param target the target vertex of the edge
- * @returns the average diameter of the edge
- */
- float GetEdgeAverageDiameter(TubeGraphVertex &source, TubeGraphVertex &target);
-
- /**
- * Comparison operation between this object and the given object.
- * @param right The object to compare with.
- * @return true, if the object is the same;false, if not.
- */
- bool operator==(const TubeGraphEdge &right) const;
-
- private:
- std::vector<TubeElement *> m_ElementVector;
-
- }; // class
-
-} // namespace
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphIO.h b/Modules/TubeGraph/include/mitkTubeGraphIO.h
deleted file mode 100644
index 9be4e611ab..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphIO.h
+++ /dev/null
@@ -1,69 +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 mitkTubeGraphIO_h
-#define mitkTubeGraphIO_h
-
-#include <mitkAbstractFileIO.h>
-#include <mitkCustomMimeType.h>
-#include <mitkIOMimeTypes.h>
-
-#include "mitkTubeGraph.h"
-
-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
diff --git a/Modules/TubeGraph/include/mitkTubeGraphObjectFactory.h b/Modules/TubeGraph/include/mitkTubeGraphObjectFactory.h
deleted file mode 100644
index 3d8548db67..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphObjectFactory.h
+++ /dev/null
@@ -1,51 +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 mitkTubeGraphObjectFactory_h
-#define mitkTubeGraphObjectFactory_h
-
-#include <MitkTubeGraphExports.h>
-
-#include <mitkCoreObjectFactory.h>
-
-namespace mitk
-{
- class MITKTUBEGRAPH_EXPORT TubeGraphObjectFactory : public CoreObjectFactoryBase
- {
- public:
- mitkClassMacro(TubeGraphObjectFactory, CoreObjectFactoryBase);
- itkFactorylessNewMacro(Self);
- itkCloneMacro(Self);
-
- Mapper::Pointer CreateMapper(mitk::DataNode *node, MapperSlotId slotId) override;
- void SetDefaultProperties(mitk::DataNode *node) override;
- std::string GetFileExtensions() override;
- mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap() override;
- std::string GetSaveFileExtensions() override;
- mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap() override;
- void RegisterIOFactories();
-
- protected:
- TubeGraphObjectFactory();
-
- private:
- void CreateFileExtensionsMap();
-
- std::string m_ExternalFileExtensions;
- std::string m_InternalFileExtensions;
- std::string m_SaveFileExtensions;
- MultimapType m_FileExtensionsMap;
- MultimapType m_SaveFileExtensionsMap;
- };
-}
-
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphPicker.h b/Modules/TubeGraph/include/mitkTubeGraphPicker.h
deleted file mode 100644
index 930b16e6a7..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphPicker.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 mitkTubeGraphPicker_h
-#define mitkTubeGraphPicker_h
-
-#include <MitkTubeGraphExports.h>
-
-#include "mitkCircularProfileTubeElement.h"
-#include "mitkTubeGraph.h"
-#include "mitkTubeGraphProperty.h"
-
-namespace mitk
-{
- class MITKTUBEGRAPH_EXPORT TubeGraphPicker
- {
- public:
- /* mitkClassMacro( TubeGraphPicker, BaseDataSource );
- itkNewMacro( Self );*/
-
- void SetTubeGraph(const TubeGraph *tubeGraph);
-
- std::pair<mitk::TubeGraph::TubeDescriptorType, mitk::TubeElement *> GetPickedTube(const Point3D pickedPosition);
-
- TubeGraphPicker();
- virtual ~TubeGraphPicker();
-
- protected:
- Point3D m_WorldPosition;
- TubeGraph::ConstPointer m_TubeGraph;
- TubeGraphProperty::Pointer m_TubeGraphProperty;
- };
-
-} // namespace
-
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphProperty.h b/Modules/TubeGraph/include/mitkTubeGraphProperty.h
deleted file mode 100644
index 95fc651efe..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphProperty.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkTubeGraphProperty_h
-#define mitkTubeGraphProperty_h
-
-#include <MitkTubeGraphExports.h>
-
-#include "mitkTubeGraph.h"
-#include <mitkBaseProperty.h>
-#include <mitkColorProperty.h>
-
-#include <itkObject.h>
-#include <map>
-#include <vector>
-
-namespace mitk
-{
- /**
- * \brief Property for tube graphs
- */
- class MITKTUBEGRAPH_EXPORT TubeGraphProperty : public BaseProperty
- {
- public:
- mitkClassMacro(TubeGraphProperty, BaseProperty);
- itkNewMacro(TubeGraphProperty);
-
- struct LabelGroup
- {
- struct Label
- {
- std::string labelName;
- bool isVisible;
- Color labelColor;
- };
- std::string labelGroupName;
- std::vector<Label *> labels;
- };
-
- ///////////////TYPEDEF///////////////
- typedef TubeGraph::TubeDescriptorType TubeDescriptorType;
- typedef std::vector<TubeGraphProperty::LabelGroup *> LabelGroupSetType;
- typedef std::pair<TubeDescriptorType, std::string> TubeToLabelGroupType;
- /////////////////////////////////////
-
- struct Annotation
- {
- std::string name;
- std::string description;
- TubeDescriptorType tube;
- };
-
- /**
- * Checks, if a given tube is visible
- * @param tube the tube id of the tube to check
- * @returns true, if the tube with id is visible or false otherwise
- */
- bool IsTubeVisible(const TubeDescriptorType &tube);
-
- /**
- * Sets a tube active.
- * @param tube the tube id of the tube, which has to be set active
- * @param active true, if the tube should be active or false if not.
- */
- void SetTubeActive(const TubeDescriptorType &tube, const bool &active);
-
- /**
- * Sets tubes active.
- *
- */
- void SetTubesActive(std::vector<TubeDescriptorType> &tubes);
-
- /**
- * Checks, if a given tube is activated
- * @param tube the to check
- * @returns true, if the tube with id is active or false otherwise
- */
- bool IsTubeActive(const TubeDescriptorType &tube);
-
- std::vector<TubeDescriptorType> GetActiveTubes();
-
- Color GetColorOfTube(const TubeDescriptorType &tube);
-
- void SetTubesToLabels(std::map<TubeToLabelGroupType, std::string> tubeToLabelMap);
-
- std::map<TubeToLabelGroupType, std::string> GetTubesToLabels();
-
- /**
- * Deactivates all tubes
- */
- void DeactivateAllTubes();
-
- void AddAnnotation(Annotation *annotation);
- Annotation *GetAnnotationByName(std::string annotation);
- std::vector<Annotation *> GetAnnotations();
- void RemoveAnnotation(Annotation *annotation);
-
- void AddLabelGroup(LabelGroup *labelGroup, unsigned int position); // Add LG by name and vec<labelName>??
- void RemoveLabelGroup(LabelGroup *labelGroup);
- LabelGroupSetType GetLabelGroups();
- unsigned int GetNumberOfLabelGroups();
- unsigned int GetIndexOfLabelGroup(LabelGroup *labelGroup);
- LabelGroup *GetLabelGroupByName(std::string labelGroup);
-
- void SetLabelVisibility(LabelGroup::Label *label, bool isVisible);
- void SetLabelColor(LabelGroup::Label *label, Color color);
- void RenameLabel(LabelGroup *labelGroup, LabelGroup::Label *label, std::string newName);
- void SetLabelForActivatedTubes(LabelGroup *labelGroup, LabelGroup::Label *label);
-
- LabelGroup::Label *GetLabelByName(LabelGroup *labelGroup, std::string labelName);
-
- std::string GetValueAsString() const override;
-
- bool ToJSON(nlohmann::json& j) const override;
- bool FromJSON(const nlohmann::json& j) override;
-
- protected:
- TubeGraphProperty();
- TubeGraphProperty(const TubeGraphProperty &other);
- ~TubeGraphProperty() override;
-
- private:
- std::vector<TubeDescriptorType> m_ActiveTubes;
- LabelGroupSetType m_LabelGroups;
- std::map<TubeToLabelGroupType, std::string> m_TubeToLabelsMap;
- std::vector<Annotation *> m_Annotations;
-
- bool TubeDescriptorsCompare(const TubeDescriptorType &tube1, const TubeDescriptorType &tube2);
-
- // purposely not implemented
- TubeGraphProperty &operator=(const TubeGraphProperty &);
-
- bool IsEqual(const BaseProperty &property) const override;
- bool Assign(const BaseProperty &property) override;
- itk::LightObject::Pointer InternalClone() const override;
- };
-
-} // namespace mitk
-
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphVertex.h b/Modules/TubeGraph/include/mitkTubeGraphVertex.h
deleted file mode 100644
index 5688b4e8af..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphVertex.h
+++ /dev/null
@@ -1,57 +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 mitkTubeGraphVertex_h
-#define mitkTubeGraphVertex_h
-
-#include <MitkTubeGraphExports.h>
-
-#include "mitkTubeElement.h"
-
-namespace mitk
-{
- /**
- * \brief Base Class for Tube Graph Vertices
- */
- class MITKTUBEGRAPH_EXPORT TubeGraphVertex
- {
- public:
- TubeGraphVertex();
- TubeGraphVertex(TubeElement *element);
- virtual ~TubeGraphVertex();
-
- /**
- * Set the TubeElement which contains the information about diameter and position.
- * @param element The TubeElement for the vertex.
- */
- void SetTubeElement(TubeElement *element);
-
- /**
- * Returns the TubeElement.
- * @returns The TubeElement
- */
- const TubeElement *GetTubeElement() const;
-
- /**
- * Comparison operation between this object and the given object.
- * @param right The object to compare with.
- * @return true, if the object is the same;false, if not.
- */
- bool operator==(const TubeGraphVertex &right) const;
-
- private:
- TubeElement *m_element;
-
- }; // class
-
-} // namespace
-#endif
diff --git a/Modules/TubeGraph/include/mitkTubeGraphVtkMapper3D.h b/Modules/TubeGraph/include/mitkTubeGraphVtkMapper3D.h
deleted file mode 100644
index a2f2bebf7e..0000000000
--- a/Modules/TubeGraph/include/mitkTubeGraphVtkMapper3D.h
+++ /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.
-
-============================================================================*/
-
-#ifndef mitkTubeGraphVtkMapper3D_h
-#define mitkTubeGraphVtkMapper3D_h
-
-#include <MitkTubeGraphExports.h>
-#include <mitkLocalStorageHandler.h>
-
-#include "mitkCircularProfileTubeElement.h"
-#include "mitkTubeGraph.h"
-#include "mitkTubeGraphProperty.h"
-#include "mitkVtkMapper.h"
-
-#include <vtkActor.h>
-#include <vtkAppendPolyData.h>
-#include <vtkAssembly.h>
-#include <vtkPolyData.h>
-#include <vtkSmartPointer.h>
-
-namespace mitk
-{
- /**
- * 3D Mapper for mitk::Graph< TubeGraphVertex, TubeGraphEdge >. This mapper creates tubes
- * around each tubular structure by using vtkTubeFilter.
- *
- */
-
- class MITKTUBEGRAPH_EXPORT TubeGraphVtkMapper3D : public VtkMapper
- {
- public:
- /* Typedefs */
- typedef TubeGraph::EdgeDescriptorType EdgeDescriptorType;
- typedef TubeGraph::VertexDescriptorType VertexDescriptorType;
-
- mitkClassMacro(TubeGraphVtkMapper3D, VtkMapper);
- itkNewMacro(Self);
- /**
- * Returns the input data object of the given filter. In this
- * case, a mitk::Graph< TubeGraphVertex, TubeGraphEdge > is returned.
- */
- virtual const TubeGraph *GetInput();
- vtkProp *GetVtkProp(mitk::BaseRenderer *renderer) override;
-
- protected:
- TubeGraphVtkMapper3D();
- ~TubeGraphVtkMapper3D() override;
-
- /**
- * This method is called, each time a specific renderer is updated.
- */
- void GenerateDataForRenderer(mitk::BaseRenderer *renderer) override;
-
- /**
- * Generate vtkPolyData containing the tube centerlines and
- * sets these as input for a vtkTubeFilter, which generates tubes
- * around the edges. Also generates vtkActors for each vertex. Here
- * the vtkPolyData are vtkSphereSources. All poly data will be clipped
- * with each other on an furcation. So you get end-caps and connecting
- * pieces from the spheres. Clipping the tubes with each other avoids
- * structures within the general view.
- */
- virtual void GenerateTubeGraphData(mitk::BaseRenderer *renderer);
-
- /**
- * Render only the visual information like color or visibility new.
- */
- virtual void RenderTubeGraphPropertyInformation(mitk::BaseRenderer *renderer);
-
- /**
- * Converts a single tube into a vtkPolyData. Each point of the
- * tube surface is labeled with the tube id.
- */
- void GeneratePolyDataForTube(TubeGraphEdge &edge,
- const TubeGraph::Pointer &graph,
- const TubeGraphProperty::Pointer &graphProperty,
- mitk::BaseRenderer *renderer);
- void GeneratePolyDataForFurcation(TubeGraphVertex &vertex,
- const TubeGraph::Pointer &graph,
- mitk::BaseRenderer *renderer);
- void ClipPolyData(TubeGraphVertex &vertex,
- const TubeGraph::Pointer &graph,
- const TubeGraphProperty::Pointer &graphProperty,
- mitk::BaseRenderer *renderer);
-
- private:
- bool ClipStructures();
-
- class LocalStorage : public mitk::Mapper::BaseLocalStorage
- {
- public:
- vtkSmartPointer<vtkAssembly> m_vtkTubeGraphAssembly;
- std::map<TubeGraph::TubeDescriptorType, vtkSmartPointer<vtkActor>> m_vtkTubesActorMap;
- std::map<TubeGraph::VertexDescriptorType, vtkSmartPointer<vtkActor>> m_vtkSpheresActorMap;
-
- itk::TimeStamp m_lastGenerateDataTime;
- itk::TimeStamp m_lastRenderDataTime;
-
- LocalStorage() { m_vtkTubeGraphAssembly = vtkSmartPointer<vtkAssembly>::New(); }
- ~LocalStorage() override {}
- };
-
- LocalStorageHandler<LocalStorage> m_LSH;
- };
-} // namespace
-
-#endif
diff --git a/Modules/TubeGraph/include/mitkUndirectedGraph.h b/Modules/TubeGraph/include/mitkUndirectedGraph.h
deleted file mode 100644
index d59150607d..0000000000
--- a/Modules/TubeGraph/include/mitkUndirectedGraph.h
+++ /dev/null
@@ -1,174 +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 mitkUndirectedGraph_h
-#define mitkUndirectedGraph_h
-
-#include <mitkBaseData.h>
-
-#ifndef Q_MOC_RUN
-#include <boost/graph/adjacency_list.hpp>
-#endif
-
-/* definition of basic boost::graph properties */
-enum vertex_properties_t
-{
- vertex_properties
-};
-enum edge_properties_t
-{
- edge_properties
-};
-
-namespace boost
-{
- BOOST_INSTALL_PROPERTY(vertex, properties);
- BOOST_INSTALL_PROPERTY(edge, properties);
-}
-
-namespace mitk
-{
- /**
- * \brief Template class for undirected graphs.Paramters should be the vertex and edge classes, which contains the
- * information.
- */
- template <class TVertex, class TEdge>
- class UndirectedGraph : public BaseData
- {
- public:
- //--- Typedefs ---//
-
- typedef TVertex VertexType;
- typedef TEdge EdgeType;
- /**
- * Creating the graph type
- * listS: Represents the OutEdgeList as a std::list
- * vecS: Represents the VertexList as a std::vector
- * undirectedS: Representation for an undirected graph
- * VertexProperty: Defines that all vertex are represented by VertexType
- * EdgeProperty: Defines that all edges are represented by EdgeType
- */
- typedef boost::adjacency_list<boost::listS,
- boost::vecS,
- boost::undirectedS, // undirected graph
- boost::property<vertex_properties_t, VertexType>,
- boost::property<edge_properties_t, EdgeType>>
- GraphType;
-
- /* a bunch of graph-specific typedefs */
- typedef typename boost::graph_traits<GraphType>::vertex_descriptor VertexDescriptorType;
- typedef typename boost::graph_traits<GraphType>::edge_descriptor EdgeDescriptorType;
-
- typedef typename boost::graph_traits<GraphType>::vertex_iterator VertexIteratorType;
- typedef typename boost::graph_traits<GraphType>::edge_iterator EdgeIteratorType;
- typedef typename boost::graph_traits<GraphType>::adjacency_iterator AdjacenyIteratorType;
- typedef typename boost::graph_traits<GraphType>::out_edge_iterator OutEdgeIteratorType;
- typedef typename boost::graph_traits<GraphType>::in_edge_iterator InEdgeIteratorType;
-
- //--- Macros ---//
- mitkClassMacro(UndirectedGraph, BaseData);
- itkNewMacro(Self);
-
- // virtual methods that need to be implemented
- void UpdateOutputInformation() override
- {
- if (this->GetSource())
- this->GetSource()->UpdateOutputInformation();
- }
- void SetRequestedRegionToLargestPossibleRegion() override {}
- bool RequestedRegionIsOutsideOfTheBufferedRegion() override { return false; }
- bool VerifyRequestedRegion() override { return true; }
- void SetRequestedRegion(const itk::DataObject *) override {}
- /** Add a new vertex to the graph */
- VertexDescriptorType AddVertex(const VertexType &vertexData);
-
- /** Remove the vertex from the graph */
- void RemoveVertex(const VertexDescriptorType &vertex);
-
- /** Get the vertex data of the given vertex descriptor */
- VertexType GetVertex(const VertexDescriptorType &vertex);
-
- /** Set the vertex data of the given vertex descriptor */
- void SetVertex(const VertexDescriptorType &vertex, const VertexType &vertexData);
-
- /**Returns the descriptor if the vertex exist in the graph, otherwise undefined*/
- VertexDescriptorType GetVertexDescriptor(const VertexType &vertexData) const;
-
- /** Add a new edge between the given vertices to the graph */
- EdgeDescriptorType AddEdge(const VertexDescriptorType &vertexA,
- const VertexDescriptorType &vertexB,
- const EdgeType &edgeData);
-
- /** Remove the edge from the graph */
- void RemoveEdge(const EdgeDescriptorType &edge);
-
- /** Get the edge data of the given edge descriptor */
- EdgeType GetEdge(const EdgeDescriptorType &edge);
-
- /** Set the edge data of the given edge descriptor */
- void SetEdge(const EdgeDescriptorType &edge, const EdgeType &edgeData);
-
- /**Returns the descriptor if the edge exist in the graph, otherwise undefined*/
- EdgeDescriptorType GetEdgeDescriptor(const EdgeType &edgeData) const;
-
- /** Get parent and target vertex of the given edge*/
- std::pair<VertexType, VertexType> GetVerticesOfAnEdge(const EdgeDescriptorType &edge) const;
-
- /** Returns the edge descriptor from the edge which has the given vertices as source and target */
- EdgeDescriptorType GetEdgeDescriptorByVerices(const VertexDescriptorType &vertexA,
- const VertexDescriptorType &vertexB) const;
-
- /** Get all edges of the given vertex */
- std::vector<EdgeType> GetAllEdgesOfAVertex(const VertexDescriptorType &vertex) const;
-
- /** Get overall number of vertices in the graph */
- int GetNumberOfVertices() const;
-
- /** get overall number of edges in the graph */
- int GetNumberOfEdges() const;
-
- /** get vector containing all the vertices of the graph*/
- std::vector<VertexType> GetVectorOfAllVertices() const;
-
- /** get vector containing all the edges of the network */
- std::vector<EdgeType> GetVectorOfAllEdges() const;
-
- /** clear the graph */
- void Clear() override;
-
- /** get the graph */
- const GraphType &GetGraph() const;
-
- UndirectedGraph<VertexType, EdgeType> &operator=(const UndirectedGraph<VertexType, EdgeType> &rhs);
-
- protected:
- UndirectedGraph();
- ~UndirectedGraph() override;
-
- GraphType m_Graph;
-
- private:
- /** property access for vertices */
- VertexType &properties(const VertexDescriptorType &vertex);
- /** property access for vertices */
- const VertexType &properties(const VertexDescriptorType &vertex) const;
- /** property access for edges */
- EdgeType &properties(const EdgeDescriptorType &edge);
- /** property access for edges */
- const EdgeType &properties(const EdgeDescriptorType &edge) const;
- };
-
-} // namespace mitk
-
-#include "mitkUndirectedGraph.txx"
-
-#endif
diff --git a/Modules/TubeGraph/include/mitkUndirectedGraph.txx b/Modules/TubeGraph/include/mitkUndirectedGraph.txx
deleted file mode 100644
index a33c826a72..0000000000
--- a/Modules/TubeGraph/include/mitkUndirectedGraph.txx
+++ /dev/null
@@ -1,336 +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 _mitkUndirectedGraph_txx
-#define _mitkUndirectedGraph_txx
-
-namespace mitk
-{
- template <class TVertex, class TEdge>
- UndirectedGraph<TVertex, TEdge>::UndirectedGraph()
- {
- }
-
- template <class TVertex, class TEdge>
- UndirectedGraph<TVertex, TEdge>::~UndirectedGraph()
- {
- }
-
- template <class TVertex, class TEdge>
- typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType UndirectedGraph<TVertex, TEdge>::AddVertex(
- const typename UndirectedGraph<TVertex, TEdge>::VertexType &vertexData)
- {
- VertexDescriptorType vertex = boost::add_vertex(m_Graph);
- this->properties(vertex) = vertexData;
-
- this->Modified();
-
- return vertex;
- }
-
- template <class TVertex, class TEdge>
- void UndirectedGraph<TVertex, TEdge>::RemoveVertex(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertex)
- {
- boost::clear_vertex(vertex, m_Graph);
- boost::remove_vertex(vertex, m_Graph);
- this->Modified();
- }
-
- template <class TVertex, class TEdge>
- typename UndirectedGraph<TVertex, TEdge>::VertexType UndirectedGraph<TVertex, TEdge>::GetVertex(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertex)
- {
- return this->properties(vertex);
- }
-
- template <class TVertex, class TEdge>
- void UndirectedGraph<TVertex, TEdge>::SetVertex(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertex,
- const typename UndirectedGraph<TVertex, TEdge>::VertexType &vertexData)
- {
- this->properties(vertex) = vertexData;
-
- this->Modified();
- }
-
- template <class TVertex, class TEdge>
- typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType UndirectedGraph<TVertex, TEdge>::GetVertexDescriptor(
- const typename UndirectedGraph<TVertex, TEdge>::VertexType &vertexData) const
- {
- typename UndirectedGraph<TVertex, TEdge>::VertexIteratorType iterator, end;
-
- boost::tie(iterator, end) = boost::vertices(m_Graph);
-
- for (; iterator != end; ++iterator)
- {
- typename UndirectedGraph<TVertex, TEdge>::VertexType tempVertex;
-
- // the value of an iterator is a descriptor
- tempVertex = this->properties(*iterator);
-
- if (vertexData == tempVertex)
- return *iterator;
- }
- MITK_ERROR << "Error in mitkUndirectedGraph::GetVertexDescriptor(...): vertex could not be found." << std::endl;
- throw std::runtime_error(
- "Exception thrown in mitkUndirectedGraph::GetVertexDescriptor(...): vertex could not be found.");
- }
-
- template <class TVertex, class TEdge>
- typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType UndirectedGraph<TVertex, TEdge>::AddEdge(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertexA,
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertexB,
- const typename UndirectedGraph<TVertex, TEdge>::EdgeType &edgeData)
- {
- EdgeDescriptorType edge;
- bool inserted = false;
-
- boost::tie(edge, inserted) = boost::add_edge(vertexA, vertexB, m_Graph);
-
- if (!inserted)
- {
- MITK_ERROR << "Error in mitkUndirectedGraph::addEdge(...): edge could not be inserted." << std::endl;
- throw std::runtime_error("Exception thrown in mitkUndirectedGraph::addEdge(...): edge could not be inserted.");
- }
- this->properties(edge) = edgeData;
-
- this->Modified();
-
- return edge;
- }
-
- template <class TVertex, class TEdge>
- void UndirectedGraph<TVertex, TEdge>::RemoveEdge(
- const typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType &edge)
- {
- boost::remove_edge(edge, m_Graph);
- this->Modified();
- }
-
- template <class TVertex, class TEdge>
- typename UndirectedGraph<TVertex, TEdge>::EdgeType UndirectedGraph<TVertex, TEdge>::GetEdge(
- const typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType &edge)
- {
- return this->properties(edge);
- }
-
- template <class TVertex, class TEdge>
- void UndirectedGraph<TVertex, TEdge>::SetEdge(
- const typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType &edge,
- const typename UndirectedGraph<TVertex, TEdge>::EdgeType &edgeData)
- {
- this->properties(edge) = edgeData;
-
- this->Modified();
- }
-
- template <class TVertex, class TEdge>
- typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType UndirectedGraph<TVertex, TEdge>::GetEdgeDescriptor(
- const typename UndirectedGraph<TVertex, TEdge>::EdgeType &edgeData) const
- {
- typename UndirectedGraph<TVertex, TEdge>::EdgeIteratorType iterator, end;
- boost::tie(iterator, end) = boost::edges(m_Graph);
-
- for (; iterator != end; ++iterator)
- {
- typename UndirectedGraph<TVertex, TEdge>::EdgeType tempEdge;
-
- // the value of an iterator is a descriptor
- tempEdge = this->properties(*iterator);
-
- if (edgeData == tempEdge)
- return iterator.dereference();
- }
- // if no edge match, throw error
- MITK_ERROR << "Error in mitkUndirectedGraph::GetEdgeDescriptor(...): edge could not be found." << std::endl;
- throw std::runtime_error(
- "Exception thrown in mitkUndirectedGraph::GetEdgeDescriptor(...): edge could not be found.");
- }
-
- template <class TVertex, class TEdge>
- std::pair<typename UndirectedGraph<TVertex, TEdge>::VertexType, typename UndirectedGraph<TVertex, TEdge>::VertexType>
- UndirectedGraph<TVertex, TEdge>::GetVerticesOfAnEdge(
- const typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType &edge) const
- {
- typename UndirectedGraph<TVertex, TEdge>::VertexType sourceNode, targetNode;
-
- sourceNode = this->properties(boost::source(edge, m_Graph));
- targetNode = this->properties(boost::target(edge, m_Graph));
- std::pair<typename UndirectedGraph<TVertex, TEdge>::VertexType,
- typename UndirectedGraph<TVertex, TEdge>::VertexType>
- nodePair(sourceNode, targetNode);
-
- return nodePair;
- }
-
- template <class TVertex, class TEdge>
- typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType
- UndirectedGraph<TVertex, TEdge>::GetEdgeDescriptorByVerices(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertexA,
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertexB) const
- {
- typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType edge;
- bool edgeExists(false);
- boost::tie(edge, edgeExists) = boost::edge(vertexA, vertexB, m_Graph);
- if (edgeExists)
- return edge;
- else
- {
- MITK_ERROR << "Error in mitkUndirectedGraph::GetEdgeDescriptorByVerices(...): edge could not be found."
- << std::endl;
- throw std::runtime_error(
- "Exception thrown in mitkUndirectedGraph::GetEdgeDescriptorByVerices(...): edge could not be found.");
- }
- }
-
- template <class TVertex, class TEdge>
- std::vector<typename UndirectedGraph<TVertex, TEdge>::EdgeType> UndirectedGraph<TVertex, TEdge>::GetAllEdgesOfAVertex(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertex) const
- {
- typename UndirectedGraph<TVertex, TEdge>::OutEdgeIteratorType iterator, end;
- boost::tie(iterator, end) = boost::out_edges(vertex, m_Graph);
-
- std::vector<typename UndirectedGraph<TVertex, TEdge>::EdgeType> vectorOfEdges;
- for (; iterator != end; ++iterator)
- {
- typename UndirectedGraph<TVertex, TEdge>::EdgeType tempEdge;
-
- // the value of an iterator is a descriptor
- tempEdge = this->properties(*iterator);
-
- vectorOfEdges.push_back(tempEdge);
- }
-
- return vectorOfEdges;
- }
-
- template <class TVertex, class TEdge>
- int UndirectedGraph<TVertex, TEdge>::GetNumberOfVertices() const
- {
- // Returns the number of vertices in the graph
- return boost::num_vertices(m_Graph);
- }
-
- template <class TVertex, class TEdge>
- int UndirectedGraph<TVertex, TEdge>::GetNumberOfEdges() const
- {
- // Returns the number of edges in the graph
- return boost::num_edges(m_Graph);
- }
-
- template <class TVertex, class TEdge>
- std::vector<typename UndirectedGraph<TVertex, TEdge>::VertexType>
- UndirectedGraph<TVertex, TEdge>::GetVectorOfAllVertices() const
- {
- typename UndirectedGraph<TVertex, TEdge>::VertexIteratorType iterator, end;
-
- // sets iterator to start end end to end
- boost::tie(iterator, end) = boost::vertices(m_Graph);
-
- std::vector<typename UndirectedGraph<TVertex, TEdge>::VertexType> vectorOfNodes;
-
- for (; iterator != end; ++iterator)
- {
- typename UndirectedGraph<TVertex, TEdge>::VertexType tempVertex;
-
- // the value of an iterator is a descriptor
- tempVertex = this->properties(*iterator);
-
- vectorOfNodes.push_back(tempVertex);
- }
-
- return vectorOfNodes;
- }
-
- template <class TVertex, class TEdge>
- std::vector<typename UndirectedGraph<TVertex, TEdge>::EdgeType> UndirectedGraph<TVertex, TEdge>::GetVectorOfAllEdges()
- const
- {
- typename UndirectedGraph<TVertex, TEdge>::EdgeIteratorType iterator, end;
-
- // sets iterator to start end end to end
- boost::tie(iterator, end) = boost::edges(m_Graph);
-
- std::vector<typename UndirectedGraph<TVertex, TEdge>::EdgeType> vectorOfEdges;
-
- for (; iterator != end; ++iterator)
- {
- typename UndirectedGraph<TVertex, TEdge>::EdgeType tempEdge;
-
- // the value of an iterator is a descriptor
- tempEdge = this->properties(*iterator);
-
- vectorOfEdges.push_back(tempEdge);
- }
-
- return vectorOfEdges;
- }
-
- template <class TVertex, class TEdge>
- void UndirectedGraph<TVertex, TEdge>::Clear()
- {
- m_Graph.clear();
- this->Modified();
- }
-
- template <class TVertex, class TEdge>
- const typename UndirectedGraph<TVertex, TEdge>::GraphType &UndirectedGraph<TVertex, TEdge>::GetGraph() const
- {
- return m_Graph;
- }
-
- /* operators */
- template <class TVertex, class TEdge>
- UndirectedGraph<TVertex, TEdge> &UndirectedGraph<TVertex, TEdge>::operator=(
- const UndirectedGraph<TVertex, TEdge> &rhs)
- {
- m_Graph = rhs.m_Graph;
- return *this;
- }
-
- template <class TVertex, class TEdge>
- TVertex &UndirectedGraph<TVertex, TEdge>::properties(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertex)
- {
- typename boost::property_map<GraphType, vertex_properties_t>::type param = boost::get(vertex_properties, m_Graph);
- return param[vertex];
- }
-
- template <class TVertex, class TEdge>
- const TVertex &UndirectedGraph<TVertex, TEdge>::properties(
- const typename UndirectedGraph<TVertex, TEdge>::VertexDescriptorType &vertex) const
- {
- typename boost::property_map<GraphType, vertex_properties_t>::const_type param =
- boost::get(vertex_properties, m_Graph);
- return param[vertex];
- }
-
- template <class TVertex, class TEdge>
- TEdge &UndirectedGraph<TVertex, TEdge>::properties(
- const typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType &edge)
- {
- typename boost::property_map<GraphType, edge_properties_t>::type param = boost::get(edge_properties, m_Graph);
- return param[edge];
- }
-
- template <class TVertex, class TEdge>
- const TEdge &UndirectedGraph<TVertex, TEdge>::properties(
- const typename UndirectedGraph<TVertex, TEdge>::EdgeDescriptorType &edge) const
- {
- typename boost::property_map<GraphType, edge_properties_t>::const_type param = boost::get(edge_properties, m_Graph);
- return param[edge];
- }
-
-} // namespace mitk
-
-#endif //_mitkUndirectedGraph_txx
diff --git a/Modules/TubeGraph/resource/Interactions/TubeGraphConfig.xml b/Modules/TubeGraph/resource/Interactions/TubeGraphConfig.xml
deleted file mode 100644
index 837a989c6f..0000000000
--- a/Modules/TubeGraph/resource/Interactions/TubeGraphConfig.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<config>
- <event_variant name="PickByDouble" class="MouseDoubleClickEvent">
- <attribute name="EventButton" value="LeftMouseButton"/>
- </event_variant>
- <event_variant name="PickByShift" class="MousePressEvent">
- <attribute name="EventButton" value="LeftMouseButton"/>
- <attribute name="Modifiers" value="shift"/>
- </event_variant>
-</config>
diff --git a/Modules/TubeGraph/resource/Interactions/TubeGraphInteraction.xml b/Modules/TubeGraph/resource/Interactions/TubeGraphInteraction.xml
deleted file mode 100644
index 41032b97af..0000000000
--- a/Modules/TubeGraph/resource/Interactions/TubeGraphInteraction.xml
+++ /dev/null
@@ -1,38 +0,0 @@
-<statemachine NAME="TubeGraph">
- <state name="start" startstate="true" >
- <transition event_class="InteractionPositionEvent" event_variant="PickByDouble" target="select">
- <condition name="isOverTube"/>
- <action name="selectTube"/>
- </transition>
- <transition event_class="InteractionPositionEvent" event_variant="PickByDouble" target="start">
- <condition name="isOverTube" inverted="true"/>
- <action name="deselectTube"/>
- </transition>
- <transition event_class="InteractionPositionEvent" event_variant="PickByShift" target="select">
- <condition name="isOverTube"/>
- <action name="selectTube"/>
- </transition>
- <transition event_class="InteractionPositionEvent" event_variant="PickByShift" target="start">
- <condition name="isOverTube" inverted="true"/>
- <action name="deselectTube"/>
- </transition>
- </state>
- <state name="select" >
- <transition event_class="InteractionPositionEvent" event_variant="PickByDouble" target="select">
- <condition name="isOverTube"/>
- <action name="selectTube"/>
- </transition>
- <transition event_class="InteractionPositionEvent" event_variant="PickByDouble" target="start">
- <condition name="isOverTube" inverted="true" />
- <action name="deselectTube"/>
- </transition>
- <transition event_class="InteractionPositionEvent" event_variant="PickByShift" target="select">
- <condition name="isOverTube"/>
- <action name="selectTube"/>
- </transition>
- <transition event_class="InteractionPositionEvent" event_variant="PickByShift" target="start">
- <condition name="isOverTube" inverted="true" />
- <action name="deselectTube"/>
- </transition>
- </state>
- </statemachine>
\ No newline at end of file
diff --git a/Modules/TubeGraph/src/DataStructure/mitkCircularProfileTubeElement.cpp b/Modules/TubeGraph/src/DataStructure/mitkCircularProfileTubeElement.cpp
deleted file mode 100644
index a7fbba8da2..0000000000
--- a/Modules/TubeGraph/src/DataStructure/mitkCircularProfileTubeElement.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 "mitkCircularProfileTubeElement.h"
-
-mitk::CircularProfileTubeElement::CircularProfileTubeElement() : m_coordinates(), m_diameter(0.0f)
-{
-}
-
-mitk::CircularProfileTubeElement::CircularProfileTubeElement(float x, float y, float z, float d) : m_diameter(d)
-{
- mitk::FillVector3D(m_coordinates, x, y, z);
-}
-
-mitk::CircularProfileTubeElement::CircularProfileTubeElement(const mitk::Point3D c, float d)
- : m_coordinates(c), m_diameter(d)
-{
-}
-
-mitk::CircularProfileTubeElement::~CircularProfileTubeElement()
-{
-}
-
-const mitk::Point3D &mitk::CircularProfileTubeElement::GetCoordinates() const
-{
- return m_coordinates;
-}
-
-void mitk::CircularProfileTubeElement::SetCoordinates(mitk::Point3D coordinates)
-{
- m_coordinates = coordinates;
-}
-
-float mitk::CircularProfileTubeElement::GetDiameter() const
-{
- return m_diameter;
-}
-
-void mitk::CircularProfileTubeElement::SetDiameter(float d)
-{
- m_diameter = d;
-}
-
-bool mitk::CircularProfileTubeElement::operator==(const mitk::TubeElement &right) const
-{
- // Check if given TubeElement is CircularProfileTubeElement
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(&right))
- {
- const auto *element = dynamic_cast<const mitk::CircularProfileTubeElement *>(&right);
- return ((m_diameter == element->m_diameter) && (m_coordinates == element->m_coordinates));
- }
- else
- return false;
-}
diff --git a/Modules/TubeGraph/src/DataStructure/mitkTubeGraph.cpp b/Modules/TubeGraph/src/DataStructure/mitkTubeGraph.cpp
deleted file mode 100644
index cdb8a26cf6..0000000000
--- a/Modules/TubeGraph/src/DataStructure/mitkTubeGraph.cpp
+++ /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.
-
-============================================================================*/
-
-#include "mitkTubeGraph.h"
-#include "mitkGeometry3D.h"
-
-const mitk::TubeGraph::TubeDescriptorType mitk::TubeGraph::ErrorId =
- std::pair<VertexDescriptorType, VertexDescriptorType>(boost::graph_traits<GraphType>::null_vertex(),
- boost::graph_traits<GraphType>::null_vertex());
-
-mitk::TubeGraph::TubeGraph()
-{
-}
-
-mitk::TubeGraph::TubeGraph(const mitk::TubeGraph &graph) : UndirectedGraph<TubeGraphVertex, TubeGraphEdge>(graph)
-{
-}
-
-mitk::TubeGraph::~TubeGraph()
-{
-}
-
-std::vector<mitk::TubeGraph::TubeDescriptorType> mitk::TubeGraph::SearchShortestPath(
- const TubeDescriptorType &, const TubeDescriptorType &)
-{
- std::vector<TubeDescriptorType> shortestPath;
- return shortestPath;
-}
-
-std::vector<mitk::TubeGraph::TubeDescriptorType> mitk::TubeGraph::SearchAllPathBetweenVertices(
- const mitk::TubeGraph::TubeDescriptorType &startTube,
- const mitk::TubeGraph::TubeDescriptorType &endTube /*, std::vector<unsigned long> barrier*/)
-{ // https://lists.boost.org/boost-users/att-9001/maze.cpp
- // https://www.boost.org/doc/libs/1_49_0/libs/graph/example/bfs.cpp
-
- typedef std::map<VertexDescriptorType, EdgeDescriptorType> EdgeMap;
- typedef boost::associative_property_map<EdgeMap> PredecessorMap;
- typedef boost::edge_predecessor_recorder<PredecessorMap, boost::on_tree_edge> PredecessorVisitor;
- typedef boost::dfs_visitor<std::pair<PredecessorVisitor, boost::null_visitor>> DFSVisitor;
-
- EdgeMap edgesMap;
- PredecessorMap predecessorMap(edgesMap);
-
- PredecessorVisitor predecessorVisitor(predecessorMap);
- boost::null_visitor nullVisitor;
- DFSVisitor visitor = boost::make_dfs_visitor(std::make_pair(predecessorVisitor, nullVisitor));
-
- std::map<VertexDescriptorType, boost::default_color_type> vertexColorMap;
- std::map<EdgeDescriptorType, boost::default_color_type> edgeColorMap;
-
- boost::undirected_dfs(
- m_Graph, visitor, make_assoc_property_map(vertexColorMap), make_assoc_property_map(edgeColorMap), startTube.second);
-
- std::vector<TubeDescriptorType> solutionPath;
- solutionPath.push_back(endTube);
- VertexDescriptorType pathEdgeSource = endTube.first;
- VertexDescriptorType pathEdgeTarget;
-
- MITK_INFO << "Source: [" << startTube.first << "," << startTube.second << "] Target: [" << endTube.first << ","
- << endTube.second << "]";
- MITK_INFO << "tube [" << endTube.first << "," << endTube.second << "]";
- do
- {
- if (pathEdgeSource == 10393696)
- break;
- EdgeDescriptorType edge = get(predecessorMap, pathEdgeSource);
- pathEdgeSource = boost::source(edge, m_Graph);
- pathEdgeTarget = boost::target(edge, m_Graph);
- TubeDescriptorType tube(pathEdgeSource, pathEdgeTarget);
- MITK_INFO << "tube [" << tube.first << "," << tube.second << "]";
- solutionPath.push_back(tube);
- } while (pathEdgeSource != startTube.second);
-
- return solutionPath;
-}
-
-std::vector<mitk::TubeGraph::TubeDescriptorType> mitk::TubeGraph::SearchPathToPeriphery(
- const mitk::TubeGraph::TubeDescriptorType &startTube /*, std::vector<unsigned long> barrier*/)
-{
- std::vector<mitk::TubeGraph::TubeDescriptorType> pathToPeriphery;
-
- if (m_RootTube == ErrorId)
- {
- m_RootTube = this->GetThickestTube();
- if (m_Root == m_RootTube.first)
- m_Root = m_RootTube.second;
- else
- m_Root = m_RootTube.first;
- }
-
- // Attention!! No check which one is the right one
- DirectedGraphType directedGraph = this->GetDirectedGraph(m_Root);
-
- // Only the target vertex: it's a directed Graph, and we want only the "after tube" tubes and the clicked ones
- // this->GetOutEdgesOfAVertex(startTube.first, directedGraph, pathToPeriphery);
- pathToPeriphery.push_back(startTube);
- this->GetOutEdgesOfAVertex(startTube.second, directedGraph, pathToPeriphery);
-
- return pathToPeriphery;
-}
-
-void mitk::TubeGraph::GetOutEdgesOfAVertex(mitk::TubeGraph::VertexDescriptorType vertex,
- mitk::TubeGraph::DirectedGraphType &directedGraph,
- std::vector<mitk::TubeGraph::TubeDescriptorType> &pathToPeriphery)
-{
- typedef boost::graph_traits<DirectedGraphType>::out_edge_iterator OutEdgeIteratorType;
- std::pair<OutEdgeIteratorType, OutEdgeIteratorType> outEdges = boost::out_edges(vertex, directedGraph);
- for (; outEdges.first != outEdges.second; ++outEdges.first)
- {
- TubeDescriptorType tube;
- tube.first = boost::source(*outEdges.first, directedGraph);
- tube.second = boost::target(*outEdges.first, directedGraph);
-
- if (std::find(pathToPeriphery.begin(), pathToPeriphery.end(), tube) == pathToPeriphery.end())
- {
- pathToPeriphery.push_back(tube);
- this->GetOutEdgesOfAVertex(tube.second, directedGraph, pathToPeriphery);
- }
- }
-}
-
-mitk::TubeGraph::TubeDescriptorType mitk::TubeGraph::GetThickestTube()
-{
- TubeDescriptorType thickestTube;
- float tubeDiameter = 0.0;
-
- EdgeIteratorType iterator, end;
-
- boost::tie(iterator, end) = boost::edges(m_Graph);
-
- for (; iterator != end; ++iterator)
- {
- TubeGraphEdge edge = this->GetEdge(*iterator);
-
- std::pair<TubeGraphVertex, TubeGraphVertex> soureTargetPair = this->GetVerticesOfAnEdge(*iterator);
-
- float tempDiameter = edge.GetEdgeAverageDiameter(soureTargetPair.first, soureTargetPair.second);
- if (tempDiameter > tubeDiameter)
- {
- tubeDiameter = tempDiameter;
- thickestTube.first = this->GetVertexDescriptor(soureTargetPair.first);
- thickestTube.second = this->GetVertexDescriptor(soureTargetPair.second);
- }
- }
- return thickestTube;
-}
-
-mitk::TubeGraph::DirectedGraphType mitk::TubeGraph::GetDirectedGraph(VertexDescriptorType startVertex)
-{
- DirectedGraphType directedGraph(boost::num_vertices(m_Graph));
- DirectedGraphBfsVisitor vis(this, directedGraph);
- boost::breadth_first_search(m_Graph, startVertex, visitor(vis));
- return directedGraph;
-}
-
-mitk::TubeGraph::Pointer mitk::TubeGraph::CreateSubGraph(std::vector<TubeDescriptorType> subGraphTubes)
-{
- TubeGraph::Pointer subGraph = new TubeGraph();
- // store the descriptor from origin graph to the correspondent new descriptors
- std::map<VertexDescriptorType, VertexDescriptorType> vertexDescriptorOldToNewMap;
-
- // add a new edge and if necessary also the vertices of each tube to the new sub graph
- for (auto it = subGraphTubes.begin(); it != subGraphTubes.end(); it++)
- {
- // search for the source vertex in the subgraph; if it is already added continue, otherwise add it
- if (vertexDescriptorOldToNewMap.find(it->first) == vertexDescriptorOldToNewMap.end())
- {
- // add the vertex to the subgraph
- VertexDescriptorType newVertexDescriptor = subGraph->AddVertex(this->GetVertex(it->first));
- // add the pair of descriptor from the origin graph to the descriptor from the subgraph
- vertexDescriptorOldToNewMap.insert(
- std::pair<VertexDescriptorType, VertexDescriptorType>(it->first, newVertexDescriptor));
- }
- // and now...search for the target vertex...
- if (vertexDescriptorOldToNewMap.find(it->second) == vertexDescriptorOldToNewMap.end())
- {
- VertexDescriptorType newVertexDescriptor = subGraph->AddVertex(this->GetVertex(it->second));
- vertexDescriptorOldToNewMap.insert(
- std::pair<VertexDescriptorType, VertexDescriptorType>(it->second, newVertexDescriptor));
- }
- // Get the EdgeDescriptor from origin graph
- EdgeDescriptorType edgeDescriptor = this->GetEdgeDescriptorByVerices(it->first, it->second);
-
- TubeGraphEdge oldEdge = this->GetEdge(edgeDescriptor);
-
- // AddEdge needs the source vertex, the target vertex and the edge data
- // source Vertex: get the subgraph VertexDescriptor by the origin descriptor (tubeDescriptor->first)from the
- // assigning map
- // target Vertex: get the subgraph VertexDescriptor by the origin descriptor (tubeDescriptor->second)from the
- // assigning map
- // edge data: copy the TubeGraphEdge object using the origin edge desciptor and the origin graph
- VertexDescriptorType sourceVertex = vertexDescriptorOldToNewMap[it->first];
- VertexDescriptorType targetVertex = vertexDescriptorOldToNewMap[it->second];
- subGraph->AddEdge(sourceVertex, targetVertex, this->GetEdge(edgeDescriptor));
- }
- subGraph->CopyInformation(this);
-
- mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New();
- geometry->Initialize();
- subGraph->SetGeometry(geometry);
-
- this->Modified();
-
- return subGraph;
-}
-
-void mitk::TubeGraph::RemoveSubGraph(std::vector<TubeDescriptorType> deletedTubes)
-{
- for (auto it = deletedTubes.begin(); it != deletedTubes.end(); it++)
- {
- VertexDescriptorType source = it->first;
- VertexDescriptorType target = it->second;
-
- EdgeDescriptorType edge = this->GetEdgeDescriptorByVerices(source, target);
- this->RemoveEdge(edge);
-
- if (this->GetAllEdgesOfAVertex(source).size() == 0)
- {
- this->RemoveVertex(source);
- }
- if (this->GetAllEdgesOfAVertex(target).size() == 0)
- {
- this->RemoveVertex(target);
- }
- }
- this->Modified();
-}
-
-void mitk::TubeGraph::SetRootTube(const TubeDescriptorType &root)
-{
- if (root != TubeGraph::ErrorId)
- {
- m_RootTube = root;
- if (m_Root == root.first)
- m_Root = root.second;
- else
- m_Root = root.first;
- this->Modified();
- }
-}
-
-void mitk::TubeGraph::SetRoot(const VertexDescriptorType &root)
-{
- if (root != TubeGraph::ErrorId.first)
- {
- m_Root = root;
- }
-}
-
-mitk::TubeGraph::TubeDescriptorType mitk::TubeGraph::GetRootTube()
-{
- return m_RootTube;
-}
-
-mitk::TubeGraph::VertexDescriptorType mitk::TubeGraph::GetRootVertex()
-{
- return m_Root;
-}
-
-mitk::TubeGraph &mitk::TubeGraph::operator=(const mitk::TubeGraph &rhs)
-{
- UndirectedGraph<TubeGraphVertex, TubeGraphEdge>::operator=(rhs);
- return *this;
-}
diff --git a/Modules/TubeGraph/src/DataStructure/mitkTubeGraphEdge.cpp b/Modules/TubeGraph/src/DataStructure/mitkTubeGraphEdge.cpp
deleted file mode 100644
index 2fc109f26e..0000000000
--- a/Modules/TubeGraph/src/DataStructure/mitkTubeGraphEdge.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 "mitkTubeGraphEdge.h"
-
-mitk::TubeGraphEdge::TubeGraphEdge() : m_ElementVector(0)
-{
-}
-
-mitk::TubeGraphEdge::~TubeGraphEdge()
-{
- /*while(!m_ElementVector.empty())
- {
- delete m_ElementVector.back();
- m_ElementVector.pop_back();
- }*/
- m_ElementVector.clear();
-}
-
-std::vector<mitk::TubeElement *> mitk::TubeGraphEdge::GetElementVector()
-{
- return m_ElementVector;
-}
-
-void mitk::TubeGraphEdge::SetElementVector(std::vector<mitk::TubeElement *> elementVector)
-{
- m_ElementVector = elementVector;
-}
-
-unsigned int mitk::TubeGraphEdge::GetNumberOfElements() const
-{
- return m_ElementVector.size();
-}
-
-void mitk::TubeGraphEdge::AddTubeElement(mitk::TubeElement *element)
-{
- m_ElementVector.push_back(element);
-}
-
-void mitk::TubeGraphEdge::AddTubeElementAt(unsigned int position, TubeElement *element)
-{
- m_ElementVector.insert(m_ElementVector.begin() + position, element);
-}
-
-mitk::TubeElement *mitk::TubeGraphEdge::GetTubeElement(unsigned int position)
-{
- if (position >= GetNumberOfElements())
- throw std::runtime_error("Exception thrown in TubeGraphEdge::getTubeElement(uint): getTubeElement(uint)");
- else
- return m_ElementVector[position];
-}
-
-float mitk::TubeGraphEdge::GetEdgeLength(mitk::TubeGraphVertex &source, mitk::TubeGraphVertex &target)
-{
- float length = 0.0f;
- mitk::Point3D pos1, pos2;
- std::vector<float> diff;
- diff.resize(3);
- unsigned int numberOfElements = this->GetNumberOfElements();
-
- // if there are no elements return 0
- if (numberOfElements == 0)
- {
- // If the edge has no elements, then take the difference between the vertices directly
- pos1 = (source.GetTubeElement())->GetCoordinates();
- pos2 = (target.GetTubeElement())->GetCoordinates();
-
- diff[0] = pos1[0] - pos2[0];
- diff[1] = pos1[1] - pos2[1];
- diff[2] = pos1[2] - pos2[2];
-
- float sum = diff[0] * diff[0] + diff[1] * diff[1] + diff[2] * diff[2];
- length = length + std::sqrt(sum);
- }
- else
- {
- // difference between source and first element of the edge
- pos1 = (source.GetTubeElement())->GetCoordinates();
- pos2 = (this->GetTubeElement(0))->GetCoordinates();
-
- diff[0] = pos1[0] - pos2[0];
- diff[1] = pos1[1] - pos2[1];
- diff[2] = pos1[2] - pos2[2];
-
- float sum = diff[0] * diff[0] + diff[1] * diff[1] + diff[2] * diff[2];
- length = length + std::sqrt(sum);
-
- // Differences within the edge
- for (unsigned int i = 0; i < numberOfElements - 1; ++i)
- {
- pos1 = (this->GetTubeElement(i))->GetCoordinates();
- pos2 = (this->GetTubeElement(i + 1))->GetCoordinates();
-
- diff[0] = pos1[0] - pos2[0];
- diff[1] = pos1[1] - pos2[1];
- diff[2] = pos1[2] - pos2[2];
-
- sum = diff[0] * diff[0] + diff[1] * diff[1] + diff[2] * diff[2];
- length = length + std::sqrt(sum);
- }
-
- // difference between last element and target of the edge
- pos1 = (this->GetTubeElement(numberOfElements - 1))->GetCoordinates();
- pos2 = (target.GetTubeElement())->GetCoordinates();
-
- diff[0] = pos1[0] - pos2[0];
- diff[1] = pos1[1] - pos2[1];
- diff[2] = pos1[2] - pos2[2];
-
- sum = diff[0] * diff[0] + diff[1] * diff[1] + diff[2] * diff[2];
- length = length + std::sqrt(sum);
- }
-
- return length;
-}
-
-float mitk::TubeGraphEdge::GetEdgeAverageDiameter(mitk::TubeGraphVertex &source, mitk::TubeGraphVertex &target)
-{
- float diameterSum = 0.0;
- unsigned int numberOfElements = this->GetNumberOfElements();
-
- // add source diameter
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(source.GetTubeElement()))
- diameterSum += (dynamic_cast<const mitk::CircularProfileTubeElement *>(source.GetTubeElement()))->GetDiameter();
- ;
-
- // add all edge element diameter
- for (unsigned int i = 0; i < numberOfElements; i++)
- {
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(this->GetTubeElement(i)))
- diameterSum += (dynamic_cast<const mitk::CircularProfileTubeElement *>(this->GetTubeElement(i)))->GetDiameter();
- }
-
- // add target diameter
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(target.GetTubeElement()))
- diameterSum += (dynamic_cast<const mitk::CircularProfileTubeElement *>(target.GetTubeElement()))->GetDiameter();
-
- return diameterSum / (numberOfElements + 2);
-}
-
-bool mitk::TubeGraphEdge::operator==(const mitk::TubeGraphEdge &right) const
-{
- return (m_ElementVector == right.m_ElementVector);
-}
diff --git a/Modules/TubeGraph/src/DataStructure/mitkTubeGraphVertex.cpp b/Modules/TubeGraph/src/DataStructure/mitkTubeGraphVertex.cpp
deleted file mode 100644
index 4a3c0aa348..0000000000
--- a/Modules/TubeGraph/src/DataStructure/mitkTubeGraphVertex.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 "mitkTubeGraphVertex.h"
-
-mitk::TubeGraphVertex::TubeGraphVertex() : m_element(nullptr)
-{
-}
-
-mitk::TubeGraphVertex::TubeGraphVertex(mitk::TubeElement *element)
-{
- m_element = element;
-}
-
-mitk::TubeGraphVertex::~TubeGraphVertex()
-{
-}
-
-void mitk::TubeGraphVertex::SetTubeElement(mitk::TubeElement *element)
-{
- m_element = element;
-}
-
-const mitk::TubeElement *mitk::TubeGraphVertex::GetTubeElement() const
-{
- return m_element;
-}
-
-bool mitk::TubeGraphVertex::operator==(const mitk::TubeGraphVertex &right) const
-{
- return (m_element == right.m_element);
-}
diff --git a/Modules/TubeGraph/src/IO/mitkTubeGraphDefinitions.cpp b/Modules/TubeGraph/src/IO/mitkTubeGraphDefinitions.cpp
deleted file mode 100644
index 648a5bddba..0000000000
--- a/Modules/TubeGraph/src/IO/mitkTubeGraphDefinitions.cpp
+++ /dev/null
@@ -1,89 +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 "mitkTubeGraphDefinitions.h"
-
-//============== XML const chars ===================
-
-//==== Header information ====
-const std::string mitk::TubeGraphDefinitions::XML_TUBEGRAPH_FILE = "tube_graph_file";
-const std::string mitk::TubeGraphDefinitions::XML_FILE_VERSION = "file_version";
-const std::string mitk::TubeGraphDefinitions::VERSION_STRING = "0.1";
-const std::string mitk::TubeGraphDefinitions::ASCII_FILE = "ascii_file";
-const std::string mitk::TubeGraphDefinitions::FILE_NAME = "file_name";
-
-//==== Geometry details ====
-const std::string mitk::TubeGraphDefinitions::XML_GEOMETRY = "geometry";
-
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_XX = "xx";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_XY = "xy";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_XZ = "xz";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_YX = "yx";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_YY = "yy";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_YZ = "yz";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_ZX = "zx";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_ZY = "zy";
-const std::string mitk::TubeGraphDefinitions::XML_MATRIX_ZZ = "zz";
-
-const std::string mitk::TubeGraphDefinitions::XML_ORIGIN_X = "origin_x";
-const std::string mitk::TubeGraphDefinitions::XML_ORIGIN_Y = "origin_y";
-const std::string mitk::TubeGraphDefinitions::XML_ORIGIN_Z = "origin_z";
-
-const std::string mitk::TubeGraphDefinitions::XML_SPACING_X = "spacing_x";
-const std::string mitk::TubeGraphDefinitions::XML_SPACING_Y = "spacing_y";
-const std::string mitk::TubeGraphDefinitions::XML_SPACING_Z = "spacing_z";
-
-//==== TubeGraph structures ====
-const std::string mitk::TubeGraphDefinitions::XML_VERTICES = "vertices";
-const std::string mitk::TubeGraphDefinitions::XML_EDGES = "edges";
-const std::string mitk::TubeGraphDefinitions::XML_LABELGROUPS = "labelgroups";
-const std::string mitk::TubeGraphDefinitions::XML_ATTRIBUTIONS = "attributions";
-const std::string mitk::TubeGraphDefinitions::XML_ANNOTATIONS = "annotations";
-const std::string mitk::TubeGraphDefinitions::XML_VERTEX = "vertex";
-const std::string mitk::TubeGraphDefinitions::XML_EDGE = "edge";
-const std::string mitk::TubeGraphDefinitions::XML_ELEMENT = "element";
-const std::string mitk::TubeGraphDefinitions::XML_LABELGROUP = "labelgroup";
-const std::string mitk::TubeGraphDefinitions::XML_LABEL = "label";
-const std::string mitk::TubeGraphDefinitions::XML_ATTRIBUTION = "attribut";
-const std::string mitk::TubeGraphDefinitions::XML_ANNOTATION = "annotation";
-
-//==== vertex properties ====
-const std::string mitk::TubeGraphDefinitions::XML_VERTEX_ID = "vertex_id";
-
-//==== edge properties ====
-const std::string mitk::TubeGraphDefinitions::XML_EDGE_ID = "edge_id";
-const std::string mitk::TubeGraphDefinitions::XML_EDGE_SOURCE_ID = "edge_source_id";
-const std::string mitk::TubeGraphDefinitions::XML_EDGE_TARGET_ID = "edge_target_id";
-
-//==== element properties ====
-const std::string mitk::TubeGraphDefinitions::XML_ELEMENT_X = "element_x";
-const std::string mitk::TubeGraphDefinitions::XML_ELEMENT_Y = "element_y";
-const std::string mitk::TubeGraphDefinitions::XML_ELEMENT_Z = "element_z";
-const std::string mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER = "element_diameter";
-
-//==== label group properties ====
-const std::string mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME = "labelgroup_name";
-
-//==== label properties ====
-const std::string mitk::TubeGraphDefinitions::XML_LABEL_NAME = "label_name";
-const std::string mitk::TubeGraphDefinitions::XML_LABEL_VISIBILITY = "label_visible";
-const std::string mitk::TubeGraphDefinitions::XML_LABEL_COLOR_R = "label_color_r";
-const std::string mitk::TubeGraphDefinitions::XML_LABEL_COLOR_G = "label_color_g";
-const std::string mitk::TubeGraphDefinitions::XML_LABEL_COLOR_B = "label_color_b";
-
-//==== tube properties ====
-const std::string mitk::TubeGraphDefinitions::XML_TUBE_ID_1 = "tube_id_1";
-const std::string mitk::TubeGraphDefinitions::XML_TUBE_ID_2 = "tube_id_2";
-
-//==== annotation properties ====
-const std::string mitk::TubeGraphDefinitions::XML_ANNOTATION_NAME = "annotation_name";
-const std::string mitk::TubeGraphDefinitions::XML_ANNOTATION_DESCRIPTION = "annotation_description";
diff --git a/Modules/TubeGraph/src/IO/mitkTubeGraphIO.cpp b/Modules/TubeGraph/src/IO/mitkTubeGraphIO.cpp
deleted file mode 100644
index 9edfb8e2d9..0000000000
--- a/Modules/TubeGraph/src/IO/mitkTubeGraphIO.cpp
+++ /dev/null
@@ -1,580 +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 "mitkTubeGraphIO.h"
-
-#include "mitkCircularProfileTubeElement.h"
-#include "mitkTubeGraphDefinitions.h"
-#include "mitkTubeGraphProperty.h"
-
-#include <mitkIOMimeTypes.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;
-
- if (tinyxml2::XML_SUCCESS == doc.Parse(string.c_str()))
- {
- TubeGraph::Pointer newTubeGraph = TubeGraph::New();
-
- 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->QueryAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_X.c_str(), &temp);
- origin[0] = temp;
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Y.c_str(), &temp);
- origin[1] = temp;
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_ORIGIN_Z.c_str(), &temp);
- origin[2] = temp;
- geometry->SetOrigin(origin);
-
- // read spacing
- Vector3D spacing;
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_SPACING_X.c_str(), &temp);
- spacing.SetElement(0, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_SPACING_Y.c_str(), &temp);
- spacing.SetElement(1, 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->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XX.c_str(), &temp);
- m->SetElement(0, 0, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XY.c_str(), &temp);
- m->SetElement(1, 0, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_XZ.c_str(), &temp);
- m->SetElement(2, 0, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YX.c_str(), &temp);
- m->SetElement(0, 1, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YY.c_str(), &temp);
- m->SetElement(1, 1, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_YZ.c_str(), &temp);
- m->SetElement(2, 1, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZX.c_str(), &temp);
- m->SetElement(0, 2, temp);
- pElem->QueryAttribute(mitk::TubeGraphDefinitions::XML_MATRIX_ZY.c_str(), &temp);
- m->SetElement(1, 2, 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.c_str()).ToElement();
- if (pElem != nullptr)
- {
- // walk through the vertices
- for (auto *vertexElement = pElem->FirstChildElement(); vertexElement != nullptr; vertexElement = vertexElement->NextSiblingElement())
- {
- int vertexID(0);
- mitk::Point3D coordinate;
- coordinate.Fill(0.0);
- double diameter(0);
-
- vertexElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_VERTEX_ID.c_str(), &vertexID);
-
- auto *tubeElement = vertexElement->FirstChildElement();
-
- tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(), &temp);
- coordinate[0] = temp;
- tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(), &temp);
- coordinate[1] = temp;
- tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(), &temp);
- coordinate[2] = temp;
- 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.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->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 (auto *tubeElement = edgeElement->FirstChildElement(mitk::TubeGraphDefinitions::XML_ELEMENT.c_str()); tubeElement != nullptr; tubeElement = tubeElement->NextSiblingElement())
- {
- tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(), &temp);
- coordinate[0] = temp;
- tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(), &temp);
- coordinate[1] = temp;
- tubeElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(), &temp);
- coordinate[2] = temp;
- 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.c_str()).ToElement();
- if (pElem != nullptr)
- {
- // walk through the label groups
- 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 (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->QueryAttribute(mitk::TubeGraphDefinitions::XML_LABEL_VISIBILITY.c_str(), &temp);
- if (temp == 0)
- isVisible = false;
- else
- isVisible = true;
- labelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_R.c_str(), &temp);
- color[0] = temp;
- labelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_G.c_str(), &temp);
- color[1] = 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.c_str()).ToElement();
- if (pElem != nullptr)
- {
- std::map<TubeGraphProperty::TubeToLabelGroupType, std::string> tubeToLabelsMap;
- 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->QueryAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1.c_str(), &temp);
- tube.first = temp;
- tubeToLabelElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_2.c_str(), &temp);
- tube.second = temp;
- const char *labelGroupName =
- tubeToLabelElement->Attribute(mitk::TubeGraphDefinitions::XML_LABELGROUP_NAME.c_str());
- if (labelGroupName)
- labelGroup = newProperty->GetLabelGroupByName(labelGroupName);
-
- const char *labelName =
- 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.c_str()).ToElement();
- if (pElem != nullptr)
- {
- for (auto *annotationElement = pElem->FirstChildElement(); annotationElement != nullptr; annotationElement = annotationElement->NextSiblingElement())
- {
- auto *annotation = new mitk::TubeGraphProperty::Annotation();
- TubeGraph::TubeDescriptorType tube;
-
- const char *annotationName =
- annotationElement->Attribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_NAME.c_str());
- annotation->name = nullptr != annotationName ? annotationName : "";
-
- const char *annotationDescription =
- annotationElement->Attribute(mitk::TubeGraphDefinitions::XML_ANNOTATION_DESCRIPTION.c_str());
- annotation->description = nullptr != annotationDescription ? annotationDescription : "";
-
- annotationElement->QueryAttribute(mitk::TubeGraphDefinitions::XML_TUBE_ID_1.c_str(), &temp);
- tube.first = 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.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
- tinyxml2::XMLDocument documentXML;
- { // Begin document
- documentXML.InsertEndChild(documentXML.NewDeclaration());
-
- 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 = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_GEOMETRY.c_str());
- { // begin geometry
- 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->InsertEndChild(geometryXML);
-
- 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 = 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 = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ELEMENT.c_str());
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(),
- element->GetCoordinates().GetElement(0));
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(),
- element->GetCoordinates().GetElement(1));
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(),
- element->GetCoordinates().GetElement(2));
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(element))
- elementXML->SetAttribute(
- mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(),
- (dynamic_cast<const mitk::CircularProfileTubeElement *>(element))->GetDiameter());
- else
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(), 2);
-
- vertexXML->InsertEndChild(elementXML);
-
- verticesXML->InsertEndChild(vertexXML);
- }
- } // end vertices section
- mainXML->InsertEndChild(verticesXML);
-
- 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 = 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.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 = documentXML.NewElement(mitk::TubeGraphDefinitions::XML_ELEMENT.c_str());
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_X.c_str(),
- elementVector[elementIndex]->GetCoordinates().GetElement(0));
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Y.c_str(),
- elementVector[elementIndex]->GetCoordinates().GetElement(1));
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_Z.c_str(),
- elementVector[elementIndex]->GetCoordinates().GetElement(2));
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(elementVector[elementIndex]))
- elementXML->SetAttribute(
- mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(),
- (dynamic_cast<const mitk::CircularProfileTubeElement *>(elementVector[elementIndex]))->GetDiameter());
- else
- elementXML->SetAttribute(mitk::TubeGraphDefinitions::XML_ELEMENT_DIAMETER.c_str(), 2);
- edgeXML->InsertEndChild(elementXML);
- // elementsXML->InsertEndChild(elementXML);
- }
- edgesXML->InsertEndChild(edgeXML);
- }
- } // end edges section
- mainXML->InsertEndChild(edgesXML);
-
- 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 = 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 = 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->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_G.c_str(),
- labelVector[labelIndex]->labelColor[1]);
- labelXML->SetAttribute(mitk::TubeGraphDefinitions::XML_LABEL_COLOR_B.c_str(),
- labelVector[labelIndex]->labelColor[2]);
- labelGroupXML->InsertEndChild(labelXML);
- }
- labelGroupsXML->InsertEndChild(labelGroupXML);
- }
- } // end labe group section
- mainXML->InsertEndChild(labelGroupsXML);
-
- 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 = 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->InsertEndChild(attributionsXML);
-
- 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 = 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->InsertEndChild(annotationsXML);
- } // end document
-
- 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/TubeGraph/src/IO/mitkTubeGraphModuleActivator.cpp b/Modules/TubeGraph/src/IO/mitkTubeGraphModuleActivator.cpp
deleted file mode 100644
index 2cb0333333..0000000000
--- a/Modules/TubeGraph/src/IO/mitkTubeGraphModuleActivator.cpp
+++ /dev/null
@@ -1,38 +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 <usModuleActivator.h>
-#include <usModuleContext.h>
-
-#include "mitkTubeGraphIO.h"
-
-namespace mitk
-{
- /**
- \brief Registers services for tube graph module.
- */
- class TubeGraphActivator : public us::ModuleActivator
- {
- std::vector<AbstractFileIO *> m_FileIOs;
-
- public:
- void Load(us::ModuleContext * /*context*/) override { m_FileIOs.push_back(new TubeGraphIO()); }
- void Unload(us::ModuleContext *) override
- {
- for (auto &elem : m_FileIOs)
- {
- delete elem;
- }
- }
- };
-}
-
-US_EXPORT_MODULE_ACTIVATOR(mitk::TubeGraphActivator)
diff --git a/Modules/TubeGraph/src/IO/mitkTubeGraphObjectFactory.cpp b/Modules/TubeGraph/src/IO/mitkTubeGraphObjectFactory.cpp
deleted file mode 100644
index 71c131963a..0000000000
--- a/Modules/TubeGraph/src/IO/mitkTubeGraphObjectFactory.cpp
+++ /dev/null
@@ -1,95 +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 "mitkTubeGraphObjectFactory.h"
-
-#include <mitkBaseRenderer.h>
-#include <mitkDataNode.h>
-#include <mitkProperties.h>
-
-#include "mitkTubeGraph.h"
-#include "mitkTubeGraphVtkMapper3D.h"
-
-mitk::TubeGraphObjectFactory::TubeGraphObjectFactory() : CoreObjectFactoryBase()
-{
- static bool alreadyDone = false;
- if (!alreadyDone)
- {
- CreateFileExtensionsMap();
- alreadyDone = true;
- }
-}
-
-mitk::Mapper::Pointer mitk::TubeGraphObjectFactory::CreateMapper(mitk::DataNode *node, MapperSlotId id)
-{
- mitk::Mapper::Pointer newMapper = nullptr;
-
- if (id == mitk::BaseRenderer::Standard3D)
- {
- if ((dynamic_cast<mitk::TubeGraph *>(node->GetData()) != nullptr))
- {
- newMapper = mitk::TubeGraphVtkMapper3D::New();
- newMapper->SetDataNode(node);
- }
- }
-
- return newMapper;
-}
-
-void mitk::TubeGraphObjectFactory::SetDefaultProperties(mitk::DataNode *node)
-{
- if ((dynamic_cast<mitk::TubeGraph *>(node->GetData()) != nullptr))
- {
- node->SetProperty("Tube Graph.Clip Structures", mitk::BoolProperty::New(false));
- mitk::TubeGraphVtkMapper3D::SetDefaultProperties(node);
- }
-}
-
-std::string mitk::TubeGraphObjectFactory::GetFileExtensions()
-{
- std::string fileExtension;
- this->CreateFileExtensions(m_FileExtensionsMap, fileExtension);
- return fileExtension.c_str();
-};
-
-mitk::CoreObjectFactoryBase::MultimapType mitk::TubeGraphObjectFactory::GetFileExtensionsMap()
-{
- return m_FileExtensionsMap;
-}
-
-std::string mitk::TubeGraphObjectFactory::GetSaveFileExtensions()
-{
- std::string fileExtension;
- this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension);
- return fileExtension.c_str();
-};
-
-mitk::CoreObjectFactoryBase::MultimapType mitk::TubeGraphObjectFactory::GetSaveFileExtensionsMap()
-{
- return m_SaveFileExtensionsMap;
-}
-
-void mitk::TubeGraphObjectFactory::CreateFileExtensionsMap()
-{
-}
-
-struct RegisterTubeGraphObjectFactory
-{
- RegisterTubeGraphObjectFactory() : m_Factory(mitk::TubeGraphObjectFactory::New())
- {
- mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(m_Factory);
- }
- ~RegisterTubeGraphObjectFactory() { mitk::CoreObjectFactory::GetInstance()->UnRegisterExtraFactory(m_Factory); }
- mitk::TubeGraphObjectFactory::Pointer m_Factory;
-};
-
-static RegisterTubeGraphObjectFactory registerTubeGraphObjectFactory;
diff --git a/Modules/TubeGraph/src/Interactions/mitkTubeGraphDataInteractor.cpp b/Modules/TubeGraph/src/Interactions/mitkTubeGraphDataInteractor.cpp
deleted file mode 100644
index bd0af564dd..0000000000
--- a/Modules/TubeGraph/src/Interactions/mitkTubeGraphDataInteractor.cpp
+++ /dev/null
@@ -1,290 +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 "mitkTubeGraphDataInteractor.h"
-
-#include <mitkInteractionConst.h>
-#include <mitkInteractionPositionEvent.h>
-#include <mitkStatusBar.h>
-
-#include "mitkTubeGraphPicker.h"
-
-#include <vtkCamera.h>
-#include <vtkInteractorStyle.h>
-#include <vtkPointData.h>
-#include <vtkPolyData.h>
-#include <vtkRenderWindowInteractor.h>
-
-namespace mitk
-{
- itkEventMacroDefinition(SelectionChangedTubeGraphEvent, itk::AnyEvent);
-}
-
-mitk::TubeGraphDataInteractor::TubeGraphDataInteractor()
- : m_LastPickedTube(TubeGraph::ErrorId),
- m_SecondLastPickedTube(TubeGraph::ErrorId),
- m_ActivationMode(None),
- m_ActionMode(AttributationMode)
-{
-}
-
-mitk::TubeGraphDataInteractor::~TubeGraphDataInteractor() {}
-
-void mitk::TubeGraphDataInteractor::ConnectActionsAndFunctions()
-{
- // **Conditions** that can be used in the state machine, to ensure that certain conditions are met, before actually
- // executing an action
- CONNECT_CONDITION("isOverTube", CheckOverTube);
-
- // **Function** in the statmachine patterns also referred to as **Actions**
- CONNECT_FUNCTION("selectTube", SelectTube);
- CONNECT_FUNCTION("deselectTube", DeselectTube);
-}
-
-void mitk::TubeGraphDataInteractor::DataNodeChanged()
-{
- if (GetDataNode() != nullptr)
- {
- if (GetDataNode()->GetData() != nullptr)
- {
- m_TubeGraph = dynamic_cast<TubeGraph *>(GetDataNode()->GetData());
- m_TubeGraphProperty = dynamic_cast<TubeGraphProperty *>(
- m_TubeGraph->GetProperty("Tube Graph.Visualization Information").GetPointer());
- if (m_TubeGraphProperty.IsNull())
- MITK_ERROR << "Something went wrong! No tube graph property!";
- }
- else
- m_TubeGraph = nullptr;
- }
- else
- m_TubeGraph = nullptr;
-}
-
-bool mitk::TubeGraphDataInteractor::CheckOverTube(const InteractionEvent *interactionEvent)
-{
- const auto *positionEvent = dynamic_cast<const InteractionPositionEvent *>(interactionEvent);
- if (positionEvent == nullptr)
- return false;
-
- auto *picker = new mitk::TubeGraphPicker();
- picker->SetTubeGraph(m_TubeGraph);
-
- auto pickedTube = picker->GetPickedTube(positionEvent->GetPositionInWorld());
-
- TubeGraph::TubeDescriptorType tubeDescriptor = pickedTube.first;
-
- if (tubeDescriptor != TubeGraph::ErrorId)
- {
- m_LastPickedElement = pickedTube.second;
- m_SecondLastPickedTube = m_LastPickedTube;
- m_LastPickedTube = tubeDescriptor;
- return true;
- }
- else // nothing picked
- return false;
-}
-
-void mitk::TubeGraphDataInteractor::SelectTube(StateMachineAction *, InteractionEvent *)
-{
- if (m_TubeGraph.IsNull())
- return;
-
- this->SelectTubesByActivationModus();
-
- RenderingManager::GetInstance()->RequestUpdateAll();
-
- if (m_ActivationMode != None)
- {
- // show tube id on status bar
- std::stringstream displayText;
- displayText << "Picked tube: ID [" << m_LastPickedTube.first << "," << m_LastPickedTube.second << "]";
- StatusBar::GetInstance()->DisplayText(displayText.str().c_str());
- // TODO!!! this->InvokeEvent(SelectionChangedTubeGraphEvent());
- }
-}
-
-void mitk::TubeGraphDataInteractor::DeselectTube(StateMachineAction *, InteractionEvent *)
-{
- if (m_TubeGraph.IsNull())
- return;
-
- if ((m_ActivationMode != Multiple) && (m_ActivationMode != Points))
- {
- m_TubeGraphProperty->DeactivateAllTubes();
- RenderingManager::GetInstance()->RequestUpdateAll();
- // TODO!!!this->InvokeEvent(SelectionChangedTubeGraphEvent());
- }
- // show info on status bar
- StatusBar::GetInstance()->DisplayText("No tube hit!");
-}
-
-void mitk::TubeGraphDataInteractor::SetActivationMode(const ActivationMode &activationMode)
-{
- m_ActivationMode = activationMode;
- if (m_TubeGraph.IsNotNull())
- if (m_LastPickedTube != mitk::TubeGraph::ErrorId)
- this->UpdateActivation();
-}
-
-mitk::TubeGraphDataInteractor::ActivationMode mitk::TubeGraphDataInteractor::GetActivationMode()
-{
- return m_ActivationMode;
-}
-
-void mitk::TubeGraphDataInteractor::SetActionMode(const ActionMode &actionMode)
-{
- m_ActionMode = actionMode;
-}
-
-mitk::TubeGraphDataInteractor::ActionMode mitk::TubeGraphDataInteractor::GetActionMode()
-{
- return m_ActionMode;
-}
-
-void mitk::TubeGraphDataInteractor::SelectTubesByActivationModus()
-{
- if (m_LastPickedTube != mitk::TubeGraph::ErrorId)
- {
- this->UpdateActivation();
- }
-}
-
-void mitk::TubeGraphDataInteractor::UpdateActivation()
-{
- if (m_ActionMode == RootMode)
- {
- m_TubeGraphProperty->DeactivateAllTubes();
- m_TubeGraphProperty->SetTubeActive(m_LastPickedTube, true);
-
- // QmitkTubeGraphSelectRootDialog* dialog = new QmitkTubeGraphSelectRootDialog(m_Parent);
- // int dialogReturnValue = dialog->exec();
- // delete dialog;
-
- // if ( dialogReturnValue != QDialog::Rejected ) // user doesn't clicked cancel or pressed Esc or something similar
- //{
- m_TubeGraph->SetRootTube(m_LastPickedTube);
- //}
- m_TubeGraphProperty->DeactivateAllTubes();
- RenderingManager::GetInstance()->RequestUpdateAll();
- }
- else
- {
- switch (m_ActivationMode)
- {
- case None:
- {
- m_TubeGraphProperty->DeactivateAllTubes();
- }
- break;
-
- case Single:
- {
- m_TubeGraphProperty->DeactivateAllTubes();
- m_TubeGraphProperty->SetTubeActive(m_LastPickedTube, true);
- }
- break;
-
- case Multiple:
- { // special deactivation for multiple modus
- // if activated--> deactivate; if not activated--> activate
- if (m_TubeGraphProperty->IsTubeActive(m_LastPickedTube))
- m_TubeGraphProperty->SetTubeActive(m_LastPickedTube, false);
- else
- m_TubeGraphProperty->SetTubeActive(m_LastPickedTube, true);
- }
- break;
-
- case ToRoot:
- {
- m_TubeGraphProperty->DeactivateAllTubes();
- std::vector<TubeGraph::TubeDescriptorType> activeTubes = this->GetTubesToRoot();
- m_TubeGraphProperty->SetTubesActive(activeTubes);
- }
- break;
- case ToPeriphery:
- {
- m_TubeGraphProperty->DeactivateAllTubes();
- std::vector<TubeGraph::TubeDescriptorType> activeTubes = this->GetPathToPeriphery();
- m_TubeGraphProperty->SetTubesActive(activeTubes);
- }
- break;
-
- case Points:
- {
- m_TubeGraphProperty->DeactivateAllTubes();
- std::vector<TubeGraph::TubeDescriptorType> activeTubes = this->GetTubesBetweenPoints();
- m_TubeGraphProperty->SetTubesActive(activeTubes);
- }
- break;
-
- default:
- MITK_WARN << "Unknown tube graph interaction mode!";
- break;
- }
- }
-}
-
-std::vector<mitk::TubeGraph::TubeDescriptorType> mitk::TubeGraphDataInteractor::GetTubesToRoot()
-{
- TubeGraph::TubeDescriptorType root = m_TubeGraph->GetRootTube();
- if (root == TubeGraph::ErrorId)
- {
- root = m_TubeGraph->GetThickestTube();
- m_TubeGraph->SetRootTube(root);
- }
-
- return this->GetPathBetweenTubes(m_LastPickedTube, root);
-}
-
-std::vector<mitk::TubeGraph::TubeDescriptorType> mitk::TubeGraphDataInteractor::GetTubesBetweenPoints()
-{
- return this->GetPathBetweenTubes(m_LastPickedTube, m_SecondLastPickedTube);
-}
-
-std::vector<mitk::TubeGraph::TubeDescriptorType> mitk::TubeGraphDataInteractor::GetPathBetweenTubes(
- const mitk::TubeGraph::TubeDescriptorType &start, const mitk::TubeGraph::TubeDescriptorType &end)
-{
- std::vector<mitk::TubeGraph::TubeDescriptorType> solutionPath;
- if ((start != TubeGraph::ErrorId) && (end != TubeGraph::ErrorId))
- {
- if (start != end)
- solutionPath = m_TubeGraph->SearchAllPathBetweenVertices(start, end);
- else
- solutionPath.push_back(start);
- }
-
- return solutionPath;
-}
-
-std::vector<mitk::TubeGraph::TubeDescriptorType> mitk::TubeGraphDataInteractor::GetPathToPeriphery()
-{
- std::vector<mitk::TubeGraph::TubeDescriptorType> solutionPath;
-
- if (m_LastPickedTube != TubeGraph::ErrorId)
- solutionPath = m_TubeGraph->SearchPathToPeriphery(m_LastPickedTube);
-
- return solutionPath;
-}
-
-void mitk::TubeGraphDataInteractor::ResetPickedTubes()
-{
- m_LastPickedTube = TubeGraph::ErrorId;
- m_SecondLastPickedTube = TubeGraph::ErrorId;
-}
-
-mitk::Point3D mitk::TubeGraphDataInteractor::GetLastPickedPosition()
-{
- if (m_LastPickedElement)
- return m_LastPickedElement->GetCoordinates();
- else
- return mitk::Point3D();
-}
diff --git a/Modules/TubeGraph/src/Interactions/mitkTubeGraphPicker.cpp b/Modules/TubeGraph/src/Interactions/mitkTubeGraphPicker.cpp
deleted file mode 100644
index 3fa1a9ca3a..0000000000
--- a/Modules/TubeGraph/src/Interactions/mitkTubeGraphPicker.cpp
+++ /dev/null
@@ -1,93 +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 "mitkTubeGraphPicker.h"
-
-mitk::TubeGraphPicker::TubeGraphPicker()
-{
- m_WorldPosition.Fill(0.0);
-}
-
-mitk::TubeGraphPicker::~TubeGraphPicker() {}
-
-void mitk::TubeGraphPicker::SetTubeGraph(const mitk::TubeGraph *tubeGraph)
-{
- m_TubeGraph = tubeGraph;
- m_TubeGraphProperty =
- dynamic_cast<TubeGraphProperty *>(m_TubeGraph->GetProperty("Tube Graph.Visualization Information").GetPointer());
-}
-
-/**
- * Implements the picking process
- */
-std::pair<mitk::TubeGraph::TubeDescriptorType, mitk::TubeElement *> mitk::TubeGraphPicker::GetPickedTube(
- const Point3D pickedPosition)
-{
- if (!m_TubeGraph)
- {
- MITK_ERROR << "mitk::TubeGraphPicker: No tube graph available. Please set an input!" << std::endl;
- mitk::TubeElement *nullPointer = nullptr;
- return std::pair<mitk::TubeGraph::TubeDescriptorType, mitk::TubeElement *>(TubeGraph::ErrorId, nullPointer);
- }
- m_WorldPosition = pickedPosition;
-
- Point3D currentPosition;
- ScalarType closestDistance = itk::NumericTraits<ScalarType>::max();
- ScalarType currentDistance = itk::NumericTraits<ScalarType>::max();
- float currentRadius = 0;
-
- TubeGraph::TubeDescriptorType currentTubeId(TubeGraph::ErrorId);
- TubeGraph::TubeDescriptorType tubeId(TubeGraph::ErrorId);
- TubeElement *tubeElement;
-
- // iterate over all edges and find the edge, which element is near by the clicked point
- std::vector<mitk::TubeGraphEdge> allEdges = m_TubeGraph->GetVectorOfAllEdges();
- for (auto edge = allEdges.begin(); edge != allEdges.end(); ++edge)
- {
- std::pair<mitk::TubeGraphVertex, mitk::TubeGraphVertex> soureTargetPair =
- m_TubeGraph->GetVerticesOfAnEdge(m_TubeGraph->GetEdgeDescriptor(*edge));
-
- currentTubeId = TubeGraph::TubeDescriptorType(m_TubeGraph->GetVertexDescriptor(soureTargetPair.first),
- m_TubeGraph->GetVertexDescriptor(soureTargetPair.second));
- // check if the tube is visible, if not pass this tube. User can not choose a tube, which he can't see
- if (m_TubeGraphProperty->IsTubeVisible(currentTubeId))
- {
- std::vector<mitk::TubeElement *> allElements = edge->GetElementVector();
- for (unsigned int index = 0; index < edge->GetNumberOfElements(); index++)
- {
- currentPosition = allElements[index]->GetCoordinates();
- if (dynamic_cast<mitk::CircularProfileTubeElement *>(allElements[index]))
- currentRadius = ((dynamic_cast<mitk::CircularProfileTubeElement *>(allElements[index]))->GetDiameter()) / 2;
- else
- currentRadius = 0;
-
- // calculate point->point distance
- itk::Index<3> worldIndex;
- m_TubeGraph->GetGeometry()->WorldToIndex(pickedPosition, worldIndex);
-
- m_WorldPosition[0] = worldIndex[0];
- m_WorldPosition[1] = worldIndex[1];
- m_WorldPosition[2] = worldIndex[2];
-
- currentDistance = m_WorldPosition.EuclideanDistanceTo(currentPosition);
- if (currentDistance < closestDistance && (currentDistance - currentRadius) < 1.0)
- {
- closestDistance = currentDistance;
- tubeId = currentTubeId;
- tubeElement = allElements[index];
- }
- }
- }
- }
-
- return std::make_pair(tubeId, tubeElement);
-}
diff --git a/Modules/TubeGraph/src/Rendering/mitkTubeGraphProperty.cpp b/Modules/TubeGraph/src/Rendering/mitkTubeGraphProperty.cpp
deleted file mode 100644
index 745be8cc85..0000000000
--- a/Modules/TubeGraph/src/Rendering/mitkTubeGraphProperty.cpp
+++ /dev/null
@@ -1,438 +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 "mitkTubeGraphProperty.h"
-
-#include <mitkRenderingManager.h>
-
-mitk::TubeGraphProperty::TubeGraphProperty()
-/*: m_LabelGroups(), m_ActiveTubes(), m_TubeToLabelsMap()*/
-{
-}
-
-mitk::TubeGraphProperty::TubeGraphProperty(const mitk::TubeGraphProperty &other)
- : BaseProperty(other),
- m_ActiveTubes(other.m_ActiveTubes),
- m_LabelGroups(other.m_LabelGroups),
- m_TubeToLabelsMap(other.m_TubeToLabelsMap),
- m_Annotations(other.m_Annotations)
-{
-}
-
-mitk::TubeGraphProperty::~TubeGraphProperty()
-{
- m_ActiveTubes.clear();
- m_TubeToLabelsMap.clear();
-
- for (auto it = m_LabelGroups.begin(); it != m_LabelGroups.end(); it++)
- delete *it;
- m_LabelGroups.clear();
-}
-
-bool mitk::TubeGraphProperty::IsTubeVisible(const TubeDescriptorType &tube)
-{
- // search for any label settings for the tube
- if (m_LabelGroups.size() > 0)
- {
- for (auto it = m_TubeToLabelsMap.begin(); it != m_TubeToLabelsMap.end(); it++)
- {
- if (this->TubeDescriptorsCompare(tube, (*it).first.first))
- {
- // At the moment only the first entry is considered
- LabelGroup *lg = this->GetLabelGroupByName((*it).first.second);
- LabelGroup::Label *label = this->GetLabelByName(lg, (*it).second);
- return label->isVisible;
- }
- }
- // If nothing is found, look if the first labelgroup is visible for "undefined" label
- LabelGroup::Label *label = this->GetLabelByName((*m_LabelGroups.begin()), "Undefined");
- return label->isVisible;
- }
- else
- return true;
-}
-
-void mitk::TubeGraphProperty::SetTubeActive(const TubeDescriptorType &tube, const bool &active)
-{
- // set active
- if (active)
- {
- for (std::vector<TubeDescriptorType>::const_iterator it = m_ActiveTubes.begin(); it != m_ActiveTubes.end(); it++)
- {
- if (this->TubeDescriptorsCompare(tube, (*it)))
- {
- return;
- }
- }
- // if not found, add it
- m_ActiveTubes.push_back(tube);
- this->Modified();
- }
- // set deactive
- else
- {
- for (auto it = m_ActiveTubes.begin(); it != m_ActiveTubes.end(); it++)
- {
- if (this->TubeDescriptorsCompare(tube, (*it)))
- { // if found, delete it
- m_ActiveTubes.erase(it);
- this->Modified();
- return;
- }
- }
- }
- //// render new activation
- // RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void mitk::TubeGraphProperty::SetTubesActive(std::vector<TubeDescriptorType> &tubes)
-{
- for (auto it = tubes.begin(); it != tubes.end(); it++)
- this->SetTubeActive(*it, true);
-}
-
-bool mitk::TubeGraphProperty::IsTubeActive(const TubeDescriptorType &tube)
-{
- for (std::vector<TubeDescriptorType>::const_iterator it = m_ActiveTubes.begin(); it != m_ActiveTubes.end(); it++)
- {
- if (this->TubeDescriptorsCompare((*it), tube))
- return true;
- }
- return false;
-}
-
-std::vector<mitk::TubeGraphProperty::TubeDescriptorType> mitk::TubeGraphProperty::GetActiveTubes()
-{
- return m_ActiveTubes;
-}
-
-void mitk::TubeGraphProperty::DeactivateAllTubes()
-{
- // if (!m_ActiveTubes.empty())
- m_ActiveTubes.clear();
- this->Modified();
-}
-
-void mitk::TubeGraphProperty::AddAnnotation(mitk::TubeGraphProperty::Annotation *annotation)
-{
- for (auto it = m_Annotations.begin(); it != m_Annotations.end(); it++)
- {
- if ((*it)->name == annotation->name)
- {
- MITK_INFO << "An Annotation with this name already exists.";
- return;
- }
- }
- m_Annotations.push_back(annotation);
-}
-mitk::TubeGraphProperty::Annotation *mitk::TubeGraphProperty::GetAnnotationByName(std::string annotation)
-{
- for (auto it = m_Annotations.begin(); it != m_Annotations.end(); it++)
- {
- if ((*it)->name == annotation)
- return *it;
- }
- return nullptr;
-}
-std::vector<mitk::TubeGraphProperty::Annotation *> mitk::TubeGraphProperty::GetAnnotations()
-{
- return m_Annotations;
-}
-void mitk::TubeGraphProperty::RemoveAnnotation(mitk::TubeGraphProperty::Annotation *annotation)
-{
- for (auto it = m_Annotations.begin(); it != m_Annotations.end(); it++)
- {
- if ((*it)->name == annotation->name)
- {
- m_Annotations.erase(it);
- return;
- }
- }
-}
-
-mitk::Color mitk::TubeGraphProperty::GetColorOfTube(const TubeDescriptorType &tube)
-{
- Color color;
- // grey as default color
- color[0] = 150;
- color[1] = 150;
- color[2] = 150;
-
- bool isActive(false);
- bool hasLabel(false);
- // search the vector with active tubes first. If the tube is active it can not have another color.
- for (std::vector<TubeDescriptorType>::const_iterator it = m_ActiveTubes.begin(); it != m_ActiveTubes.end(); it++)
- {
- if (this->TubeDescriptorsCompare(tube, (*it)))
- {
- color[0] = 255;
- color[1] = 255;
- color[2] = 0;
- isActive = true;
- break;
- }
- }
-
- if (!isActive)
- {
- // So let see which label is activ on this tube and which color is set.
- if (m_LabelGroups.size() > 0)
- {
- for (auto it = m_TubeToLabelsMap.begin(); it != m_TubeToLabelsMap.end(); it++)
- {
- if (this->TubeDescriptorsCompare(tube, (*it).first.first))
- { // At the moment only the first entry is considered
- LabelGroup *lg = this->GetLabelGroupByName((*it).first.second);
- LabelGroup::Label *label = this->GetLabelByName(lg, (*it).second);
- color = label->labelColor;
- hasLabel = true;
- }
- }
- // If nothing is found, look if the first labelgroup is visible for "undefined" label
- if (!hasLabel)
- {
- LabelGroup::Label *label = this->GetLabelByName(*(m_LabelGroups.begin()), "Undefined");
- color = label->labelColor;
- }
- }
- }
-
- return color;
-}
-
-void mitk::TubeGraphProperty::SetLabelForActivatedTubes(LabelGroup *labelGroup, LabelGroup::Label *label)
-{
- bool isUndefined(label->labelName.compare("Undefined") == 0);
- for (unsigned int i = 0; i < m_ActiveTubes.size(); i++)
- {
- bool isInList(false);
- for (auto it = m_TubeToLabelsMap.begin(); it != m_TubeToLabelsMap.end(); it++)
- {
- if ((this->TubeDescriptorsCompare(it->first.first, m_ActiveTubes[i])) &&
- (labelGroup->labelGroupName.compare(it->first.second) == 0))
- {
- // If tube has a label fromlabel group, deleted if "undefined" is clicked.
- if (isUndefined)
- {
- m_TubeToLabelsMap.erase(it);
- break;
- }
- else
- {
- it->second = label->labelName;
- isInList = true;
- }
- }
- }
- if (!isInList && !isUndefined)
- {
- TubeToLabelGroupType tubeToLabelGroup(m_ActiveTubes[i], labelGroup->labelGroupName);
- m_TubeToLabelsMap.insert(std::pair<TubeToLabelGroupType, std::string>(tubeToLabelGroup, label->labelName));
- }
- }
- this->Modified();
- m_ActiveTubes.clear();
-}
-
-void mitk::TubeGraphProperty::SetTubesToLabels(std::map<TubeToLabelGroupType, std::string> tubeToLabelMap)
-{
- m_TubeToLabelsMap = tubeToLabelMap;
-}
-
-std::map<mitk::TubeGraphProperty::TubeToLabelGroupType, std::string> mitk::TubeGraphProperty::GetTubesToLabels()
-{
- return m_TubeToLabelsMap;
-}
-
-void mitk::TubeGraphProperty::AddLabelGroup(LabelGroup *labelGroup, unsigned int position)
-{
- // Check if the name is unique
- for (auto it = m_LabelGroups.begin(); it != m_LabelGroups.end(); it++)
- {
- if (labelGroup->labelGroupName.compare((*it)->labelGroupName) == 0)
- {
- MITK_ERROR << "The label group must be unique! This name already exists!";
- return;
- }
- }
-
- // Add the label group at position, if you can, otherwise put it at the end of the vector
- if (position < m_LabelGroups.size() - 1)
- {
- auto it = m_LabelGroups.begin() + position;
- m_LabelGroups.insert(it, labelGroup);
- }
- else
- {
- m_LabelGroups.push_back(labelGroup);
-
- // when given position is larger then vector size, the label group will be added at the last position
- if (position >= m_LabelGroups.size())
- MITK_INFO << "Position is out of space. So the label group was added on last position: "
- << m_LabelGroups.size() - 1;
- }
-}
-
-void mitk::TubeGraphProperty::RemoveLabelGroup(LabelGroup *labelGroup)
-{
- // find labelGroup in vector
- auto foundElement = std::find(m_LabelGroups.begin(), m_LabelGroups.end(), labelGroup);
- unsigned int pos = foundElement - m_LabelGroups.begin();
-
- // found it? delete it!
- if (pos < m_LabelGroups.size())
- {
- // delete every assignment to a tube
- for (auto it = m_TubeToLabelsMap.begin(); it != m_TubeToLabelsMap.end(); it++)
- {
- if (labelGroup->labelGroupName.compare((*it).first.second) == 0)
- m_TubeToLabelsMap.erase(it);
- }
-
- m_LabelGroups.erase(foundElement);
- }
- else
- {
- MITK_ERROR << "Could not find the label group!";
- return;
- }
-}
-
-void mitk::TubeGraphProperty::SetLabelColor(LabelGroup::Label *label, mitk::Color color)
-{
- // LabelGroup? Check if it is a label in property class
- if (label)
- {
- label->labelColor = color;
- this->Modified();
- }
-}
-
-void mitk::TubeGraphProperty::SetLabelVisibility(LabelGroup::Label *label, bool isVisible)
-{
- // LabelGroup? Check if it is a label in property class
- if (label)
- {
- label->isVisible = isVisible;
- this->Modified();
- }
-}
-
-void mitk::TubeGraphProperty::RenameLabel(LabelGroup *labelGroup, LabelGroup::Label *label, std::string newName)
-{
- // LabelGroup? Check if it is a label in property class
- if (label)
- {
- // rename the label in the assignement vector for tubes
- for (auto it = m_TubeToLabelsMap.begin(); it != m_TubeToLabelsMap.end(); it++)
- {
- // Label group fit?
- if (labelGroup->labelGroupName.compare((*it).first.second) == 0)
- // label fit?
- if (label->labelName.compare((*it).second) == 0)
- // rename it
- (*it).second = newName;
- }
-
- // rename the label in label group
- label->labelName = newName;
- }
-}
-
-mitk::TubeGraphProperty::LabelGroupSetType mitk::TubeGraphProperty::GetLabelGroups()
-{
- return m_LabelGroups;
-}
-
-unsigned int mitk::TubeGraphProperty::GetNumberOfLabelGroups()
-{
- return m_LabelGroups.size();
-}
-
-unsigned int mitk::TubeGraphProperty::GetIndexOfLabelGroup(mitk::TubeGraphProperty::LabelGroup *labelGroup)
-{
- unsigned int pos = std::find(m_LabelGroups.begin(), m_LabelGroups.end(), labelGroup) - m_LabelGroups.begin();
-
- if (pos < m_LabelGroups.size())
- return pos;
- // label group is not in property class
- else
- {
- MITK_ERROR << "Could not find such a label group!";
- return m_LabelGroups.size();
- }
-}
-
-mitk::TubeGraphProperty::LabelGroup *mitk::TubeGraphProperty::GetLabelGroupByName(std::string labelGroup)
-{
- for (auto it = m_LabelGroups.begin(); it != m_LabelGroups.end(); it++)
- {
- if (labelGroup.compare((*it)->labelGroupName) == 0)
- return (*it);
- }
-
- MITK_ERROR << "Could not find such a label group!";
- return nullptr;
-}
-
-mitk::TubeGraphProperty::LabelGroup::Label *mitk::TubeGraphProperty::GetLabelByName(LabelGroup *labelGroup,
- std::string labelName)
-{
- for (auto it = labelGroup->labels.begin(); it != labelGroup->labels.end(); it++)
- {
- if (labelName.compare((*it)->labelName) == 0)
- return (*it);
- }
-
- MITK_ERROR << "Could not find such a label!";
- return nullptr;
-}
-
-bool mitk::TubeGraphProperty::TubeDescriptorsCompare(const TubeDescriptorType &tube1, const TubeDescriptorType &tube2)
-{
- if (((tube1.first == tube2.first) && (tube1.second == tube2.second)) ||
- ((tube1.first == tube2.second) && (tube1.second == tube2.first)))
- return true;
- else
- return false;
-}
-
-bool mitk::TubeGraphProperty::IsEqual(const BaseProperty &) const
-{ // TODO see ResectionProposalDescriptorProperty
- return true;
-}
-
-bool mitk::TubeGraphProperty::Assign(const BaseProperty &)
-{ // TODO see ResectionProposalDescriptorProperty
- return true;
-}
-
-std::string mitk::TubeGraphProperty::GetValueAsString() const
-{ // TODO
- return "";
-}
-
-itk::LightObject::Pointer mitk::TubeGraphProperty::InternalClone() const
-{
- itk::LightObject::Pointer result(new Self(*this));
- return result;
-}
-
-bool mitk::TubeGraphProperty::ToJSON(nlohmann::json&) const
-{
- return false; // Not implemented
-}
-
-bool mitk::TubeGraphProperty::FromJSON(const nlohmann::json&)
-{
- return false; // Not implemented
-}
diff --git a/Modules/TubeGraph/src/Rendering/mitkTubeGraphVtkMapper3D.cpp b/Modules/TubeGraph/src/Rendering/mitkTubeGraphVtkMapper3D.cpp
deleted file mode 100644
index 864d163416..0000000000
--- a/Modules/TubeGraph/src/Rendering/mitkTubeGraphVtkMapper3D.cpp
+++ /dev/null
@@ -1,753 +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 "mitkTubeGraphVtkMapper3D.h"
-
-#include <mitkColorProperty.h>
-
-#include <vtkCellArray.h>
-#include <vtkClipPolyData.h>
-#include <vtkContourFilter.h>
-#include <vtkCylinder.h>
-#include <vtkFloatArray.h>
-#include <vtkGeneralTransform.h>
-#include <vtkImplicitBoolean.h>
-#include <vtkImplicitModeller.h>
-#include <vtkPlane.h>
-#include <vtkPointData.h>
-#include <vtkPoints.h>
-#include <vtkPolyDataMapper.h>
-#include <vtkProperty.h>
-#include <vtkRenderer.h>
-#include <vtkSampleFunction.h>
-#include <vtkSphereSource.h>
-#include <vtkTubeFilter.h>
-#include <vtkUnsignedCharArray.h>
-
-mitk::TubeGraphVtkMapper3D::TubeGraphVtkMapper3D()
-{
-}
-
-mitk::TubeGraphVtkMapper3D::~TubeGraphVtkMapper3D()
-{
-}
-
-const mitk::TubeGraph *mitk::TubeGraphVtkMapper3D::GetInput()
-{
- return dynamic_cast<const TubeGraph *>(GetDataNode()->GetData());
-}
-
-vtkProp *mitk::TubeGraphVtkMapper3D::GetVtkProp(mitk::BaseRenderer *renderer)
-{
- return m_LSH.GetLocalStorage(renderer)->m_vtkTubeGraphAssembly;
-}
-
-void mitk::TubeGraphVtkMapper3D::GenerateDataForRenderer(mitk::BaseRenderer *renderer)
-{
- bool renderTubeGraph(false);
- LocalStorage *ls = m_LSH.GetLocalStorage(renderer);
-
- TubeGraph::Pointer tubeGraph = const_cast<mitk::TubeGraph *>(this->GetInput());
- TubeGraphProperty::Pointer tubeGraphProperty =
- dynamic_cast<TubeGraphProperty *>(tubeGraph->GetProperty("Tube Graph.Visualization Information").GetPointer());
-
- if (tubeGraph.IsNull() || tubeGraphProperty.IsNull())
- {
- itkWarningMacro(<< "Input of tube graph mapper is nullptr!");
- return;
- }
- // Check if the tube graph has changed; if the data has changed, generate the spheres and tubes new;
- if (tubeGraph->GetMTime() > ls->m_lastGenerateDataTime)
- {
- this->GenerateTubeGraphData(renderer);
- renderTubeGraph = true;
- }
- else
- {
- // Check if the tube graph property has changed; if the property has changed, render the visualization information
- // new;
- if (tubeGraphProperty->GetMTime() > ls->m_lastRenderDataTime)
- {
- this->RenderTubeGraphPropertyInformation(renderer);
- renderTubeGraph = true;
- }
- }
-
- if (renderTubeGraph)
- {
- std::vector<TubeGraph::VertexDescriptorType> alreadyRenderedVertexList;
- // don't render the sphere which is the root of the graph; so add it to the list before;
- // TODO check both spheres
- TubeGraph::VertexDescriptorType root = tubeGraph->GetRootVertex();
- alreadyRenderedVertexList.push_back(root);
-
- for (auto itTubes =
- ls->m_vtkTubesActorMap.begin();
- itTubes != ls->m_vtkTubesActorMap.end();
- itTubes++)
- {
- if (tubeGraphProperty->IsTubeVisible(itTubes->first))
- {
- // add tube actor to assembly
- ls->m_vtkTubeGraphAssembly->AddPart(itTubes->second);
-
- // render the clipped spheres as end-cups of a tube and connections between tubes
- if (std::find(alreadyRenderedVertexList.begin(), alreadyRenderedVertexList.end(), itTubes->first.first) ==
- alreadyRenderedVertexList.end())
- {
- auto itSourceSphere =
- ls->m_vtkSpheresActorMap.find(itTubes->first.first);
- if (itSourceSphere != ls->m_vtkSpheresActorMap.end())
- ls->m_vtkTubeGraphAssembly->AddPart(itSourceSphere->second);
- alreadyRenderedVertexList.push_back(itSourceSphere->first);
- }
- if (std::find(alreadyRenderedVertexList.begin(), alreadyRenderedVertexList.end(), itTubes->first.second) ==
- alreadyRenderedVertexList.end())
- {
- auto itTargetSphere =
- ls->m_vtkSpheresActorMap.find(itTubes->first.second);
- if (itTargetSphere != ls->m_vtkSpheresActorMap.end())
- ls->m_vtkTubeGraphAssembly->AddPart(itTargetSphere->second);
- alreadyRenderedVertexList.push_back(itTargetSphere->first);
- }
- }
- }
- }
-
- //// Opacity TODO
- //{
- // float opacity = 1.0f;
- // if( this->GetDataNode()->GetOpacity(opacity,renderer) )
- // ls->m_vtkTubesActor->GetProperty()->SetOpacity( opacity );
- //}
-}
-
-void mitk::TubeGraphVtkMapper3D::RenderTubeGraphPropertyInformation(mitk::BaseRenderer *renderer)
-{
- MITK_INFO << "Render tube graph property information!";
- LocalStorage *ls = m_LSH.GetLocalStorage(renderer);
- TubeGraph::ConstPointer tubeGraph = this->GetInput();
- TubeGraphProperty::Pointer tubeGraphProperty =
- dynamic_cast<TubeGraphProperty *>(tubeGraph->GetProperty("Tube Graph.Visualization Information").GetPointer());
-
- if (tubeGraphProperty.IsNull())
- {
- MITK_INFO << "No tube graph property!! So no special render information...";
- return;
- }
-
- std::vector<TubeGraphVertex> allVertices = tubeGraph->GetVectorOfAllVertices();
- for (auto vertex = allVertices.begin(); vertex != allVertices.end(); ++vertex)
- {
- TubeGraph::VertexDescriptorType vertexDesc = tubeGraph->GetVertexDescriptor(*vertex);
-
- double sphereColorR = 0;
- double sphereColorG = 0;
- double sphereColorB = 0;
-
- int numberOfVisibleEdges = 0;
- std::vector<TubeGraphEdge> allEdgesOfVertex = tubeGraph->GetAllEdgesOfAVertex(vertexDesc);
- for (auto edge = allEdgesOfVertex.begin(); edge != allEdgesOfVertex.end(); ++edge)
- {
- // get edge descriptor
- EdgeDescriptorType edgeDesc = tubeGraph->GetEdgeDescriptor(*edge);
-
- // get source and target vertex descriptor
- std::pair<TubeGraphVertex, TubeGraphVertex> soureTargetPair = tubeGraph->GetVerticesOfAnEdge(edgeDesc);
- TubeGraphVertex source = soureTargetPair.first;
- TubeGraphVertex target = soureTargetPair.second;
-
- // build tube descriptor [sourceId,targetId]
- TubeGraph::TubeDescriptorType tube;
- tube.first = tubeGraph->GetVertexDescriptor(source);
- tube.second = tubeGraph->GetVertexDescriptor(target);
-
- if (tubeGraphProperty->IsTubeVisible(tube))
- {
- mitk::Color tubeColor = tubeGraphProperty->GetColorOfTube(tube);
-
- vtkSmartPointer<vtkDataArray> scalars =
- ls->m_vtkTubesActorMap[tube]->GetMapper()->GetInput()->GetPointData()->GetScalars();
- double color[3];
- scalars->GetTuple(0, color);
-
- if (color[0] != tubeColor[0] || color[1] != tubeColor[1] || color[2] != tubeColor[2])
- {
- int numberOfPoints = scalars->GetSize();
-
- vtkSmartPointer<vtkUnsignedCharArray> colorScalars = vtkSmartPointer<vtkUnsignedCharArray>::New();
- colorScalars->SetName("colorScalars");
- colorScalars->SetNumberOfComponents(3);
- colorScalars->SetNumberOfTuples(numberOfPoints);
- for (int i = 0; i < numberOfPoints; i++)
- {
- scalars->InsertTuple3(i, tubeColor[0], tubeColor[1], tubeColor[2]);
- }
- ls->m_vtkTubesActorMap[tube]->GetMapper()->GetInput()->GetPointData()->SetActiveScalars("colorScalars");
- }
-
- sphereColorR += tubeColor[0];
- sphereColorG += tubeColor[1];
- sphereColorB += tubeColor[2];
- numberOfVisibleEdges++;
- }
- }
- if (numberOfVisibleEdges > 0)
- {
- sphereColorR /= 255 * numberOfVisibleEdges;
- sphereColorG /= 255 * numberOfVisibleEdges;
- sphereColorB /= 255 * numberOfVisibleEdges;
- }
-
- ls->m_vtkSpheresActorMap[vertexDesc]->GetProperty()->SetColor(sphereColorR, sphereColorG, sphereColorB);
- }
- ls->m_lastRenderDataTime.Modified();
-}
-
-void mitk::TubeGraphVtkMapper3D::GenerateTubeGraphData(mitk::BaseRenderer *renderer)
-{
- MITK_INFO << "Render tube graph!";
- LocalStorage *ls = m_LSH.GetLocalStorage(renderer);
-
- ls->m_vtkTubesActorMap.clear();
- ls->m_vtkSpheresActorMap.clear();
-
- TubeGraph::Pointer tubeGraph = const_cast<mitk::TubeGraph *>(this->GetInput());
- TubeGraphProperty::Pointer tubeGraphProperty =
- dynamic_cast<TubeGraphProperty *>(tubeGraph->GetProperty("Tube Graph.Visualization Information").GetPointer());
- if (tubeGraphProperty.IsNull())
- MITK_INFO << "No tube graph property!! So no special render information...";
-
- // render all edges as tubular structures using the vtkTubeFilter
- std::vector<TubeGraphEdge> allEdges = tubeGraph->GetVectorOfAllEdges();
- for (auto edge = allEdges.begin(); edge != allEdges.end(); ++edge)
- {
- this->GeneratePolyDataForTube(*edge, tubeGraph, tubeGraphProperty, renderer);
- }
-
- // Generate all vertices as spheres
- std::vector<TubeGraphVertex> allVertices = tubeGraph->GetVectorOfAllVertices();
- for (auto vertex = allVertices.begin(); vertex != allVertices.end(); ++vertex)
- {
- this->GeneratePolyDataForFurcation(*vertex, tubeGraph, renderer);
- if (this->ClipStructures())
- {
- this->ClipPolyData(*vertex, tubeGraph, tubeGraphProperty, renderer);
- }
-
- ls->m_lastGenerateDataTime.Modified();
- }
-}
-
-void mitk::TubeGraphVtkMapper3D::GeneratePolyDataForFurcation(mitk::TubeGraphVertex &vertex,
- const mitk::TubeGraph::Pointer &graph,
- mitk::BaseRenderer *renderer)
-{
- LocalStorage *ls = this->m_LSH.GetLocalStorage(renderer);
-
- mitk::Point3D coordinates;
- float diameter = 2;
-
- coordinates = (vertex.GetTubeElement())->GetCoordinates();
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(vertex.GetTubeElement()))
- {
- diameter = (dynamic_cast<const mitk::CircularProfileTubeElement *>(vertex.GetTubeElement()))->GetDiameter();
- }
- vtkSmartPointer<vtkSphereSource> sphereSource = vtkSmartPointer<vtkSphereSource>::New();
- sphereSource->SetCenter(coordinates[0], coordinates[1], coordinates[2]);
- sphereSource->SetRadius(diameter / 2.0f);
- sphereSource->SetThetaResolution(12);
- sphereSource->SetPhiResolution(12);
- sphereSource->Update();
-
- // generate a actor with a mapper for the sphere
- vtkSmartPointer<vtkPolyDataMapper> sphereMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
- vtkSmartPointer<vtkActor> sphereActor = vtkSmartPointer<vtkActor>::New();
-
- sphereMapper->SetInputConnection(sphereSource->GetOutputPort());
- sphereActor->SetMapper(sphereMapper);
-
- ls->m_vtkSpheresActorMap.insert(std::make_pair(graph->GetVertexDescriptor(vertex), sphereActor));
-}
-
-void mitk::TubeGraphVtkMapper3D::GeneratePolyDataForTube(mitk::TubeGraphEdge &edge,
- const mitk::TubeGraph::Pointer &graph,
- const mitk::TubeGraphProperty::Pointer &graphProperty,
- mitk::BaseRenderer *renderer)
-{
- LocalStorage *ls = this->m_LSH.GetLocalStorage(renderer);
-
- // get edge descriptor
- EdgeDescriptorType edgeDesc = graph->GetEdgeDescriptor(edge);
-
- // get source and target vertex descriptor
- std::pair<TubeGraphVertex, TubeGraphVertex> soureTargetPair = graph->GetVerticesOfAnEdge(edgeDesc);
- TubeGraphVertex source = soureTargetPair.first;
- TubeGraphVertex target = soureTargetPair.second;
-
- // build tube descriptor [sourceId,targetId]
- TubeGraph::TubeDescriptorType tube;
- tube.first = graph->GetVertexDescriptor(source);
- tube.second = graph->GetVertexDescriptor(target);
-
- Color color;
- if (graphProperty.IsNotNull())
- {
- color = graphProperty->GetColorOfTube(tube);
- }
- else
- {
- color[0] = 150;
- color[1] = 150;
- color[2] = 150;
- }
-
- // add 2 points for the source and target vertices.
- unsigned int numberOfPoints = edge.GetNumberOfElements() + 2;
-
- // Initialize the required data-structures for building
- // an appropriate input to the tube filter
- vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
- points->SetNumberOfPoints(numberOfPoints);
-
- vtkSmartPointer<vtkFloatArray> radii = vtkSmartPointer<vtkFloatArray>::New();
- radii->SetName("radii");
- radii->SetNumberOfComponents(1);
-
- vtkSmartPointer<vtkCellArray> lines = vtkSmartPointer<vtkCellArray>::New();
-
- vtkSmartPointer<vtkUnsignedCharArray> colorScalars = vtkSmartPointer<vtkUnsignedCharArray>::New();
- colorScalars->SetName("colorScalars");
- colorScalars->SetNumberOfComponents(3);
-
- // resize the data-arrays
- radii->SetNumberOfTuples(numberOfPoints);
- colorScalars->SetNumberOfTuples(numberOfPoints);
- lines->InsertNextCell(numberOfPoints);
-
- // Add the positions of the source node, the elements along the edge and
- // the target node as lines to a cell. This cell is used as input
- // for a Tube Filter
- mitk::Point3D coordinates;
- float diameter = 2;
- unsigned int id = 0;
-
- // Source Node
- coordinates = (source.GetTubeElement())->GetCoordinates();
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(source.GetTubeElement()))
- {
- diameter = (dynamic_cast<const mitk::CircularProfileTubeElement *>(source.GetTubeElement()))->GetDiameter();
- }
- points->InsertPoint(id, coordinates[0], coordinates[1], coordinates[2]);
- radii->InsertTuple1(id, diameter / 2.0f);
-
- colorScalars->InsertTuple3(id, color[0], color[1], color[2]);
- lines->InsertCellPoint(id);
- ++id;
-
- // Iterate along the edge
- std::vector<mitk::TubeElement *> allElements = edge.GetElementVector();
- for (unsigned int index = 0; index < edge.GetNumberOfElements(); index++)
- {
- coordinates = allElements[index]->GetCoordinates();
- if (dynamic_cast<mitk::CircularProfileTubeElement *>(allElements[index]))
- {
- diameter = (dynamic_cast<mitk::CircularProfileTubeElement *>(allElements[index]))->GetDiameter();
- }
- points->InsertPoint(id, coordinates[0], coordinates[1], coordinates[2]);
- radii->InsertTuple1(id, diameter / 2.0f);
- colorScalars->InsertTuple3(id, color[0], color[1], color[2]);
- lines->InsertCellPoint(id);
- ++id;
- }
-
- // Target Node
- coordinates = (target.GetTubeElement())->GetCoordinates();
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(target.GetTubeElement()))
- {
- diameter = (dynamic_cast<const mitk::CircularProfileTubeElement *>(target.GetTubeElement()))->GetDiameter();
- }
- points->InsertPoint(id, coordinates[0], coordinates[1], coordinates[2]);
- radii->InsertTuple1(id, diameter / 2.0f);
- colorScalars->InsertTuple3(id, color[0], color[1], color[2]);
- lines->InsertCellPoint(id);
- ++id;
-
- // Initialize poly data from the point set and the cell array
- // (representing topology)
- vtkSmartPointer<vtkPolyData> polyData = vtkSmartPointer<vtkPolyData>::New();
- polyData->SetPoints(points);
- polyData->SetLines(lines);
- polyData->GetPointData()->AddArray(radii);
- polyData->GetPointData()->AddArray(colorScalars);
- polyData->GetPointData()->SetActiveScalars(radii->GetName());
-
- // Generate a tube for all lines in the polydata object
- double *range = radii->GetRange();
-
- assert(range[0] != 0.0f && range[1] != 0.0f);
-
- vtkSmartPointer<vtkTubeFilter> tubeFilter = vtkSmartPointer<vtkTubeFilter>::New();
- tubeFilter->SetInputData(polyData);
- tubeFilter->SetRadius(range[0]);
- tubeFilter->SetRadiusFactor(range[1] / range[0]);
-
- if (range[0] != range[1])
- tubeFilter->SetVaryRadiusToVaryRadiusByScalar();
-
- tubeFilter->SetNumberOfSides(9);
- tubeFilter->SidesShareVerticesOn();
- tubeFilter->CappingOff();
- tubeFilter->Update();
-
- tubeFilter->GetOutput()->GetPointData()->SetActiveScalars("colorScalars");
-
- // generate a actor with a mapper for the
- vtkSmartPointer<vtkPolyDataMapper> tubeMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
- vtkSmartPointer<vtkActor> tubeActor = vtkSmartPointer<vtkActor>::New();
-
- tubeMapper->SetInputConnection(tubeFilter->GetOutputPort());
- tubeActor->SetMapper(tubeMapper);
- tubeActor->GetProperty()->SetColor(color[0], color[1], color[2]);
-
- ls->m_vtkTubesActorMap.insert(std::pair<TubeGraph::TubeDescriptorType, vtkSmartPointer<vtkActor>>(tube, tubeActor));
-}
-
-void mitk::TubeGraphVtkMapper3D::ClipPolyData(mitk::TubeGraphVertex &vertex,
- const mitk::TubeGraph::Pointer &graph,
- const mitk::TubeGraphProperty::Pointer &graphProperty,
- mitk::BaseRenderer *renderer)
-{
- LocalStorage *ls = this->m_LSH.GetLocalStorage(renderer);
-
- mitk::Point3D centerVertex = vertex.GetTubeElement()->GetCoordinates();
- float diameter = 2;
- if (dynamic_cast<const mitk::CircularProfileTubeElement *>(vertex.GetTubeElement()))
- {
- diameter = (dynamic_cast<const mitk::CircularProfileTubeElement *>(vertex.GetTubeElement()))->GetDiameter();
- }
-
- TubeGraph::VertexDescriptorType vertexDesc = graph->GetVertexDescriptor(vertex);
-
- std::map<TubeGraph::TubeDescriptorType, vtkSmartPointer<vtkImplicitBoolean>> cylinderForClipping;
-
- // generate for all edges/tubes cylinders. With this structure you can clip the sphere and the other tubes, so that no
- // fragments are shown in the tube.
- std::vector<TubeGraphEdge> allEdgesOfVertex = graph->GetAllEdgesOfAVertex(vertexDesc);
- for (auto edge = allEdgesOfVertex.begin(); edge != allEdgesOfVertex.end(); ++edge)
- {
- // get edge descriptor
- EdgeDescriptorType edgeDesc = graph->GetEdgeDescriptor(*edge);
-
- // get source and target vertex descriptor
- auto soureTargetPair = graph->GetVerticesOfAnEdge(edgeDesc);
- TubeGraphVertex source = soureTargetPair.first;
- TubeGraphVertex target = soureTargetPair.second;
-
- // build tube descriptor [sourceId,targetId]
- TubeGraph::TubeDescriptorType tube;
- tube.first = graph->GetVertexDescriptor(source);
- tube.second = graph->GetVertexDescriptor(target);
-
- // get reference point in the tube for the direction
- mitk::Point3D edgeDirectionPoint;
- // get reference diameter
- double cylinderDiameter = diameter;
- float radius = diameter / 2;
- // if the vertex is the source vertex of the edge get the first element of elementVector; otherwise get the last
- // element.
- if (source == vertex)
- {
- // if the edge has no element get the other vertex
- if ((*edge).GetNumberOfElements() != 0)
- {
- double lastDistance = 0, distance = 0;
-
- unsigned int index = 0;
- // Get the first element behind the radius of the sphere
- for (; index < (*edge).GetNumberOfElements(); index++)
- {
- mitk::Vector3D diffVec = (*edge).GetTubeElement(index)->GetCoordinates() - centerVertex;
- distance = std::sqrt(pow(diffVec[0], 2) + pow(diffVec[1], 2) + pow(diffVec[2], 2));
- if (distance > radius)
- break;
- lastDistance = distance;
- }
- // if the last element is not inside the sphere
- if (index < (*edge).GetNumberOfElements())
- {
- double withinSphereDiameter = diameter, outsideSphereDiameter = diameter, interpolationValue = 0.5;
-
- interpolationValue = (radius - lastDistance) / (distance - lastDistance);
- // if first element is outside of the sphere use sphere diameter and the element diameter for interpolation
- if (index == 0)
- {
- if (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(0)))
- outsideSphereDiameter =
- (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(0)))->GetDiameter();
- }
- else
- {
- if (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index - 1)))
- withinSphereDiameter =
- (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index - 1)))->GetDiameter();
-
- if (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index)))
- outsideSphereDiameter =
- (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index)))->GetDiameter();
- }
- // interpolate the diameter for clipping
- cylinderDiameter =
- (1 - interpolationValue) * withinSphereDiameter + interpolationValue * outsideSphereDiameter;
- }
- // Get the reference point, so the direction of the tube can be calculated
- edgeDirectionPoint = (*edge).GetTubeElement(0)->GetCoordinates();
- }
- else
- {
- // Get the reference point, so the direction of the tube can be calculated
- edgeDirectionPoint = target.GetTubeElement()->GetCoordinates();
- }
- }
-
- // if vertex is target of the tube
- else
- {
- // if the edge has no element, get the other vertex
- if ((*edge).GetNumberOfElements() != 0)
- {
- double lastDistance = 0, distance = 0;
- // Get the first element behind the radius of the sphere; now backwards through the element list
- int index = (*edge).GetNumberOfElements();
- for ( ; index >= 0; --index)
- {
- mitk::Vector3D diffVec = (*edge).GetTubeElement(index)->GetCoordinates() - centerVertex;
- distance = std::sqrt(pow(diffVec[0], 2) + pow(diffVec[1], 2) + pow(diffVec[2], 2));
- if (distance > radius)
- break;
- lastDistance = distance;
- }
-
- if (index >= 0)
- {
- double withinSphereDiameter = diameter, outsideSphereDiameter = diameter, interpolationValue = 0.5;
-
- interpolationValue = (radius - lastDistance) / (distance - lastDistance);
-
- if (index == static_cast<int>((*edge).GetNumberOfElements() - 1))
- {
- if (dynamic_cast<mitk::CircularProfileTubeElement *>(
- (*edge).GetTubeElement((*edge).GetNumberOfElements() - 1)))
- outsideSphereDiameter = (dynamic_cast<mitk::CircularProfileTubeElement *>(
- (*edge).GetTubeElement((*edge).GetNumberOfElements() - 1)))
- ->GetDiameter();
- }
- else
- {
- if (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index + 1)))
- withinSphereDiameter =
- (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index + 1)))->GetDiameter();
-
- if (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index)))
- outsideSphereDiameter =
- (dynamic_cast<mitk::CircularProfileTubeElement *>((*edge).GetTubeElement(index)))->GetDiameter();
- }
- // interpolate the diameter for clipping
- cylinderDiameter =
- (1 - interpolationValue) * withinSphereDiameter + interpolationValue * outsideSphereDiameter;
- }
- // Get the reference point, so the direction of the tube can be calculated
- edgeDirectionPoint = (*edge).GetTubeElement((*edge).GetNumberOfElements() - 1)->GetCoordinates();
- }
- else
- {
- // Get the reference point, so the direction of the tube can be calculated
- edgeDirectionPoint = source.GetTubeElement()->GetCoordinates();
- }
- }
-
- //////Calculate the matrix for rotation and translation////
- // get the normalized vector for the orientation (tube element direction)
- mitk::Vector3D vecOrientation;
- mitk::FillVector3D(vecOrientation,
- (edgeDirectionPoint[0] - centerVertex[0]),
- (edgeDirectionPoint[1] - centerVertex[1]),
- (edgeDirectionPoint[2] - centerVertex[2]));
- vecOrientation.Normalize();
-
- // generate a random vector
- mitk::Vector3D vecRandom;
- mitk::FillVector3D(vecRandom, (rand() % 100 - 50), (rand() % 100 - 50), (rand() % 100 - 50));
- // project the random vector on the plane-->orthogonal vector to plane normal; normalize it!
- mitk::Vector3D vecOrthoToOrientation;
- vecOrthoToOrientation = vecRandom - (vecRandom * vecOrientation) * vecOrientation;
- vecOrthoToOrientation.Normalize();
-
- // get the cross product of both orthogonale vectors to get a third one
- mitk::Vector3D vecCrossProduct;
- vecCrossProduct = itk::CrossProduct(vecOrientation, vecOrthoToOrientation);
- vecCrossProduct.Normalize();
-
- // Fill matrix
- vtkSmartPointer<vtkMatrix4x4> vtkTransformMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
- vtkTransformMatrix->Identity();
- // 1. column
- vtkTransformMatrix->SetElement(0, 0, vecOrthoToOrientation[0]);
- vtkTransformMatrix->SetElement(1, 0, vecOrthoToOrientation[1]);
- vtkTransformMatrix->SetElement(2, 0, vecOrthoToOrientation[2]);
- // 2. column
- vtkTransformMatrix->SetElement(0, 1, vecOrientation[0]);
- vtkTransformMatrix->SetElement(1, 1, vecOrientation[1]);
- vtkTransformMatrix->SetElement(2, 1, vecOrientation[2]);
- // 3. column
- vtkTransformMatrix->SetElement(0, 2, vecCrossProduct[0]);
- vtkTransformMatrix->SetElement(1, 2, vecCrossProduct[1]);
- vtkTransformMatrix->SetElement(2, 2, vecCrossProduct[2]);
- // 4. column
- vtkTransformMatrix->SetElement(0, 3, centerVertex[0]);
- vtkTransformMatrix->SetElement(1, 3, centerVertex[1]);
- vtkTransformMatrix->SetElement(2, 3, centerVertex[2]);
-
- vtkSmartPointer<vtkGeneralTransform> transform = vtkSmartPointer<vtkGeneralTransform>::New();
- transform->Concatenate(vtkTransformMatrix);
- // transform->Translate(centerVertex[0],centerVertex[1],centerVertex[2]);
-
- transform->Inverse();
- transform->Update();
-
- // Generate plane in center [0,0,0] with n= (0,1,0) as normal vector
- vtkSmartPointer<vtkPlane> plane = vtkSmartPointer<vtkPlane>::New();
- plane->SetOrigin(0, 0, 0);
- plane->SetNormal(0, 1, 0);
-
- // Generate a cylinder in center [0,0,0] and the axes of rotation is along the y-axis; radius is vertex diameter/2;
- vtkSmartPointer<vtkCylinder> cylinder = vtkSmartPointer<vtkCylinder>::New();
- cylinder->SetCenter(0, 0, 0);
- cylinder->SetRadius(cylinderDiameter / 2);
- // cylinder->SetTransform(transform);
-
- // Truncate the infinite cylinder with the plane
- vtkSmartPointer<vtkImplicitBoolean> cutCylinder = vtkSmartPointer<vtkImplicitBoolean>::New();
- cutCylinder->SetOperationTypeToDifference();
- cutCylinder->SetTransform(transform);
- cutCylinder->AddFunction(cylinder);
- cutCylinder->AddFunction(plane);
-
- cylinderForClipping.insert(
- std::pair<TubeGraph::TubeDescriptorType, vtkSmartPointer<vtkImplicitBoolean>>(tube, cutCylinder));
-
- //// Sample the function
- // vtkSmartPointer<vtkSampleFunction> sample = vtkSmartPointer<vtkSampleFunction>::New();
- // sample->SetSampleDimensions(100,100,100);
- // sample->SetImplicitFunction(cutCylinder);
- ////double value = 200.0;
- // double xmin = centerVertex[0]-(2*diameter), xmax = centerVertex[0]+(2*diameter),
- // ymin = centerVertex[1]-(2*diameter), ymax = centerVertex[1]+(2*diameter),
- // zmin = centerVertex[2]-(2*diameter), zmax = centerVertex[2]+(2*diameter);
- // sample->SetModelBounds(xmin, xmax, ymin, ymax, zmin, zmax);
-
- // vtkSmartPointer<vtkContourFilter> contour =vtkSmartPointer<vtkContourFilter>::New();
- // contour->SetInputConnection(sample->GetOutputPort());
- // contour->SetValue( 0, 0.25);
-
- // vtkSmartPointer<vtkPolyDataMapper> impMapper = vtkSmartPointer<vtkPolyDataMapper>::New();
- // impMapper->SetInputConnection (contour->GetOutputPort());
- // impMapper->ScalarVisibilityOff();
- // vtkSmartPointer<vtkActor> impActor = vtkSmartPointer<vtkActor>::New();
- // impActor->SetMapper(impMapper);
-
- // ls->m_vtkTubeGraphAssembly->AddPart(impActor);
- }
-
- double sphereColorR = 0;
- double sphereColorG = 0;
- double sphereColorB = 0;
-
- for (auto itClipStructure =
- cylinderForClipping.begin();
- itClipStructure != cylinderForClipping.end();
- itClipStructure++)
- {
- vtkSmartPointer<vtkPolyDataMapper> sphereMapper =
- dynamic_cast<vtkPolyDataMapper *>(ls->m_vtkSpheresActorMap[vertexDesc]->GetMapper());
-
- if (sphereMapper != nullptr)
- {
- // first clip the sphere with the cylinder
- vtkSmartPointer<vtkClipPolyData> clipperSphere = vtkSmartPointer<vtkClipPolyData>::New();
- clipperSphere->SetInputData(sphereMapper->GetInput());
- clipperSphere->SetClipFunction(itClipStructure->second);
- clipperSphere->GenerateClippedOutputOn();
- clipperSphere->Update();
-
- sphereMapper->SetInputConnection(clipperSphere->GetOutputPort());
- sphereMapper->Update();
- }
-
- mitk::Color tubeColor = graphProperty->GetColorOfTube(itClipStructure->first);
- sphereColorR += tubeColor[0];
- sphereColorG += tubeColor[1];
- sphereColorB += tubeColor[2];
-
- // than clip with all other tubes
- for (auto itTobBeClipped =
- cylinderForClipping.begin();
- itTobBeClipped != cylinderForClipping.end();
- itTobBeClipped++)
- {
- TubeGraph::TubeDescriptorType toBeClippedTube = itTobBeClipped->first;
-
- if (itClipStructure->first != toBeClippedTube)
- {
- vtkSmartPointer<vtkPolyDataMapper> tubeMapper =
- dynamic_cast<vtkPolyDataMapper *>(ls->m_vtkTubesActorMap[toBeClippedTube]->GetMapper());
-
- if (tubeMapper != nullptr)
- {
- // first clip the sphere with the cylinder
- vtkSmartPointer<vtkClipPolyData> clipperTube = vtkSmartPointer<vtkClipPolyData>::New();
- tubeMapper->Update();
- clipperTube->SetInputData(tubeMapper->GetInput());
- clipperTube->SetClipFunction(itClipStructure->second);
- clipperTube->GenerateClippedOutputOn();
- clipperTube->Update();
-
- tubeMapper->SetInputConnection(clipperTube->GetOutputPort());
- tubeMapper->Update();
- }
- }
- }
- }
- if (cylinderForClipping.size() != 0)
- {
- sphereColorR /= 255 * cylinderForClipping.size();
- sphereColorG /= 255 * cylinderForClipping.size();
- sphereColorB /= 255 * cylinderForClipping.size();
- }
-
- ls->m_vtkSpheresActorMap[vertexDesc]->GetProperty()->SetColor(sphereColorR, sphereColorG, sphereColorB);
-}
-
-bool mitk::TubeGraphVtkMapper3D::ClipStructures()
-{
- DataNode::Pointer node = this->GetDataNode();
- if (node.IsNull())
- {
- itkWarningMacro(<< "associated node is nullptr!");
- return false;
- }
-
- bool clipStructures = false;
- node->GetBoolProperty("Tube Graph.Clip Structures", clipStructures);
-
- return clipStructures;
-}
diff --git a/Plugins/PluginList.cmake b/Plugins/PluginList.cmake
index 231542bd9e..4e73a65a56 100644
--- a/Plugins/PluginList.cmake
+++ b/Plugins/PluginList.cmake
@@ -1,84 +1,76 @@
# 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.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.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.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.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.overlaymanager:OFF
org.mitk.gui.qt.igt.app.hummelprotocolmeasurements: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.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.concentration.mri:OFF
org.mitk.gui.qt.pharmacokinetics.curvedescriptor: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.flowapplication:OFF
org.mitk.gui.qt.flow.segmentation:OFF
org.mitk.gui.qt.pixelvalue:ON
)
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/CMakeLists.txt b/Plugins/org.mitk.gui.qt.deformableclippingplane/CMakeLists.txt
deleted file mode 100644
index 8dd1c33292..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/CMakeLists.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-project(org_mitk_gui_qt_deformableclippingplane)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE DEFORMABLECLIPPINGPLANE_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
-)
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox
deleted file mode 100644
index e4eb5ea593..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane.dox
+++ /dev/null
@@ -1,73 +0,0 @@
-/**
-\page org_mitk_views_deformableclippingplane The Clipping Plane View
-
-\imageMacro{QmitkClippingPlane_Icon.png,"Icon of the Clipping Plane Plugin",5.00}
-
-
-\imageMacro{QmitkClippingPlane_Overview2.png,"Clipping Plane view",16.00}
-
-\tableofcontents
-
-\section org_mitk_views_clippingPlaneManualOverview Overview
-
-The <b>Clipping Plane view</b> allows you to create clipping planes and calculate the volumina of the divided parts.
-
-
-\section org_mitk_views_clippingPlaneTechnicalIssue Technical Issue
-
-To use the Update Volumina function your image should be binary.
-
-\section org_mitk_views_clippingPlaneManualImageSelection Image Selection
-
-The Clipping Plane view makes use of the Data Manager view to give you an overview of all images, segmentations and clipping planes.
-
-\imageMacro{QmitkClippingPlane_DataManager.png,"Data Manager is used for selecting the current clipping plane. The reference plane is selected in the drop down box of the control area.",8.00}
-
-To select the reference plane use the drop down box in the control area of the Clipping Plane view or the Data Manager. The clipping plane selected in the Data Manager is displayed below the drop down box. If no clipping plane exists or none is selected create a new clipping plane by using the "Create new clipping plane" button.
-Some items of the graphical user interface might be disabled when no plane is selected.
-In any case, the application will give you hints if a selection is needed.
-
-\section org_mitk_views_clippingPlaneCreating Creating New Clipping Plane
-
-If you want to create a new clipping plane select an image from the Data Manager and press the button "Create new clipping plane". Optionally you can enable the "...with surface model" option.
-
-\section org_mitk_views_clippingPlaneInteraction Interaction with the planes
-\imageMacro{QmitkClippingPlane_Interaction.png,"The interaction buttons",5.00}
-
-You have different options to interact with the clipping planes:
-
-\subsection org_mitk_views_clippingPlaneTranslation Translation
-
-In Translation mode you can change the position of the clipping plane.
- - Click the Translation Button
- - Move mouse over the selected clipping plane (the plane changes its color from blue to green)
- - Hold mouse-left button and move the mouse orthogonally to the plane
-
-\subsection org_mitk_views_clippingPlaneRotation Rotation
-
-In Rotation mode you can change the angle of the clipping plane.
- - Click the Rotation Button
- - Move mouse over the selected clipping plane (the plane changes its color from blue to green)
- - Hold mouse-left button and move the mouse in the direction it should be rotated
-
-\subsection org_mitk_views_clippingPlaneDeformation Deformation
-
-In Deformation mode you can change the surface of the clipping plane.
- - Click the Deformation Button
- - Move mouse over the selected clipping plane (the plane changes its color from blue to green). The deformation area is highlighted in red and yellow.
- - On mouse-scrolling you can change the size of the deformation area (Scroll-Down = smaller / Scroll-Up = bigger).
- - Hold mouse-left button and move the mouse orthogonally to the plane to deformate the plane
-
-\section org_mitk_views_clippingPlaneUpdateVolumina Update Volumina
-
-\imageMacro{QmitkClippingPlane_UpdateVolumina.png,"The 'Update Volumina' button",5.00}
-
-Calculating the volumina of the segmentation parts, which are divided by the clipping plane(s).
- - Create a segmentation (see Segmentation-Manual)
- - Create one or more clipping plane(s)
- - Use the interaction buttons (Translation, Rotation, Deformation) to adjust the clipping plane for intersecting the segmentation
- - (You can decide which planes shouldn't be included for the calculation by changing their visibility to invisible)
- - Click button "Update Volumina" button
- - The intersected parts are displayed in different colors and their volumina are shown beneath the "Update Volumina" button
-
-**/
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_DataManager.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_DataManager.png
deleted file mode 100644
index d786549d26..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_DataManager.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Icon.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Icon.png
deleted file mode 100644
index c8e3ab8953..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Icon.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Interaction.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Interaction.png
deleted file mode 100644
index 0ed78e487f..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Interaction.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview.png
deleted file mode 100644
index 3e1de5fb08..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview2.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview2.png
deleted file mode 100644
index c261f169b4..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_Overview2.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_UpdateVolumina.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_UpdateVolumina.png
deleted file mode 100644
index 11baa0631c..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/documentation/UserManual/QmitkClippingPlane_UpdateVolumina.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/files.cmake b/Plugins/org.mitk.gui.qt.deformableclippingplane/files.cmake
deleted file mode 100644
index d6fb308c8c..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/files.cmake
+++ /dev/null
@@ -1,21 +0,0 @@
-set(CPP_FILES
- src/internal/QmitkDeformableClippingPlaneView.cpp
- src/internal/mitkPluginActivator.cpp
-)
-
-set(MOC_H_FILES
- src/internal/mitkPluginActivator.h
- src/internal/QmitkDeformableClippingPlaneView.h
-)
-
-set(UI_FILES
- src/internal/QmitkDeformableClippingPlaneViewControls.ui
-)
-
-set(CACHED_RESOURCE_FILES
- resources/deformablePlane.png
- resources/clipping_plane_translate_48x48.png
- resources/clipping_plane_rotate48x48.png
- resources/clipping_plane_deform48x48.png
- plugin.xml
-)
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.deformableclippingplane/manifest_headers.cmake
deleted file mode 100644
index b64619ac32..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Clipping Plane")
-set(Plugin-Version "1.0.0")
-set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
-set(Plugin-ContactAddress "https://www.mitk.org")
-set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.datamanager)
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/plugin.xml b/Plugins/org.mitk.gui.qt.deformableclippingplane/plugin.xml
deleted file mode 100644
index 09a9fd4c0c..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/plugin.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.deformableclippingplane"
- name="Clipping Plane"
- category="Segmentation"
- class="QmitkDeformableClippingPlaneView"
- icon="resources/deformablePlane.png">
- <description>Allow the clipping of a volume using a deformable plane.</description>
- <keywordReference id="org.mitk.views.deformableclippingplane.ViewKeyword" />
- </view>
- </extension>
- <extension point="org.blueberry.ui.keywords">
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Plane" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Volume calculation" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Splitting" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Deformation" />
- <keyword id="org.mitk.views.deformableclippingplane.ViewKeyword" label="Volume analysis" />
- </extension>
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png
deleted file mode 100644
index 74af5fa6eb..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png
deleted file mode 100644
index 19018f23fc..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png
deleted file mode 100644
index 01fe80f023..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/deformablePlane.png b/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/deformablePlane.png
deleted file mode 100644
index c8e3ab8953..0000000000
Binary files a/Plugins/org.mitk.gui.qt.deformableclippingplane/resources/deformablePlane.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp
deleted file mode 100644
index 6f72a2c5df..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.cpp
+++ /dev/null
@@ -1,584 +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 "QmitkDeformableClippingPlaneView.h"
-
-#include <usModuleRegistry.h>
-
-// mitk core
-#include <mitkImageToSurfaceFilter.h>
-#include <mitkInteractionConst.h>
-#include <mitkLevelWindowProperty.h>
-#include <mitkLookupTableProperty.h>
-#include <mitkNodePredicateDataType.h>
-#include <mitkNodePredicateNot.h>
-#include <mitkRenderingModeProperty.h>
-#include <mitkRotationOperation.h>
-#include <mitkSurfaceVtkMapper3D.h>
-#include <mitkVtkRepresentationProperty.h>
-#include <mitkVtkResliceInterpolationProperty.h>
-
-#include <mitkHeightFieldSurfaceClipImageFilter.h>
-#include <mitkClippingPlaneInteractor3D.h>
-#include <mitkLabeledImageLookupTable.h>
-#include <mitkLabeledImageVolumeCalculator.h>
-#include <mitkSurfaceDeformationDataInteractor3D.h>
-
-#include <vtkFloatArray.h>
-#include <vtkPointData.h>
-#include <vtkPlaneSource.h>
-#include <vtkProperty.h>
-
-#include <mitkILinkedRenderWindowPart.h>
-
-#include <array>
-
-const std::string QmitkDeformableClippingPlaneView::VIEW_ID = "org.mitk.views.deformableclippingplane";
-
-QmitkDeformableClippingPlaneView::QmitkDeformableClippingPlaneView()
- : QmitkAbstractView()
- , m_Controls(new Ui::QmitkDeformableClippingPlaneViewControls)
- , m_WorkingNode(nullptr)
-{
- auto isImage = mitk::TNodePredicateDataType<mitk::Image>::New();
- auto isNotHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true)));
-
- m_IsImagePredicate = mitk::NodePredicateAnd::New(isImage, isNotHelperObject);
-
- m_IsClippingPlanePredicate = mitk::NodePredicateProperty::New("clippingPlane", mitk::BoolProperty::New(true));
-}
-
-QmitkDeformableClippingPlaneView::~QmitkDeformableClippingPlaneView()
-{
- if (m_WorkingNode.IsNotNull())
- m_WorkingNode->SetDataInteractor(nullptr);
-}
-
-void QmitkDeformableClippingPlaneView::SetFocus()
-{
- m_Controls->createNewPlanePushButton->setFocus();
-}
-
-void QmitkDeformableClippingPlaneView::CreateQtPartControl(QWidget *parent)
-{
- m_Controls->setupUi(parent);
-
- m_Controls->imageSelectionWidget->SetDataStorage(GetDataStorage());
- m_Controls->imageSelectionWidget->SetNodePredicate(m_IsImagePredicate);
- m_Controls->imageSelectionWidget->SetSelectionIsOptional(false);
- m_Controls->imageSelectionWidget->SetInvalidInfo("Select an image or segmentation.");
- m_Controls->imageSelectionWidget->SetPopUpTitel("Select an image or segmentation.");
-
- m_Controls->clippingPlaneSelector->SetDataStorage(this->GetDataStorage());
- m_Controls->clippingPlaneSelector->SetPredicate(m_IsClippingPlanePredicate);
-
- m_Controls->volumeGroupBox->setEnabled(false);
- m_Controls->interactionSelectionBox->setEnabled(false);
- m_Controls->planesWarningLabel->hide();
-
- this->CreateConnections();
-
- m_Controls->imageSelectionWidget->SetAutoSelectNewNodes(true);
-}
-
-void QmitkDeformableClippingPlaneView::OnCurrentSelectionChanged(const QList<mitk::DataNode::Pointer>& /*nodes*/)
-{
- this->UpdateView();
-}
-
-void QmitkDeformableClippingPlaneView::OnComboBoxSelectionChanged(const mitk::DataNode* node)
-{
- this->DeactivateInteractionButtons();
-
- auto selectedNode = const_cast<mitk::DataNode*>(node);
- if(nullptr != selectedNode)
- {
- if(m_WorkingNode.IsNotNull())
- selectedNode->SetDataInteractor(m_WorkingNode->GetDataInteractor());
-
- m_WorkingNode = selectedNode;
- }
-
- this->UpdateView();
-}
-
-void QmitkDeformableClippingPlaneView::OnCreateNewClippingPlane()
-{
- this->DeactivateInteractionButtons();
-
- auto plane = mitk::Surface::New();
- auto planeSource = vtkSmartPointer<vtkPlaneSource>::New();
-
- planeSource->SetOrigin(-32.0, -32.0, 0.0);
- planeSource->SetPoint1(32.0, -32.0, 0.0);
- planeSource->SetPoint2(-32.0, 32.0, 0.0);
- planeSource->SetResolution(128, 128);
- planeSource->Update();
-
- plane->SetVtkPolyData(planeSource->GetOutput());
-
- mitk::ScalarType imageDiagonal = 200.0;
-
- auto selectedNode = m_Controls->imageSelectionWidget->GetSelectedNode();
- if (selectedNode.IsNotNull())
- {
- auto selectedImage = dynamic_cast<mitk::Image*>(selectedNode->GetData());
- if (nullptr != selectedImage)
- {
- // check if user wants a surface model
- if (m_Controls->surfaceModelCheckBox->isChecked())
- {
- //Check if there is a surface node from the image. If not, create one
- bool createSurfaceFromImage = true;
- auto isSurface = mitk::NodePredicateDataType::New("Surface");
- auto childNodes = GetDataStorage()->GetDerivations(selectedNode, isSurface, true);
-
- for (mitk::DataStorage::SetOfObjects::ConstIterator it = childNodes->Begin();
- it != childNodes->End(); it++)
- {
- if (it.Value().IsNotNull() && it->Value()->GetName() == selectedNode->GetName())
- {
- createSurfaceFromImage = false;
- it.Value()->SetVisibility(true);
- }
- }
-
- if (createSurfaceFromImage)
- {
- //Lsg 2: Surface for the 3D-perspective
- auto surfaceFilter = mitk::ImageToSurfaceFilter::New();
- surfaceFilter->SetInput(selectedImage);
- surfaceFilter->SetThreshold(1);
- surfaceFilter->SetSmooth(true);
- //Downsampling
- surfaceFilter->SetDecimate(mitk::ImageToSurfaceFilter::DecimatePro);
-
- auto surfaceNode = mitk::DataNode::New();
- surfaceNode->SetData(surfaceFilter->GetOutput());
- surfaceNode->SetProperty("color", selectedNode->GetProperty("color"));
- surfaceNode->SetOpacity(0.5);
- surfaceNode->SetName(selectedNode->GetName());
- this->GetDataStorage()->Add(surfaceNode, selectedNode);
- }
- }
-
- //If an image is selected trim the plane to this.
- imageDiagonal = selectedImage->GetGeometry()->GetDiagonalLength();
- plane->SetOrigin(selectedImage->GetGeometry()->GetCenter());
-
- // Rotate plane
- mitk::Vector3D rotationAxis;
- mitk::FillVector3D(rotationAxis, 0.0, 1.0, 0.0);
- mitk::RotationOperation op(mitk::OpROTATE, selectedImage->GetGeometry()->GetCenter(), rotationAxis, 90.0);
- plane->GetGeometry()->ExecuteOperation(&op);
- }
- }
-
- // equivalent to the extent and resolution function of the clipping plane
- const auto x = imageDiagonal * 0.9;
- planeSource->SetOrigin(-x / 2.0, -x / 2.0, 0.0);
- planeSource->SetPoint1(x / 2.0, -x / 2.0, 0.0);
- planeSource->SetPoint2(-x / 2.0, x / 2.0, 0.0);
- planeSource->SetResolution(64, 64);
- planeSource->Update();
-
- plane->SetVtkPolyData(planeSource->GetOutput());
-
- // Set scalars (for colorization of plane)
- vtkFloatArray *scalars = vtkFloatArray::New();
- scalars->SetName("Distance");
- scalars->SetNumberOfComponents(1);
-
- const auto numerOfPoints = plane->GetVtkPolyData(0)->GetNumberOfPoints();
- for (std::remove_const_t<decltype(numerOfPoints)> i = 0; i < plane->GetVtkPolyData(0)->GetNumberOfPoints(); ++i)
- {
- scalars->InsertNextValue(-1.0);
- }
- plane->GetVtkPolyData(0)->GetPointData()->SetScalars(scalars);
- plane->GetVtkPolyData(0)->GetPointData()->Update();
-
- auto planeNode = mitk::DataNode::New();
- planeNode->SetData(plane);
-
- std::stringstream planeName;
- planeName << "ClippingPlane ";
- planeName << this->GetAllClippingPlanes()->Size() + 1;
-
- planeNode->SetName(planeName.str());
- planeNode->AddProperty("clippingPlane", mitk::BoolProperty::New(true));
- // Make plane pickable
- planeNode->SetBoolProperty("pickable", true);
-
- mitk::SurfaceVtkMapper3D::SetDefaultProperties(planeNode);
-
- // Don't include plane in bounding box!
- planeNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false));
-
- // Set lookup table for plane surface visualization
- auto lookupTablevtk = vtkSmartPointer<vtkLookupTable>::New();
- lookupTablevtk->SetHueRange(0.6, 0.0);
- lookupTablevtk->SetSaturationRange(1.0, 1.0);
- lookupTablevtk->SetValueRange(1.0, 1.0);
- lookupTablevtk->SetTableRange(-1.0, 1.0);
- lookupTablevtk->Build();
-
- auto lookupTable = mitk::LookupTable::New();
- lookupTable->SetVtkLookupTable(lookupTablevtk);
-
- auto prop = mitk::LookupTableProperty::New(lookupTable);
-
- planeNode->SetProperty("LookupTable", prop);
- planeNode->SetBoolProperty("scalar visibility", true);
- planeNode->SetBoolProperty("color mode", true);
- planeNode->SetFloatProperty("ScalarsRangeMinimum", -1.0);
- planeNode->SetFloatProperty("ScalarsRangeMaximum", 1.0);
-
- // Configure material so that only scalar colors are shown
- planeNode->SetColor(0.0f, 0.0f, 0.0f);
- planeNode->SetOpacity(1.0f);
- planeNode->SetFloatProperty("material.wireframeLineWidth", 2.0f);
-
- //Set view of plane to wireframe
- planeNode->SetProperty("material.representation", mitk::VtkRepresentationProperty::New(VTK_WIREFRAME));
-
- //Add the plane to data storage
- this->GetDataStorage()->Add(planeNode);
-
- //Change the index of the selector to the new generated node
- m_Controls->clippingPlaneSelector->setCurrentIndex(m_Controls->clippingPlaneSelector->Find(planeNode));
-
- m_Controls->interactionSelectionBox->setEnabled(true);
-
- if (auto renderWindowPart = dynamic_cast<mitk::ILinkedRenderWindowPart*>(this->GetRenderWindowPart()))
- {
- renderWindowPart->EnableSlicingPlanes(false);
- }
-
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void QmitkDeformableClippingPlaneView::OnCalculateClippingVolume()
-{
- auto selectedNode = m_Controls->imageSelectionWidget->GetSelectedNode();
- if (selectedNode.IsNull())
- {
- MITK_ERROR << "No segmentation selected! Can't calculate volume";
- return;
- }
-
- bool isSegmentation = false;
- selectedNode->GetBoolProperty("binary", isSegmentation);
- if (!isSegmentation)
- {
- MITK_ERROR << "No segmentation selected! Can't calculate volume";
- return;
- }
-
- std::vector<mitk::Surface*> clippingPlanes;
- mitk::DataStorage::SetOfObjects::ConstPointer allClippingPlanes = this->GetAllClippingPlanes();
- for (mitk::DataStorage::SetOfObjects::ConstIterator itPlanes = allClippingPlanes->Begin(); itPlanes != allClippingPlanes->End(); itPlanes++)
- {
- bool isVisible = false;
- itPlanes.Value()->GetBoolProperty("visible", isVisible);
- auto plane = dynamic_cast<mitk::Surface*>(itPlanes.Value()->GetData());
-
- if (isVisible && nullptr != plane)
- clippingPlanes.push_back(plane);
- }
-
- if (clippingPlanes.empty())
- {
- MITK_ERROR << "No clipping plane selected! Can't calculate volume";
- return;
- }
-
- // deactivate Tools
- this->DeactivateInteractionButtons();
- //Clear the list of volumes, before calculating the new values
- m_Controls->volumeList->clear();
-
- selectedNode->SetBoolProperty("visible", false);
-
- //set some properties for clipping the image-->Output: labeled Image
- mitk::HeightFieldSurfaceClipImageFilter::Pointer surfaceClipFilter = mitk::HeightFieldSurfaceClipImageFilter::New();
-
- surfaceClipFilter->SetInput(dynamic_cast<mitk::Image*>(selectedNode->GetData()));
- surfaceClipFilter->SetClippingModeToMultiPlaneValue();
- surfaceClipFilter->SetClippingSurfaces(clippingPlanes);
- surfaceClipFilter->Update();
-
- //delete the old clipped image node
- mitk::DataStorage::SetOfObjects::ConstPointer oldClippedNode = this->GetDataStorage()->GetSubset(mitk::NodePredicateProperty::New("name", mitk::StringProperty::New("Clipped Image")));
- if (oldClippedNode.IsNotNull())
- this->GetDataStorage()->Remove(oldClippedNode);
-
- //add the new clipped image node
- auto clippedNode = mitk::DataNode::New();
- mitk::Image::Pointer clippedImage = surfaceClipFilter->GetOutput();
- clippedImage->DisconnectPipeline();
- clippedNode->SetData(clippedImage);
- clippedNode->SetName("Clipped Image");
- clippedNode->SetColor(1.0, 1.0, 1.0); // color property will not be used, labeled image lookuptable will be used instead
- clippedNode->SetProperty("use color", mitk::BoolProperty::New(false));
- clippedNode->SetProperty("reslice interpolation", mitk::VtkResliceInterpolationProperty::New(VTK_RESLICE_NEAREST));
- clippedNode->SetOpacity(0.4);
- this->GetDataStorage()->Add(clippedNode);
-
- auto volumeCalculator = mitk::LabeledImageVolumeCalculator::New();
- volumeCalculator->SetImage(clippedImage);
- volumeCalculator->Calculate();
-
- auto volumes = volumeCalculator->GetVolumes();
-
- auto lookupTable = mitk::LabeledImageLookupTable::New();
- int lablesWithVolume = 0;
- const auto numberOfVolumes = volumes.size();
- for (std::remove_const_t<decltype(numberOfVolumes)> i = 1; i < numberOfVolumes; ++i)
- {
- if (0 != volumes[0])
- {
- lablesWithVolume++;
-
- mitk::Color color(GetLabelColor(lablesWithVolume));
- lookupTable->SetColorForLabel(i, color.GetRed(), color.GetGreen(), color.GetBlue(), 1.0);
-
- QColor qcolor;
- qcolor.setRgbF(color.GetRed(), color.GetGreen(), color.GetBlue(), 0.7);
-
- //output volume as string "x.xx ml"
- std::stringstream stream;
- stream << std::fixed << std::setprecision(2) << 0.001 * volumes[i] << " ml";
- stream << " ml";
-
- auto item = new QListWidgetItem();
- item->setText(QString::fromStdString(stream.str()));
- item->setBackground(qcolor);
- m_Controls->volumeList->addItem(item);
- }
- }
-
- //set the rendering mode to use the lookup table and level window
- clippedNode->SetProperty("Image Rendering.Mode", mitk::RenderingModeProperty::New(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR));
- mitk::LookupTableProperty::Pointer lutProp = mitk::LookupTableProperty::New(lookupTable.GetPointer());
- clippedNode->SetProperty("LookupTable", lutProp);
- // it is absolutely important, to use the LevelWindow settings provided by
- // the LUT generator, otherwise, it is not guaranteed, that colors show
- // up correctly.
- clippedNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(lookupTable->GetLevelWindow()));
-}
-
-void QmitkDeformableClippingPlaneView::OnTranslationMode(bool check)
-{
- if (check)
- { //uncheck all other buttons
- m_Controls->rotationPushButton->setChecked(false);
- m_Controls->deformationPushButton->setChecked(false);
-
- mitk::ClippingPlaneInteractor3D::Pointer affineDataInteractor = mitk::ClippingPlaneInteractor3D::New();
- affineDataInteractor->LoadStateMachine("ClippingPlaneInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- affineDataInteractor->SetEventConfig("ClippingPlaneTranslationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- affineDataInteractor->SetDataNode(m_WorkingNode);
- }
- else
- m_WorkingNode->SetDataInteractor(nullptr);
-}
-
-void QmitkDeformableClippingPlaneView::OnRotationMode(bool check)
-{
- if (check)
- { //uncheck all other buttons
- m_Controls->translationPushButton->setChecked(false);
- m_Controls->deformationPushButton->setChecked(false);
-
- mitk::ClippingPlaneInteractor3D::Pointer affineDataInteractor = mitk::ClippingPlaneInteractor3D::New();
- affineDataInteractor->LoadStateMachine("ClippingPlaneInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- affineDataInteractor->SetEventConfig("ClippingPlaneRotationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- affineDataInteractor->SetDataNode(m_WorkingNode);
- }
- else
- m_WorkingNode->SetDataInteractor(nullptr);
-}
-
-void QmitkDeformableClippingPlaneView::OnDeformationMode(bool check)
-{
- if (check)
- { //uncheck all other buttons
- m_Controls->translationPushButton->setChecked(false);
- m_Controls->rotationPushButton->setChecked(false);
-
- mitk::SurfaceDeformationDataInteractor3D::Pointer surfaceDataInteractor = mitk::SurfaceDeformationDataInteractor3D::New();
- surfaceDataInteractor->LoadStateMachine("ClippingPlaneInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- surfaceDataInteractor->SetEventConfig("ClippingPlaneDeformationConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- surfaceDataInteractor->SetDataNode(m_WorkingNode);
- }
- else
- m_WorkingNode->SetDataInteractor(nullptr);
-}
-
-void QmitkDeformableClippingPlaneView::CreateConnections()
-{
- connect(m_Controls->imageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
- this, &QmitkDeformableClippingPlaneView::OnCurrentSelectionChanged);
- connect(m_Controls->translationPushButton, &QPushButton::toggled,
- this, &QmitkDeformableClippingPlaneView::OnTranslationMode);
- connect(m_Controls->rotationPushButton, &QPushButton::toggled,
- this, &QmitkDeformableClippingPlaneView::OnRotationMode);
- connect(m_Controls->deformationPushButton, &QPushButton::toggled,
- this, &QmitkDeformableClippingPlaneView::OnDeformationMode);
- connect(m_Controls->createNewPlanePushButton, &QPushButton::clicked,
- this, &QmitkDeformableClippingPlaneView::OnCreateNewClippingPlane);
- connect(m_Controls->updateVolumePushButton, &QPushButton::clicked,
- this, &QmitkDeformableClippingPlaneView::OnCalculateClippingVolume);
- connect(m_Controls->clippingPlaneSelector, &QmitkDataStorageComboBox::OnSelectionChanged,
- this, &QmitkDeformableClippingPlaneView::OnComboBoxSelectionChanged);
-}
-
-void QmitkDeformableClippingPlaneView::NodeRemoved(const mitk::DataNode* node)
-{
- if (m_IsClippingPlanePredicate->CheckNode(node))
- {
- if (this->GetAllClippingPlanes()->Size() <= 1)
- {
- m_WorkingNode = nullptr;
- this->UpdateView();
- }
- }
-}
-
-void::QmitkDeformableClippingPlaneView::NodeChanged(const mitk::DataNode*)
-{
- this->UpdateView();
-}
-
-void QmitkDeformableClippingPlaneView::UpdateView()
-{
- auto selectedNode = m_Controls->imageSelectionWidget->GetSelectedNode();
- if (selectedNode.IsNotNull())
- {
- m_Controls->selectedReferenceImageLabel->setText(QString::fromUtf8(selectedNode->GetName().c_str()));
- if (m_WorkingNode.IsNotNull())
- {
- bool isSegmentation = false;
- selectedNode->GetBoolProperty("binary", isSegmentation);
- m_Controls->interactionSelectionBox->setEnabled(true);
-
- m_Controls->volumeGroupBox->setEnabled(isSegmentation);
-
- //clear list --> than search for all shown clipping plans (max 7 planes)
- m_Controls->selectedClippingPlanesLabel->setText("");
- m_Controls->planesWarningLabel->hide();
- int volumePlanes = 0;
-
- auto allClippingPlanes = this->GetAllClippingPlanes();
- for (mitk::DataStorage::SetOfObjects::ConstIterator itPlanes = allClippingPlanes->Begin(); itPlanes != allClippingPlanes->End(); itPlanes++)
- {
- bool isVisible = false;
- itPlanes.Value()->GetBoolProperty("visible", isVisible);
- if (isVisible)
- {
- if (volumePlanes < 7)
- {
- ++volumePlanes;
- m_Controls->selectedClippingPlanesLabel->setText(m_Controls->selectedClippingPlanesLabel->text().append(QString::fromStdString(itPlanes.Value()->GetName()+"\n")));
- }
- else
- {
- m_Controls->planesWarningLabel->show();
- return;
- }
- }
- }
- }
- else
- {
- m_Controls->volumeGroupBox->setEnabled(false);
- m_Controls->interactionSelectionBox->setEnabled(false);
- m_Controls->selectedClippingPlanesLabel->setText("");
- m_Controls->volumeList->clear();
- }
- }
- else
- {
- m_Controls->volumeGroupBox->setEnabled(false);
- m_Controls->selectedReferenceImageLabel->setText("");
- m_Controls->selectedClippingPlanesLabel->setText("");
- m_Controls->planesWarningLabel->hide();
-
- m_Controls->interactionSelectionBox->setEnabled(m_WorkingNode.IsNotNull());
- }
-}
-
-mitk::DataStorage::SetOfObjects::ConstPointer QmitkDeformableClippingPlaneView::GetAllClippingPlanes()
-{
- auto allPlanes = GetDataStorage()->GetSubset(m_IsClippingPlanePredicate);
- return allPlanes;
-}
-
-mitk::Color QmitkDeformableClippingPlaneView::GetLabelColor(int label)
-{
- std::array<float, 3> color = { 0.0f, 0.0f, 0.0f };
-
- switch (label % 6)
- {
- case 0: // red
- color[0] = 1.0f;
- break;
- case 1: // green
- color[1] = 1.0f;
- break;
- case 2: // blue
- color[2] = 1.0f;
- break;
- case 3: // yellow
- color[0] = 1.0f;
- color[1] = 1.0f;
- break;
- case 4: // magenta
- color[0] = 1.0f;
- color[2] = 1.0f;
- break;
- case 5: // cyan
- color[1] = 1.0f;
- color[2] = 1.0f;
- default: // black
- break;
- }
-
- int outerCycleNr = label / 6;
- int cycleSize = std::min(1, static_cast<int>(std::pow(2.0, std::log(outerCycleNr) / std::log(2.0))));
- int insideCycleCounter = outerCycleNr % cycleSize;
-
- float factor;
- if (0 == outerCycleNr)
- {
- factor = 255.0f;
- }
- else
- {
- factor = 256.0f / (2.0f * cycleSize) + insideCycleCounter * (256.0f / cycleSize);
- }
-
- color = {
- std::min(1.0f, color[0] / 256.0f * factor),
- std::min(1.0f, color[1] / 256.0f * factor),
- std::min(1.0f, color[2] / 256.0f * factor)
- };
-
- return mitk::Color(color.data());
-}
-
-void QmitkDeformableClippingPlaneView::DeactivateInteractionButtons()
-{
- m_Controls->translationPushButton->setChecked(false);
- m_Controls->rotationPushButton->setChecked(false);
- m_Controls->deformationPushButton->setChecked(false);
-}
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.h b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.h
deleted file mode 100644
index 9b2a17dccb..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneView.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 QmitkDeformableClippingPlaneView_h
-#define QmitkDeformableClippingPlaneView_h
-
-#include <ui_QmitkDeformableClippingPlaneViewControls.h>
-
-#include <mitkImage.h>
-#include <mitkNodePredicateAnd.h>
-#include <mitkNodePredicateProperty.h>
-#include <QmitkAbstractView.h>
-
-typedef itk::RGBPixel< float > Color;
-
-/**
- * @brief
- */
-class QmitkDeformableClippingPlaneView : public QmitkAbstractView
-{
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- QmitkDeformableClippingPlaneView();
- ~QmitkDeformableClippingPlaneView() override;
-
- void SetFocus() override;
-
-private Q_SLOTS:
-
- void OnCurrentSelectionChanged(const QList<mitk::DataNode::Pointer>& nodes);
- void OnComboBoxSelectionChanged(const mitk::DataNode* node);
- void OnCreateNewClippingPlane();
- void OnCalculateClippingVolume();
-
- void OnTranslationMode(bool check);
- void OnRotationMode(bool check);
- void OnDeformationMode(bool check);
-
-private:
-
- void CreateQtPartControl(QWidget *parent) override;
- virtual void CreateConnections();
-
- void NodeRemoved(const mitk::DataNode* node) override;
- void NodeChanged(const mitk::DataNode* node) override;
-
- void UpdateView();
-
- mitk::DataStorage::SetOfObjects::ConstPointer GetAllClippingPlanes();
- mitk::Color GetLabelColor(int label);
- void DeactivateInteractionButtons();
-
- Ui::QmitkDeformableClippingPlaneViewControls* m_Controls;
-
- mitk::NodePredicateAnd::Pointer m_IsImagePredicate;
- mitk::NodePredicateProperty::Pointer m_IsClippingPlanePredicate;
-
- mitk::DataNode::Pointer m_WorkingNode;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneViewControls.ui b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneViewControls.ui
deleted file mode 100644
index f19a2edcc3..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/QmitkDeformableClippingPlaneViewControls.ui
+++ /dev/null
@@ -1,429 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkDeformableClippingPlaneViewControls</class>
- <widget class="QWidget" name="QmitkDeformableClippingPlaneViewControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>300</width>
- <height>600</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="windowTitle">
- <string>Deformable surface</string>
- </property>
- <layout class="QVBoxLayout">
- <item>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QLabel" name="imageSelectionLabel">
- <property name="text">
- <string>Selected image</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QmitkSingleNodeSelectionWidget" name="imageSelectionWidget" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>40</height>
- </size>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QGroupBox" name="planeGroupBox">
- <property name="checkable">
- <bool>false</bool>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_1">
- <item>
- <widget class="QPushButton" name="createNewPlanePushButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Create new clipping plane</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QCheckBox" name="surfaceModelCheckBox">
- <property name="layoutDirection">
- <enum>Qt::RightToLeft</enum>
- </property>
- <property name="text">
- <string>...with surface model</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QLabel" name="clippingPlaneSelectorLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Maximum" 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="text">
- <string>Plane</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QmitkDataStorageComboBox" name="clippingPlaneSelector">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="sizeAdjustPolicy">
- <enum>QComboBox::AdjustToMinimumContentsLength</enum>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QGroupBox" name="interactionSelectionBox">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <widget class="QPushButton" name="translationPushButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>50</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Translation</string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="icon">
- <iconset>
- <normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png</normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_translate_48x48.png</iconset>
- </property>
- <property name="iconSize">
- <size>
- <width>32</width>
- <height>32</height>
- </size>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="autoRepeat">
- <bool>false</bool>
- </property>
- <property name="autoExclusive">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="rotationPushButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>50</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Rotation</string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="icon">
- <iconset>
- <normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png</normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_rotate48x48.png</iconset>
- </property>
- <property name="iconSize">
- <size>
- <width>32</width>
- <height>32</height>
- </size>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="autoExclusive">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="deformationPushButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimumSize">
- <size>
- <width>20</width>
- <height>50</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Deformation</string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="icon">
- <iconset>
- <normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png</normaloff>:/org.mitk.gui.qt.deformableclippingplane/resources/clipping_plane_deform48x48.png</iconset>
- </property>
- <property name="iconSize">
- <size>
- <width>32</width>
- <height>32</height>
- </size>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="autoExclusive">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="planesWarningLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Maximum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Please select less or equal 6 clipping planes!</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="volumeGroupBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="title">
- <string/>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_5">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <widget class="QLabel" name="referenceImageLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Referenced image</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="clippingPlanesLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Clipping planes</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QLabel" name="selectedReferenceImageLabel">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="selectedClippingPlanesLabel">
- <property name="font">
- <font>
- <pointsize>8</pointsize>
- </font>
- </property>
- <property name="alignment">
- <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QPushButton" name="updateVolumePushButton">
- <property name="text">
- <string>Update Volumina</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QListWidget" name="volumeList">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <customwidgets>
- <customwidget>
- <class>QmitkSingleNodeSelectionWidget</class>
- <extends>QWidget</extends>
- <header location="global">QmitkSingleNodeSelectionWidget.h</header>
- </customwidget>
- <customwidget>
- <class>QmitkDataStorageComboBox</class>
- <extends>QComboBox</extends>
- <header location="global">QmitkDataStorageComboBox.h</header>
- </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.cpp
deleted file mode 100644
index 6fdaaa8cdd..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.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 "mitkPluginActivator.h"
-#include "QmitkDeformableClippingPlaneView.h"
-
-void mitk::PluginActivator::start(ctkPluginContext *context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(QmitkDeformableClippingPlaneView, context)
-}
-
-void mitk::PluginActivator::stop(ctkPluginContext *)
-{
-}
diff --git a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.h
deleted file mode 100644
index 0adc31438c..0000000000
--- a/Plugins/org.mitk.gui.qt.deformableclippingplane/src/internal/mitkPluginActivator.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 mitkPluginActivator_h
-#define mitkPluginActivator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk
-{
- class PluginActivator : public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_deformableclippingplane")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
- void start(ctkPluginContext *context) override;
- void stop(ctkPluginContext *context) override;
- };
-}
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/CMakeLists.txt b/Plugins/org.mitk.gui.qt.eventrecorder/CMakeLists.txt
deleted file mode 100644
index 2f08c6d36d..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_eventrecorder)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE EVENTRECORDER_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt
-)
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/files.cmake b/Plugins/org.mitk.gui.qt.eventrecorder/files.cmake
deleted file mode 100644
index 858711fa87..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/files.cmake
+++ /dev/null
@@ -1,46 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_eventrecorder_Activator.cpp
- InteractionEventRecorder.cpp
-)
-
-set(UI_FILES
- src/internal/InteractionEventRecorderControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_eventrecorder_Activator.h
- src/internal/InteractionEventRecorder.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
- plugin.xml
- resources/play.png
- resources/rec.png
- resources/stop_rec.png
- resources/stop.png
- resources/icon.png
-)
-
-# 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.eventrecorder/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.eventrecorder/manifest_headers.cmake
deleted file mode 100644
index ea9bb6e6f3..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Eventrecorder")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
-set(Plugin-ContactAddress "")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/plugin.xml b/Plugins/org.mitk.gui.qt.eventrecorder/plugin.xml
deleted file mode 100644
index c412788f66..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/plugin.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.interactioneventrecorder"
- name="Interaction Event Recorder"
- class="InteractionEventRecorder"
- icon="resources/icon.png" >
- <description>Records and plays interaction to test the GUI</description>
- <keywordReference id="org.mitk.views.interactioneventrecorder.Keyword"/>
- </view>
- </extension>
- <extension point="org.blueberry.ui.keywords">
- <keyword label="Testing" id="org.mitk.views.interactioneventrecorder.Keyword"/>
- <keyword label="Recording" id="org.mitk.views.interactioneventrecorder.Keyword"/>
- <keyword label="GUI" id="org.mitk.views.interactioneventrecorder.Keyword"/>
- <keyword label="Interaction" id="org.mitk.views.interactioneventrecorder.Keyword"/>
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/resources/icon.png b/Plugins/org.mitk.gui.qt.eventrecorder/resources/icon.png
deleted file mode 100644
index 7f2545d959..0000000000
Binary files a/Plugins/org.mitk.gui.qt.eventrecorder/resources/icon.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/resources/play.png b/Plugins/org.mitk.gui.qt.eventrecorder/resources/play.png
deleted file mode 100644
index b352da58ad..0000000000
Binary files a/Plugins/org.mitk.gui.qt.eventrecorder/resources/play.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/resources/rec.png b/Plugins/org.mitk.gui.qt.eventrecorder/resources/rec.png
deleted file mode 100644
index 26c424ca75..0000000000
Binary files a/Plugins/org.mitk.gui.qt.eventrecorder/resources/rec.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/resources/stop.png b/Plugins/org.mitk.gui.qt.eventrecorder/resources/stop.png
deleted file mode 100644
index e9e377b46c..0000000000
Binary files a/Plugins/org.mitk.gui.qt.eventrecorder/resources/stop.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/resources/stop_rec.png b/Plugins/org.mitk.gui.qt.eventrecorder/resources/stop_rec.png
deleted file mode 100644
index 25c782ac37..0000000000
Binary files a/Plugins/org.mitk.gui.qt.eventrecorder/resources/stop_rec.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorder.cpp b/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorder.cpp
deleted file mode 100644
index cfdecd38f2..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorder.cpp
+++ /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.
-
-============================================================================*/
-
-
-// Blueberry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// Qmitk
-#include "InteractionEventRecorder.h"
-
-// Qt
-#include <QMessageBox>
-#include <QFileDialog>
-// us
-#include "usGetModuleContext.h"
-#include "usModuleContext.h"
-#include "usModuleResource.h"
-
-#include <usModuleInitialization.h>
-#include <mitkXML2EventParser.h>
-#include <vtkSmartPointer.h>
-#include "QmitkRenderWindow.h"
-
-
-US_INITIALIZE_MODULE
-
-
-const std::string InteractionEventRecorder::VIEW_ID = "org.mitk.views.interactioneventrecorder";
-
-void InteractionEventRecorder::SetFocus()
-{
- m_Controls.textFileName->setFocus();
-}
-
-void InteractionEventRecorder::StartRecording()
-{
-
- MITK_INFO << "Start Recording";
- MITK_INFO << "Performing Reinit";
- mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage());
-
- m_CurrentObserver->SetOutputFile(m_Controls.textFileName->text().toStdString());
- m_CurrentObserver->StartRecording();
-}
-
-void InteractionEventRecorder::StopRecording()
-{
- MITK_INFO << "Stop Recording";
- m_CurrentObserver->StopRecording();
-}
-
-void InteractionEventRecorder::Play()
-{
- std::ifstream xmlStream(m_Controls.textFileName->text().toStdString().c_str());
- mitk::XML2EventParser parser(xmlStream);
- mitk::XML2EventParser::EventContainerType events = parser.GetInteractions();
-
- MITK_INFO << "parsed events";
-
- for (std::size_t i=0; i < events.size(); ++i)
- events.at(i)->GetSender()->GetDispatcher()->ProcessEvent(events.at(i));
-
- MITK_INFO << "DONE";
-}
-
-void InteractionEventRecorder::OpenFile()
-{
- QString fn = QFileDialog::getOpenFileName(nullptr, "Open File...",
- QString(), "All Files (*)");
- if (!fn.isEmpty())
- this->m_Controls.textFileName->setText(fn);
-}
-
-void InteractionEventRecorder::RotatePlanes()
-{
- mitk::Point3D center;
- center.Fill(0);
- mitk::Vector3D firstVec;
- mitk::Vector3D secondVec;
-
- firstVec[0] = 1.0;
- firstVec[1] = .5;
- firstVec[2] = .25;
-
- secondVec[0] = 1;
- secondVec[1] = .25;
- secondVec[2] = 1;
-
- // Rotate Planes to a predefined state which can later be used again in tests
- auto* axialRenderWindow = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("axial");
- axialRenderWindow->GetSliceNavigationController()->ReorientSlices( center, firstVec,secondVec );
- axialRenderWindow->GetRenderer()->RequestUpdate();
-
-}
-
-void InteractionEventRecorder::RotateView()
-{
- // Rotate the view in 3D to a predefined state which can later be used again in tests
- // this simulates a prior VTK Interaction
- auto allRenderWindows = mitk::BaseRenderer::GetAll3DRenderWindows();
- for (auto mapit = allRenderWindows.begin(); mapit != allRenderWindows.end(); ++mapit)
- {
- vtkRenderWindow* renderWindow = mapit->first;
- if (renderWindow == nullptr)
- continue;
-
- mitk::Stepper* stepper = mapit->second->GetCameraRotationController()->GetStepper();
- if (stepper == nullptr)
- return;
-
- unsigned int newPos = 17;
- stepper->SetPos(newPos);
- }
-}
-
-void InteractionEventRecorder::CreateQtPartControl( QWidget *parent )
-{
- // create GUI widgets from the Qt Designer's .ui file
- m_Controls.setupUi( parent );
- connect( m_Controls.btnStopRecording, SIGNAL(clicked()), this, SLOT(StopRecording()) );
- connect( m_Controls.btnStartRecording, SIGNAL(clicked()), this, SLOT(StartRecording()) );
- connect( m_Controls.btnPlay, SIGNAL(clicked()), this, SLOT(Play()) );
- connect( m_Controls.btnOpenFile, SIGNAL(clicked()), this, SLOT(OpenFile()) );
- connect( m_Controls.rotatePlanes, SIGNAL(clicked()), this, SLOT(RotatePlanes()) );
- connect( m_Controls.rotate3D, SIGNAL(clicked()), this, SLOT(RotateView()) );
-
- m_CurrentObserver = new mitk::EventRecorder();
- // Register as listener via micro services
- us::ServiceProperties props;
-
- props["name"] = std::string("EventRecorder");
- m_ServiceRegistration = us::GetModuleContext()->RegisterService<mitk::InteractionEventObserver>(m_CurrentObserver,props);
-
-
- /*
-
-delete m_CurrentObserverDEBUG;
- m_ServiceRegistrationDEBUG.Unregister();
- */
-}
-
-
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorder.h b/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorder.h
deleted file mode 100644
index c3a8fe5374..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorder.h
+++ /dev/null
@@ -1,74 +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 InteractionEventRecorder_h
-#define InteractionEventRecorder_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-
-#include "ui_InteractionEventRecorderControls.h"
-
-#include "mitkInteractionEventObserver.h"
-#include "mitkEventRecorder.h"
-
-/**
- \brief InteractionEventRecorder
-
- Demontrates the use of InteractionOversers.
-
- Allows to record all mouse interaction in the renderwindows save it as XML file. And also replay the interaction.
-
- \sa QmitkAbstractView
- \ingroup ${plugin_target}_internal
-*/
-class InteractionEventRecorder : 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 StartRecording();
- void StopRecording();
- void OpenFile();
- void RotatePlanes();
- void RotateView();
- void Play();
-
- protected:
-
- void CreateQtPartControl(QWidget *parent) override;
-
- void SetFocus() override;
-
-
-
- Ui::InteractionEventRecorderControls m_Controls;
-
- private:
- mitk::EventRecorder* m_CurrentObserver;
-
- us::ServiceRegistration<mitk::InteractionEventObserver> m_ServiceRegistration;
-
-};
-
-#endif // InteractionEventRecorder_h
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorderControls.ui b/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorderControls.ui
deleted file mode 100644
index cbf775f228..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/InteractionEventRecorderControls.ui
+++ /dev/null
@@ -1,197 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>InteractionEventRecorderControls</class>
- <widget class="QWidget" name="InteractionEventRecorderControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>432</width>
- <height>359</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="label">
- <property name="text">
- <string>Filename to store interaction</string>
- </property>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLineEdit" name="textFileName"/>
- </item>
- <item>
- <spacer name="horizontalSpacer">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Fixed</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>5</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="btnOpenFile">
- <property name="maximumSize">
- <size>
- <width>30</width>
- <height>20</height>
- </size>
- </property>
- <property name="toolTip">
- <string>Open file</string>
- </property>
- <property name="text">
- <string>...</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QPushButton" name="btnStartRecording">
- <property name="toolTip">
- <string>Record</string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="icon">
- <iconset resource="../../../../../bin-MITK/MITK-build/Plugins/org.mitk.gui.qt.eventrecorder/org_mitk_gui_qt_eventrecorder_cached.qrc">
- <normaloff>:/org.mitk.gui.qt.eventrecorder/resources/rec.png</normaloff>:/org.mitk.gui.qt.eventrecorder/resources/rec.png</iconset>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_2">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Fixed</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="btnStopRecording">
- <property name="toolTip">
- <string>Stop recording</string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="icon">
- <iconset resource="../../../../../bin-MITK/MITK-build/Plugins/org.mitk.gui.qt.eventrecorder/org_mitk_gui_qt_eventrecorder_cached.qrc">
- <normaloff>:/org.mitk.gui.qt.eventrecorder/resources/stop_rec.png</normaloff>:/org.mitk.gui.qt.eventrecorder/resources/stop_rec.png</iconset>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_3">
- <property name="orientation">
- <enum>Qt::Horizontal</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Fixed</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="btnPlay">
- <property name="toolTip">
- <string>Play</string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="icon">
- <iconset resource="../../../../../bin-MITK/MITK-build/Plugins/org.mitk.gui.qt.eventrecorder/org_mitk_gui_qt_eventrecorder_cached.qrc">
- <normaloff>:/org.mitk.gui.qt.eventrecorder/resources/play.png</normaloff>:/org.mitk.gui.qt.eventrecorder/resources/play.png</iconset>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="horizontalSpacer_4">
- <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="QPushButton" name="rotate3D">
- <property name="text">
- <string>Rotate 3D View</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="rotatePlanes">
- <property name="text">
- <string>Rotated Planes</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>200</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <resources>
- <include location="../../../../../bin-MITK/MITK-build/Plugins/org.mitk.gui.qt.eventrecorder/org_mitk_gui_qt_eventrecorder_cached.qrc"/>
- </resources>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/org_mitk_gui_qt_eventrecorder_Activator.cpp b/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/org_mitk_gui_qt_eventrecorder_Activator.cpp
deleted file mode 100644
index ff11c49a72..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/org_mitk_gui_qt_eventrecorder_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_eventrecorder_Activator.h"
-#include "InteractionEventRecorder.h"
-
-namespace mitk {
-
-void org_mitk_gui_qt_eventrecorder_Activator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(InteractionEventRecorder, context)
-}
-
-void org_mitk_gui_qt_eventrecorder_Activator::stop(ctkPluginContext* context)
-{
- Q_UNUSED(context)
-}
-
-}
diff --git a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/org_mitk_gui_qt_eventrecorder_Activator.h b/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/org_mitk_gui_qt_eventrecorder_Activator.h
deleted file mode 100644
index 1f340d2b3d..0000000000
--- a/Plugins/org.mitk.gui.qt.eventrecorder/src/internal/org_mitk_gui_qt_eventrecorder_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_eventrecorder_Activator_h
-#define org_mitk_gui_qt_eventrecorder_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
-class org_mitk_gui_qt_eventrecorder_Activator :
- public QObject, public ctkPluginActivator
-{
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_eventrecorder")
- Q_INTERFACES(ctkPluginActivator)
-
-public:
-
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
-}; // org_mitk_gui_qt_eventrecorder_Activator
-
-}
-
-#endif // org_mitk_gui_qt_eventrecorder_Activator_h
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/CMakeLists.txt b/Plugins/org.mitk.gui.qt.geometrytools/CMakeLists.txt
deleted file mode 100644
index 315504774f..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_geometrytools)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE GEOMETRYTOOLS_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt
-)
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/Manual.dox
deleted file mode 100644
index 3baf2840a5..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/Manual.dox
+++ /dev/null
@@ -1,18 +0,0 @@
-/**
-\page org_mitk_gui_qt_geometrytools The Geometry Tools
-
-\imageMacro{geometrytools-dox.xpm,"Icon of Geometry Tools",2.00}
-
-\tableofcontents
-
-\section org_mitk_gui_qt_geometrytoolsOverview Overview
-
-A plugin to modify geometry of mitkBaseData via interaction. Currently, the following
-operations can be performed:
-
-<ul>
-<li>Translation
-<li>Rotation
-<li>Scaling (not supported for images, yet, and will not happen in coordinate origin)
-</ul>
-*/
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/geometrytools-dox.xpm b/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/geometrytools-dox.xpm
deleted file mode 100644
index 7b3b16dec1..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/documentation/UserManual/geometrytools-dox.xpm
+++ /dev/null
@@ -1,896 +0,0 @@
-/* XPM */
-static char * geometrytools_color_xpm[] = {
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diff --git a/Plugins/org.mitk.gui.qt.geometrytools/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.geometrytools/documentation/doxygen/modules.dox
deleted file mode 100644
index 80ce9d8232..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/documentation/doxygen/modules.dox
+++ /dev/null
@@ -1,23 +0,0 @@
-/**
- \defgroup org_mitk_gui_qt_geometrytools org.mitk.gui.qt.geometrytools
- \ingroup MITKPlugins
-
- \brief A plugin to modify geometry of mitkBaseData via interaction. Currently, the following
-operations can be performed:
-
-<ul>
-<li>Translation
-<li>Rotation
-<li>Scaling (not supported for images, yet, and will not happen in coordinate origin)
-</ul>
-
-*/
-
-/**
- \defgroup org_mitk_gui_qt_geometrytools_internal Internal
- \ingroup org_mitk_gui_qt_geometrytools
-
- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.geometrytools 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.geometrytools/files.cmake b/Plugins/org.mitk.gui.qt.geometrytools/files.cmake
deleted file mode 100644
index 599f90d2a6..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/files.cmake
+++ /dev/null
@@ -1,52 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_geometrytools_Activator.cpp
- QmitkGeometryToolsView.cpp
-)
-
-set(UI_FILES
- src/internal/QmitkGeometryToolsViewControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_geometrytools_Activator.h
- src/internal/QmitkGeometryToolsView.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
- resources/key_ctrl.png
- resources/key_alt.png
- resources/key_dash.png
- resources/key_down.png
- resources/key_left.png
- resources/key_plus.png
- resources/key_right.png
- resources/key_shift.png
- resources/key_up.png
-
- 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.geometrytools/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.geometrytools/manifest_headers.cmake
deleted file mode 100644
index 17165dc97f..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Geometry Tools")
-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.geometrytools/plugin.xml b/Plugins/org.mitk.gui.qt.geometrytools/plugin.xml
deleted file mode 100644
index a9f448907a..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/plugin.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.geometrytools"
- name="Geometry Tools"
- class="QmitkGeometryToolsView"
- icon="resources/icon.xpm" >
- <description>Modify the geometry of objects</description>
- <keywordReference id="org.mitk.views.geometrytools.Keyword"/>
- </view>
- </extension>
- <extension point="org.blueberry.ui.keywords">
- <keyword label="Rotate" id="org.mitk.views.geometrytools.Keyword"/>
- <keyword label="Translate" id="org.mitk.views.geometrytools.Keyword"/>
- <keyword label="Geometry" id="org.mitk.views.geometrytools.Keyword"/>
- <keyword label="Interaction" id="org.mitk.views.geometrytools.Keyword"/>
- <keyword label="Move" id="org.mitk.views.geometrytools.Keyword"/>
- <keyword label="Shift" id="org.mitk.views.geometrytools.Keyword"/>
- </extension>
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/icon.xpm b/Plugins/org.mitk.gui.qt.geometrytools/resources/icon.xpm
deleted file mode 100644
index 7b3b16dec1..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/resources/icon.xpm
+++ /dev/null
@@ -1,896 +0,0 @@
-/* XPM */
-static char * geometrytools_color_xpm[] = {
-"100 97 796 2",
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-"! c #71AF48",
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-"^ c #6AA443",
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diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_alt.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_alt.png
deleted file mode 100644
index e18d3767bf..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_alt.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_ctrl.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_ctrl.png
deleted file mode 100644
index 4b8486046e..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_ctrl.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_dash.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_dash.png
deleted file mode 100644
index 245d42ec5f..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_dash.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_down.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_down.png
deleted file mode 100644
index 70a8550573..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_down.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_left.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_left.png
deleted file mode 100644
index 5fd44d92ad..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_left.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_plus.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_plus.png
deleted file mode 100644
index a6d6761a87..0000000000
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diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_right.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_right.png
deleted file mode 100644
index 0401161ea1..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_right.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_shift.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_shift.png
deleted file mode 100644
index 0ad24dc5ea..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_shift.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_up.png b/Plugins/org.mitk.gui.qt.geometrytools/resources/key_up.png
deleted file mode 100644
index 64fa3d8412..0000000000
Binary files a/Plugins/org.mitk.gui.qt.geometrytools/resources/key_up.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsView.cpp b/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsView.cpp
deleted file mode 100644
index 79f79e07be..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsView.cpp
+++ /dev/null
@@ -1,209 +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 "QmitkGeometryToolsView.h"
-
-//mitk
-#include <mitkImage.h>
-#include <mitkAffineBaseDataInteractor3D.h>
-
-//micro services
-#include <usModuleRegistry.h>
-#include <usGetModuleContext.h>
-
-const std::string QmitkGeometryToolsView::VIEW_ID = "org.mitk.views.geometrytools";
-
-void QmitkGeometryToolsView::SetFocus()
-{
- m_Controls.m_AddInteractor->setFocus();
-}
-
-void QmitkGeometryToolsView::CreateQtPartControl( QWidget *parent )
-{
- m_Controls.setupUi( parent );
- connect( m_Controls.m_AddInteractor, SIGNAL(clicked()), this, SLOT(AddInteractor()) );
- connect( m_Controls.m_RemoveInteractor, SIGNAL(clicked()), this, SLOT(RemoveInteractor()) );
- connect( m_Controls.m_TranslationStep, SIGNAL(valueChanged(double)), this, SLOT(OnTranslationSpinBoxChanged(double)) );
- connect( m_Controls.m_RotationStep, SIGNAL(valueChanged(double)), this, SLOT(OnRotationSpinBoxChanged(double)) );
- connect( m_Controls.m_ScaleFactor, SIGNAL(valueChanged(double)), this, SLOT(OnScaleSpinBoxChanged(double)) );
- connect( m_Controls.m_AnchorPointX, SIGNAL(valueChanged(double)), this, SLOT(OnAnchorPointChanged(double)) );
- connect( m_Controls.m_AnchorPointY, SIGNAL(valueChanged(double)), this, SLOT(OnAnchorPointChanged(double)) );
- connect( m_Controls.m_AnchorPointZ, SIGNAL(valueChanged(double)), this, SLOT(OnAnchorPointChanged(double)) );
- connect( m_Controls.m_UsageInfoCheckBox, SIGNAL(clicked(bool)), this, SLOT(OnUsageInfoBoxChanged(bool)) );
-
- connect( m_Controls.m_CustomAnchorPointRadioButton, SIGNAL(toggled(bool)), this, SLOT(OnCustomPointRadioButtonToggled(bool)) );
-
- connect( m_Controls.m_OriginPointRadioButton, SIGNAL(clicked(bool)), this, SLOT(OnOriginPointRadioButton(bool)) );
- connect( m_Controls.m_CenterPointRadioButton, SIGNAL(clicked(bool)), this, SLOT(OnCenterPointRadioButton(bool)) );
-
-
-
- m_Controls.m_UsageInfo->hide();
- m_Controls.m_CustomAnchorPoint->hide();
-
-}
-
-void QmitkGeometryToolsView::OnUsageInfoBoxChanged(bool flag)
-{
- m_Controls.m_UsageInfo->setVisible(flag);
-}
-
-void QmitkGeometryToolsView::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*source*/,
- const QList<mitk::DataNode::Pointer>& nodes )
-{
- for (mitk::DataNode::Pointer node: nodes)
- {
- if( node.IsNotNull() )
- {
- m_Controls.m_AddInteractor->setEnabled( true );
- return;
- }
- }
- m_Controls.m_AddInteractor->setEnabled( false );
-}
-
-void QmitkGeometryToolsView::OnCustomPointRadioButtonToggled(bool status)
-{
- m_Controls.m_CustomAnchorPoint->setVisible(status);
- //change the anchor point to be the custom point
- OnAnchorPointChanged(0.0);
-}
-
-void QmitkGeometryToolsView::OnCenterPointRadioButton(bool)
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( node.IsNotNull() && (node->GetDataInteractor().IsNotNull()) )
- {
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point X", node->GetData()->GetGeometry()->GetCenter()[0]);
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Y", node->GetData()->GetGeometry()->GetCenter()[1]);
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Z", node->GetData()->GetGeometry()->GetCenter()[2]);
- }
- }
-}
-
-void QmitkGeometryToolsView::OnOriginPointRadioButton(bool)
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( node.IsNotNull() && (node->GetDataInteractor().IsNotNull()) )
- {
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point X", node->GetData()->GetGeometry()->GetOrigin()[0]);
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Y", node->GetData()->GetGeometry()->GetOrigin()[1]);
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Z", node->GetData()->GetGeometry()->GetOrigin()[2]);
- }
- }
-}
-
-
-void QmitkGeometryToolsView::AddInteractor()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( node.IsNotNull() )
- {
-
- mitk::AffineBaseDataInteractor3D::Pointer affineDataInteractor = mitk::AffineBaseDataInteractor3D::New();
- if (m_Controls.m_KeyboardMode->isChecked())
- {
- affineDataInteractor->LoadStateMachine("AffineInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- affineDataInteractor->SetEventConfig("AffineKeyConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- }
- else if(m_Controls.m_MouseMode->isChecked())
- {
- affineDataInteractor->LoadStateMachine("AffineInteraction3D.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- affineDataInteractor->SetEventConfig("AffineMouseConfig.xml", us::ModuleRegistry::GetModule("MitkDataTypesExt"));
- }
-
- affineDataInteractor->SetDataNode(node);
-
- node->SetBoolProperty("pickable", true);
- node->SetFloatProperty("AffineBaseDataInteractor3D.Translation Step Size", m_Controls.m_TranslationStep->value());
- node->SetFloatProperty("AffineBaseDataInteractor3D.Rotation Step Size", m_Controls.m_RotationStep->value());
- node->SetFloatProperty("AffineBaseDataInteractor3D.Scale Step Size", m_Controls.m_ScaleFactor->value());
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point X", m_Controls.m_AnchorPointX->value());
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Y", m_Controls.m_AnchorPointY->value());
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Z", m_Controls.m_AnchorPointZ->value());
- }
- }
-}
-
-void QmitkGeometryToolsView::RemoveInteractor()
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( (node.IsNotNull()) && (node->GetDataInteractor().IsNotNull()) )
- {
- node->SetDataInteractor(nullptr);
- }
- }
-}
-
-void QmitkGeometryToolsView::OnTranslationSpinBoxChanged(double step)
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( node.IsNotNull() && (node->GetDataInteractor().IsNotNull()) )
- {
- node->SetFloatProperty("AffineBaseDataInteractor3D.Translation Step Size", step);
- }
- }
-}
-
-void QmitkGeometryToolsView::OnRotationSpinBoxChanged(double step)
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( node.IsNotNull() && (node->GetDataInteractor().IsNotNull()) )
- {
- node->SetFloatProperty("AffineBaseDataInteractor3D.Rotation Step Size", step);
- }
- }
-}
-
-void QmitkGeometryToolsView::OnScaleSpinBoxChanged(double factor)
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( node.IsNotNull() && (node->GetDataInteractor().IsNotNull()) )
- {
- node->SetFloatProperty("AffineBaseDataInteractor3D.Scale Step Size", factor);
- }
- }
-}
-
-void QmitkGeometryToolsView::OnAnchorPointChanged(double /*value*/)
-{
- QList<mitk::DataNode::Pointer> nodes = this->GetDataManagerSelection();
- foreach( mitk::DataNode::Pointer node, nodes )
- {
- if( node.IsNotNull() && (node->GetDataInteractor().IsNotNull()) )
- {
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point X", m_Controls.m_AnchorPointX->value());
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Y", m_Controls.m_AnchorPointY->value());
- node->SetFloatProperty("AffineBaseDataInteractor3D.Anchor Point Z", m_Controls.m_AnchorPointZ->value());
- }
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsView.h b/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsView.h
deleted file mode 100644
index 8da09f1922..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsView.h
+++ /dev/null
@@ -1,103 +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 QmitkGeometryToolsView_h
-#define QmitkGeometryToolsView_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-#include <mitkAffineBaseDataInteractor3D.h>
-
-#include "ui_QmitkGeometryToolsViewControls.h"
-
-/**
- \brief QmitkGeometryToolsView to modify geometry of mitkBaseData via interaction.
-
- \warning This is an experimental view to play with the geometry of all mitkBaseDatas.
- The current implementation allows to translate, rotate and scale objects with the
- keyboard.
-
- \warning Scaling is not supported for images, yet.
-
- \sa QmitkAbstractView
- \ingroup ${plugin_target}_internal
-*/
-class QmitkGeometryToolsView : 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;
-
-public slots:
-protected slots:
-
- /**
- * @brief Add/remove the affine interactor.
- */
- void AddInteractor();
- void RemoveInteractor();
-
- /**
- * @brief Slots to adapt the step size for interaction.
- */
- void OnRotationSpinBoxChanged(double step);
- void OnScaleSpinBoxChanged(double factor);
- void OnTranslationSpinBoxChanged(double step);
-
- /**
- * @brief OnUsageInfoBoxChanged show help.
- * @param flag yes/no.
- */
- void OnUsageInfoBoxChanged(bool flag);
-
- /**
- * @brief OnCustomPointRadioButtonToggled hide/show custom anchor point
- *
- */
- void OnCustomPointRadioButtonToggled(bool status);
-
- /**
- * @brief OnAnchorPointChanged sets the anchor point for rotation or translation.
- */
- void OnAnchorPointChanged(double);
-
- /**
- * @brief OnOriginPointRadioButton sets the anchor point to the origin of the
- * mitk::DataNode mitk::BaseGeometry.
- */
- void OnOriginPointRadioButton(bool);
-
- /**
- * @brief OnCenterPointRadioButton sets the anchor point to the center of the
- * mitk::DataNode mitk::BaseGeometry.
- */
- void OnCenterPointRadioButton(bool);
-protected:
-
- void CreateQtPartControl(QWidget *parent) override;
-
- void SetFocus() override;
-
- /// \brief called by QmitkAbstractView when DataManager's selection has changed
- void OnSelectionChanged( berry::IWorkbenchPart::Pointer source,
- const QList<mitk::DataNode::Pointer>& nodes ) override;
-
- Ui::QmitkGeometryToolsViewControls m_Controls;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsViewControls.ui b/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsViewControls.ui
deleted file mode 100644
index 4c93313294..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/QmitkGeometryToolsViewControls.ui
+++ /dev/null
@@ -1,588 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkGeometryToolsViewControls</class>
- <widget class="QWidget" name="QmitkGeometryToolsViewControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>369</width>
- <height>919</height>
- </rect>
- </property>
- <property name="minimumSize">
- <size>
- <width>0</width>
- <height>0</height>
- </size>
- </property>
- <property name="windowTitle">
- <string>QmitkTemplate</string>
- </property>
- <layout class="QGridLayout" name="gridLayout_2">
- <item row="6" column="0">
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Rotation step size (°)</string>
- </property>
- </widget>
- </item>
- <item row="5" column="0">
- <widget class="QDoubleSpinBox" name="m_TranslationStep">
- <property name="decimals">
- <number>2</number>
- </property>
- <property name="maximum">
- <double>1000.000000000000000</double>
- </property>
- <property name="value">
- <double>1.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QRadioButton" name="m_KeyboardMode">
- <property name="text">
- <string>Keyboard Mode (default)</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="8" column="0">
- <widget class="QLabel" name="label_3">
- <property name="text">
- <string>Scale factor (%)</string>
- </property>
- </widget>
- </item>
- <item row="12" column="0">
- <widget class="QCheckBox" name="m_UsageInfoCheckBox">
- <property name="text">
- <string>Show usage information</string>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QRadioButton" name="m_MouseMode">
- <property name="text">
- <string>Mouse Mode (not implemented, yet)</string>
- </property>
- </widget>
- </item>
- <item row="7" column="0">
- <widget class="QDoubleSpinBox" name="m_RotationStep">
- <property name="maximum">
- <double>360.000000000000000</double>
- </property>
- <property name="value">
- <double>1.000000000000000</double>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Translation step size (mm)</string>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QPushButton" name="m_RemoveInteractor">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Remove Interactor</string>
- </property>
- </widget>
- </item>
- <item row="9" column="0">
- <widget class="QDoubleSpinBox" name="m_ScaleFactor">
- <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="10" column="0">
- <widget class="QGroupBox" name="groupBox">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="title">
- <string>Anchor point (for scaling and rotation)</string>
- </property>
- <property name="checkable">
- <bool>false</bool>
- </property>
- <layout class="QGridLayout" name="gridLayout_4">
- <item row="0" column="0">
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QRadioButton" name="m_OriginPointRadioButton">
- <property name="text">
- <string>Origin</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="m_CenterPointRadioButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Center</string>
- </property>
- <property name="checked">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="m_CustomAnchorPointRadioButton">
- <property name="text">
- <string>Custom</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="1" column="0">
- <widget class="QWidget" name="m_CustomAnchorPoint" native="true">
- <layout class="QGridLayout" name="gridLayout_6">
- <item row="0" column="0">
- <layout class="QGridLayout" name="gridLayout_3">
- <item row="0" column="0">
- <widget class="QLabel" name="label_33">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>X:</string>
- </property>
- </widget>
- </item>
- <item row="0" column="1">
- <widget class="QDoubleSpinBox" name="m_AnchorPointX">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimum">
- <double>-9999.989999999999782</double>
- </property>
- <property name="maximum">
- <double>9999.989999999999782</double>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_34">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Y:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QDoubleSpinBox" name="m_AnchorPointY">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimum">
- <double>-9999.989999999999782</double>
- </property>
- <property name="maximum">
- <double>9999.989999999999782</double>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_35">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Z:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="1">
- <widget class="QDoubleSpinBox" name="m_AnchorPointZ">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="minimum">
- <double>-9999.989999999999782</double>
- </property>
- <property name="maximum">
- <double>9999.989999999999782</double>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="0" column="0">
- <widget class="QPushButton" name="m_AddInteractor">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <string>Do image processing</string>
- </property>
- <property name="text">
- <string>Add Interactor</string>
- </property>
- </widget>
- </item>
- <item row="14" column="0" rowspan="3" colspan="2">
- <widget class="QWidget" name="m_UsageInfo" native="true">
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QLabel" name="label_32">
- <property name="text">
- <string>Select a data node in the data storage and add an interactor. The color property will be set blue if the interactor is added. Next, pick the object you want move (in case there are multiple interactors) with the mouse in a render window. If it turns green, the interactor is active. Keyboard mode provides the following functions:</string>
- </property>
- <property name="wordWrap">
- <bool>true</bool>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <layout class="QGridLayout" name="m_UsageInfoLayout">
- <item row="4" column="6">
- <widget class="QLabel" name="label_24">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_up.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="2" column="2">
- <widget class="QLabel" name="label_18">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_shift.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="3" column="3">
- <widget class="QLabel" name="label_7">
- <property name="text">
- <string>+</string>
- </property>
- </widget>
- </item>
- <item row="3" column="6">
- <widget class="QLabel" name="label_8">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_up.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="2" column="3">
- <widget class="QLabel" name="label_11">
- <property name="text">
- <string>+</string>
- </property>
- </widget>
- </item>
- <item row="1" column="4">
- <widget class="QLabel" name="label_12">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_right.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="1" column="2">
- <widget class="QLabel" name="label_16">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_left.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="1" column="3">
- <widget class="QLabel" name="label_14">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_up.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="4" column="5">
- <widget class="QLabel" name="label_28">
- <property name="text">
- <string>+</string>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_19">
- <property name="text">
- <string><html><head/><body><p>Translate <br/>Coronal</p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="1" column="5">
- <widget class="QLabel" name="label_13">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_down.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="4" column="2">
- <widget class="QLabel" name="label_25">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_ctrl.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="4" column="0">
- <widget class="QLabel" name="label_27">
- <property name="text">
- <string><html><head/><body><p>Rotate <br/>Coronal</p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="3" column="2">
- <widget class="QLabel" name="label_6">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_ctrl.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="3" column="7">
- <widget class="QLabel" name="label_9">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_down.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="3" column="0">
- <widget class="QLabel" name="label_10">
- <property name="text">
- <string><html><head/><body><p>Rotate <br/>Sagittal/Axial</p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="4" column="3">
- <widget class="QLabel" name="label_20">
- <property name="text">
- <string>+</string>
- </property>
- </widget>
- </item>
- <item row="3" column="5">
- <widget class="QLabel" name="label_5">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_down.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="2" column="5">
- <widget class="QLabel" name="label_21">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_down.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="4" column="7">
- <widget class="QLabel" name="label_22">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_down.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="4" column="4">
- <widget class="QLabel" name="label_26">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_shift.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="2" column="4">
- <widget class="QLabel" name="label_15">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_up.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_17">
- <property name="text">
- <string><html><head/><body><p>Translate <br/>Sagittal/Axial</p></body></html></string>
- </property>
- </widget>
- </item>
- <item row="3" column="4">
- <widget class="QLabel" name="label_4">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_left.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="5" column="0">
- <widget class="QLabel" name="label_23">
- <property name="text">
- <string>Scale*</string>
- </property>
- </widget>
- </item>
- <item row="5" column="2">
- <widget class="QLabel" name="label_29">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_plus.png</pixmap>
- </property>
- </widget>
- </item>
- <item row="5" column="3">
- <widget class="QLabel" name="label_30">
- <property name="text">
- <string/>
- </property>
- <property name="pixmap">
- <pixmap resource="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc">:/org.mitk.gui.qt.geometrytools/resources/key_dash.png</pixmap>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- <item row="2" column="0">
- <widget class="QLabel" name="label_31">
- <property name="text">
- <string>*currently does not work with images</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item row="17" column="0">
- <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>
- <layoutdefault spacing="6" margin="11"/>
- <tabstops>
- <tabstop>m_AddInteractor</tabstop>
- <tabstop>m_KeyboardMode</tabstop>
- <tabstop>m_MouseMode</tabstop>
- <tabstop>m_RemoveInteractor</tabstop>
- <tabstop>m_TranslationStep</tabstop>
- <tabstop>m_RotationStep</tabstop>
- <tabstop>m_ScaleFactor</tabstop>
- <tabstop>m_OriginPointRadioButton</tabstop>
- <tabstop>m_CenterPointRadioButton</tabstop>
- <tabstop>m_CustomAnchorPointRadioButton</tabstop>
- <tabstop>m_AnchorPointX</tabstop>
- <tabstop>m_AnchorPointY</tabstop>
- <tabstop>m_AnchorPointZ</tabstop>
- <tabstop>m_UsageInfoCheckBox</tabstop>
- </tabstops>
- <resources>
- <include location="../../../../../mitk-super-master-release/MITK-build/Plugins/org.mitk.gui.qt.geometrytools/org_mitk_gui_qt_geometrytools_cached.qrc"/>
- </resources>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/org_mitk_gui_qt_geometrytools_Activator.cpp b/Plugins/org.mitk.gui.qt.geometrytools/src/internal/org_mitk_gui_qt_geometrytools_Activator.cpp
deleted file mode 100644
index d57c5411e1..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/org_mitk_gui_qt_geometrytools_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_geometrytools_Activator.h"
-#include "QmitkGeometryToolsView.h"
-
-namespace mitk {
-
-void org_mitk_gui_qt_geometrytools_Activator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(QmitkGeometryToolsView, context)
-}
-
-void org_mitk_gui_qt_geometrytools_Activator::stop(ctkPluginContext* context)
-{
- Q_UNUSED(context)
-}
-
-}
diff --git a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/org_mitk_gui_qt_geometrytools_Activator.h b/Plugins/org.mitk.gui.qt.geometrytools/src/internal/org_mitk_gui_qt_geometrytools_Activator.h
deleted file mode 100644
index 455d85d4bc..0000000000
--- a/Plugins/org.mitk.gui.qt.geometrytools/src/internal/org_mitk_gui_qt_geometrytools_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_geometrytools_Activator_h
-#define org_mitk_gui_qt_geometrytools_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
-class org_mitk_gui_qt_geometrytools_Activator :
- public QObject, public ctkPluginActivator
-{
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_geometrytools")
- Q_INTERFACES(ctkPluginActivator)
-
-public:
-
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
-}; // org_mitk_gui_qt_geometrytools_Activator
-
-}
-
-#endif // org_mitk_gui_qt_geometrytools_Activator_h
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/CMakeLists.txt b/Plugins/org.mitk.gui.qt.materialeditor/CMakeLists.txt
deleted file mode 100644
index b8f112a380..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/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_materialeditor)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE MATERIALEDITOR_EXPORTS
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgets
-)
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox b/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox
deleted file mode 100644
index 1a6935a94d..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor.dox
+++ /dev/null
@@ -1,10 +0,0 @@
-/**
-\page org_surfacematerialeditor The Surface Material Editor
-
-\imageMacro{QmitkSurfaceMaterialEditor_Icon.png,"Icon of the Surface Material Editor",2.00}
-
-The Surface Material Editor shows the properties of the selected data that are relevant for the selected shader. These properties can be filtered to find a specific property. The preview window shows the representation of a neutral 3D object with the currently selected settings.
-
-\imageMacro{QmitkSurfaceMaterialEditor_Gui.png,"The Surface Material Editor",10.92}
-
-*/
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor_Gui.png b/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor_Gui.png
deleted file mode 100644
index 9b81744250..0000000000
Binary files a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor_Gui.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor_Icon.png b/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor_Icon.png
deleted file mode 100644
index 9a660225a5..0000000000
Binary files a/Plugins/org.mitk.gui.qt.materialeditor/documentation/UserManual/QmitkSurfaceMaterialEditor_Icon.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.materialeditor/documentation/doxygen/modules.dox
deleted file mode 100644
index 34c292bcfe..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/documentation/doxygen/modules.dox
+++ /dev/null
@@ -1,16 +0,0 @@
-/**
- \defgroup org_mitk_gui_qt_materialeditor org.mitk.gui.qt.materialeditor
- \ingroup MITKPlugins
-
- \brief Describe your plugin here.
-
-*/
-
-/**
- \defgroup org_mitk_gui_qt_materialeditor_internal Internal
- \ingroup org_mitk_gui_qt_materialeditor
-
- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.materialeditor 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.materialeditor/files.cmake b/Plugins/org.mitk.gui.qt.materialeditor/files.cmake
deleted file mode 100644
index 81413caeb9..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/files.cmake
+++ /dev/null
@@ -1,34 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- QmitkMITKSurfaceMaterialEditorView.cpp
- mitkMaterialEditorPluginActivator.cpp
-)
-
-set(UI_FILES
- src/internal/QmitkMITKSurfaceMaterialEditorViewControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/QmitkMITKSurfaceMaterialEditorView.h
- src/internal/mitkMaterialEditorPluginActivator.h
-)
-
-set(CACHED_RESOURCE_FILES
- resources/SurfaceMaterialEditor.png
- plugin.xml
-)
-
-set(QRC_FILES
- resources/QmitkMITKSurfaceMaterialEditorView.qrc
-)
-
-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})
\ No newline at end of file
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.materialeditor/manifest_headers.cmake
deleted file mode 100644
index a76fffae0a..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "MITK Material Editor")
-set(Plugin-Version "0.9")
-set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
-set(Plugin-ContactAddress "https://www.mitk.org")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/plugin.xml b/Plugins/org.mitk.gui.qt.materialeditor/plugin.xml
deleted file mode 100644
index 2046abdd81..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/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.mitksurfacematerialeditor"
- name="Surface Material Editor"
- class="QmitkMITKSurfaceMaterialEditorView"
- icon="resources/SurfaceMaterialEditor.png" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/resources/QmitkMITKSurfaceMaterialEditorView.qrc b/Plugins/org.mitk.gui.qt.materialeditor/resources/QmitkMITKSurfaceMaterialEditorView.qrc
deleted file mode 100644
index b8caba7494..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/resources/QmitkMITKSurfaceMaterialEditorView.qrc
+++ /dev/null
@@ -1,5 +0,0 @@
-<!DOCTYPE RCC><RCC version="1.0">
- <qresource prefix="/QmitkTemplate">
- <file>SurfaceMaterialEditor.png</file>
- </qresource>
- </RCC>
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/resources/SurfaceMaterialEditor.png b/Plugins/org.mitk.gui.qt.materialeditor/resources/SurfaceMaterialEditor.png
deleted file mode 100644
index 9a660225a5..0000000000
Binary files a/Plugins/org.mitk.gui.qt.materialeditor/resources/SurfaceMaterialEditor.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorView.cpp b/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorView.cpp
deleted file mode 100644
index c9771ad3a3..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorView.cpp
+++ /dev/null
@@ -1,240 +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 "QmitkMITKSurfaceMaterialEditorView.h"
-
-#include "mitkBaseRenderer.h"
-#include "mitkNodePredicateDataType.h"
-#include "mitkProperties.h"
-#include "mitkIDataStorageService.h"
-#include "mitkDataNodeObject.h"
-
-#include "berryIEditorPart.h"
-#include "berryIWorkbenchPage.h"
-
-#include "QmitkDataStorageComboBox.h"
-
-#include <vtkSphereSource.h>
-#include <vtkPolyData.h>
-#include <vtkCamera.h>
-#include <vtkRenderer.h>
-#include <vtkTextActor.h>
-#include <vtkRenderer.h>
-#include <vtkTextProperty.h>
-#include <vtkCoordinate.h>
-#include <vtkActor.h>
-#include <vtkProperty.h>
-
-#include <mitkVtkPropRenderer.h>
-#include <mitkVtkLayerController.h>
-
-#include <qmessagebox.h>
-
-#include "mitkStandaloneDataStorage.h"
-
-
-
-const std::string QmitkMITKSurfaceMaterialEditorView::VIEW_ID = "org.mitk.views.mitksurfacematerialeditor";
-
-QmitkMITKSurfaceMaterialEditorView::QmitkMITKSurfaceMaterialEditorView()
-: QmitkAbstractView(),
- m_Controls(nullptr)
-{
- fixedProperties.push_back( "shader" );
- fixedProperties.push_back( "material.representation" );
- fixedProperties.push_back( "color" );
- fixedProperties.push_back( "opacity" );
- fixedProperties.push_back( "material.wireframeLineWidth" );
-
- fixedProperties.push_back( "material.ambientCoefficient" );
- fixedProperties.push_back( "material.diffuseCoefficient" );
- fixedProperties.push_back( "material.ambientColor" );
- fixedProperties.push_back( "material.diffuseColor" );
- fixedProperties.push_back( "material.specularColor" );
- fixedProperties.push_back( "material.specularCoefficient" );
- fixedProperties.push_back( "material.specularPower" );
- fixedProperties.push_back( "material.interpolation" );
-
- shaderProperties.push_back( "shader" );
- shaderProperties.push_back( "material.representation" );
- shaderProperties.push_back( "color" );
- shaderProperties.push_back( "opacity" );
- shaderProperties.push_back( "material.wireframeLineWidth" );
-
- observerAllocated = false;
-}
-
-QmitkMITKSurfaceMaterialEditorView::~QmitkMITKSurfaceMaterialEditorView()
-{
-}
-
-void QmitkMITKSurfaceMaterialEditorView::InitPreviewWindow()
-{
- usedTimer=0;
-
- vtkSphereSource* sphereSource = vtkSphereSource::New();
- sphereSource->SetThetaResolution(25);
- sphereSource->SetPhiResolution(25);
- sphereSource->Update();
-
- vtkPolyData* sphere = sphereSource->GetOutput();
-
- m_Surface = mitk::Surface::New();
- m_Surface->SetVtkPolyData( sphere );
-
- m_DataNode = mitk::DataNode::New();
- m_DataNode->SetData( m_Surface );
-
- m_DataTree = mitk::StandaloneDataStorage::New();
-
- m_DataTree->Add( m_DataNode , (mitk::DataNode *)nullptr );
-
- m_Controls->m_PreviewRenderWindow->GetRenderer()->SetDataStorage( m_DataTree );
- m_Controls->m_PreviewRenderWindow->GetRenderer()->SetMapperID( mitk::BaseRenderer::Standard3D );
-
- sphereSource->Delete();
-}
-
-
-void QmitkMITKSurfaceMaterialEditorView::RefreshPropertiesList()
-{
- mitk::DataNode* SrcND = m_SelectedDataNode;
- mitk::DataNode* DstND = m_DataNode;
-
- mitk::PropertyList* DstPL = DstND->GetPropertyList();
-
-
- m_Controls->m_ShaderPropertyList->SetPropertyList( nullptr );
-
- DstPL->Clear();
-
- if(observerAllocated)
- {
- observerAllocated=false;
- }
-
- if(SrcND)
- {
- mitk::PropertyList* SrcPL = SrcND->GetPropertyList();
-
- std::string shaderState = "fixed";
-
-// if(shaderEnum.IsNotNull())
-// {
-// shaderState = shaderEnum->GetValueAsString();
-
-// itk::MemberCommand<QmitkMITKSurfaceMaterialEditorView>::Pointer propertyModifiedCommand = itk::MemberCommand<QmitkMITKSurfaceMaterialEditorView>::New();
-// propertyModifiedCommand->SetCallbackFunction(this, &QmitkMITKSurfaceMaterialEditorView::shaderEnumChange);
-// observerIndex = shaderEnum->AddObserver(itk::ModifiedEvent(), propertyModifiedCommand);
-// observedProperty = shaderEnum;
-// observerAllocated=true;
-// }
-
- MITK_INFO << "PROPERTIES SCAN BEGIN";
-
- for(mitk::PropertyList::PropertyMap::const_iterator it=SrcPL->GetMap()->begin(); it!=SrcPL->GetMap()->end(); it++)
- {
- std::string name=it->first;
- mitk::BaseProperty *p=it->second;
-
- // MITK_INFO << "property '" << name << "' found";
-
- if(shaderState.compare("fixed")==0)
- {
- if(std::find(fixedProperties.begin(), fixedProperties.end(), name) != fixedProperties.end())
- {
- DstPL->SetProperty(name,p);
- }
- }
- else
- {
- //if(std::find(shaderProperties.begin(), shaderProperties.end(), name) != shaderProperties.end())
- {
- DstPL->SetProperty(name,p);
- }
- }
- }
-
- MITK_INFO << "PROPERTIES SCAN END";
- }
-
- m_Controls->m_ShaderPropertyList->SetPropertyList( DstPL );
- //m_Controls->m_PreviewRenderWindow->GetRenderer()->GetVtkRenderer()->ResetCameraClippingRange();
-}
-
-void QmitkMITKSurfaceMaterialEditorView::CreateQtPartControl(QWidget *parent)
-{
- if (!m_Controls)
- {
- // create GUI widgets
- m_Controls = new Ui::QmitkMITKSurfaceMaterialEditorViewControls;
- m_Controls->setupUi(parent);
- this->CreateConnections();
-
- InitPreviewWindow();
- RefreshPropertiesList();
-
- }
-}
-
-void QmitkMITKSurfaceMaterialEditorView::SetFocus()
-{
- m_Controls->m_ShaderPropertyList->setFocus();
-}
-
-void QmitkMITKSurfaceMaterialEditorView::CreateConnections()
-{
-}
-
-void QmitkMITKSurfaceMaterialEditorView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& nodes)
-{
- if(!nodes.empty())
- {
- m_SelectedDataNode = nodes.at(0);
- MITK_INFO << "Node '" << m_SelectedDataNode->GetName() << "' selected";
- SurfaceSelected();
- }
-}
-
-void QmitkMITKSurfaceMaterialEditorView::SurfaceSelected()
-{
- postRefresh();
-}
-
-void QmitkMITKSurfaceMaterialEditorView::shaderEnumChange(const itk::Object * /*caller*/, const itk::EventObject & /*event*/)
-{
- postRefresh();
-}
-
-void QmitkMITKSurfaceMaterialEditorView::postRefresh()
-{
- if(usedTimer)
- return;
-
- usedTimer=startTimer(0);
-}
-
-void QmitkMITKSurfaceMaterialEditorView::timerEvent( QTimerEvent *e )
-{
- if(usedTimer!=e->timerId())
- {
- MITK_ERROR << "INTERNAL ERROR: usedTimer[" << usedTimer << "] != timerId[" << e->timerId() << "]";
- }
-
- if(usedTimer)
- {
- killTimer(usedTimer);
- usedTimer=0;
- }
-
- RefreshPropertiesList();
-}
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorView.h b/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorView.h
deleted file mode 100644
index e6429f6276..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorView.h
+++ /dev/null
@@ -1,108 +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 QmitkMITKSurfaceMaterialEditorView_h
-#define QmitkMITKSurfaceMaterialEditorView_h
-
-#include <QmitkAbstractView.h>
-#include <berryIStructuredSelection.h>
-#include <string>
-
-#include "ui_QmitkMITKSurfaceMaterialEditorViewControls.h"
-
-/*
-#include <QtCore/QVariant>
-#include <QtGui/QAction>
-#include <QtGui/QApplication>
-#include <QtGui/QButtonGroup>
-#include <QtGui/QVBoxLayout>
-#include <QtGui/QWidget>
-#include "QtGui/QMenubarUpdatedEvent"
-*/
-
-#include "QmitkRenderWindow.h"
-#include "mitkCommon.h"
-#include "mitkDataStorage.h"
-#include "mitkDataNode.h"
-#include "mitkSurface.h"
-#include "vtkRenderer.h"
-#include "vtkTextActor.h"
-
-/*!
-
- \brief QmitkMITKSurfaceMaterialEditorView
-*/
-class QmitkMITKSurfaceMaterialEditorView : public QmitkAbstractView
-{
-
- // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
- Q_OBJECT
-
- public:
-
- static const std::string VIEW_ID;
-
- QmitkMITKSurfaceMaterialEditorView();
- ~QmitkMITKSurfaceMaterialEditorView() override;
-
- void CreateQtPartControl(QWidget *parent) override;
-
- /// \brief Creation of the connections of main and control widget
- virtual void CreateConnections();
-
- ///
- /// Sets the focus to an internal widget.
- ///
- void SetFocus() override;
-
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
-
-protected slots:
-
- void SurfaceSelected();
-
-protected:
-
- Ui::QmitkMITKSurfaceMaterialEditorViewControls* m_Controls;
-
-private:
-
- mitk::Surface::Pointer m_Surface;
- mitk::DataStorage::Pointer m_DataTree;
- mitk::DataNode::Pointer m_DataNode;
- mitk::DataNode::Pointer m_SelectedDataNode;
-
- std::list<std::string> fixedProperties;
- std::list<std::string> shaderProperties;
-
- unsigned long observerIndex;
- bool observerAllocated;
-
- void InitPreviewWindow();
-
- int usedTimer;
-
- void timerEvent( QTimerEvent *e ) override;
-
- void RefreshPropertiesList();
-
- void postRefresh();
-
- void shaderEnumChange(const itk::Object *caller, const itk::EventObject &event);
-
- berry::IStructuredSelection::ConstPointer m_CurrentSelection;
-};
-
-
-
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorViewControls.ui b/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorViewControls.ui
deleted file mode 100644
index ffd4094926..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/QmitkMITKSurfaceMaterialEditorViewControls.ui
+++ /dev/null
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkMITKSurfaceMaterialEditorViewControls</class>
- <widget class="QWidget" name="QmitkMITKSurfaceMaterialEditorViewControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>240</width>
- <height>794</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="QGroupBox" name="groupBox_Preview">
- <property name="title">
- <string>Preview</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <item>
- <widget class="QmitkRenderWindow" name="m_PreviewRenderWindow">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="groupBox_ShaderSelect">
- <property name="title">
- <string>Properties</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_6">
- <item>
- <widget class="QmitkPropertiesTableEditor" name="m_ShaderPropertyList"/>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <customwidgets>
- <customwidget>
- <class>QmitkRenderWindow</class>
- <extends>QListView</extends>
- <header>QmitkRenderWindow.h</header>
- </customwidget>
- <customwidget>
- <class>QmitkPropertiesTableEditor</class>
- <extends>QListView</extends>
- <header>QmitkPropertiesTableEditor.h</header>
- </customwidget>
- </customwidgets>
- <includes>
- <include location="local">QmitkDataStorageComboBox.h</include>
- </includes>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/mitkMaterialEditorPluginActivator.cpp b/Plugins/org.mitk.gui.qt.materialeditor/src/internal/mitkMaterialEditorPluginActivator.cpp
deleted file mode 100644
index 48baa722c6..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/mitkMaterialEditorPluginActivator.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 "mitkMaterialEditorPluginActivator.h"
-#include "QmitkMITKSurfaceMaterialEditorView.h"
-
-namespace mitk {
-
- void MaterialEditorPluginActivator::start(ctkPluginContext* context)
- {
- BERRY_REGISTER_EXTENSION_CLASS(QmitkMITKSurfaceMaterialEditorView, context)
- }
-
- void MaterialEditorPluginActivator::stop(ctkPluginContext* context)
- {
- Q_UNUSED(context)
- }
-
-}
diff --git a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/mitkMaterialEditorPluginActivator.h b/Plugins/org.mitk.gui.qt.materialeditor/src/internal/mitkMaterialEditorPluginActivator.h
deleted file mode 100644
index 49fb414956..0000000000
--- a/Plugins/org.mitk.gui.qt.materialeditor/src/internal/mitkMaterialEditorPluginActivator.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 mitkMaterialEditorPluginActivator_h
-#define mitkMaterialEditorPluginActivator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
- class MaterialEditorPluginActivator :
- public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_materialeditor")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
-
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
- }; // MaterialEditorPluginActivator
-
-}
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/CMakeLists.txt b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/CMakeLists.txt
deleted file mode 100644
index 3b57c693bb..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_pointsetinteractionmultispectrum)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE POINTSETINTERACTIONMULTISPECTRUM_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt
-)
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/files.cmake b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/files.cmake
deleted file mode 100644
index 99f891e589..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/files.cmake
+++ /dev/null
@@ -1,42 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator.cpp
- PointSetInteractionMultispectrum.cpp
-)
-
-set(UI_FILES
- src/internal/PointSetInteractionMultispectrumControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator.h
- src/internal/PointSetInteractionMultispectrum.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 ${INTERNAL_CPP_FILES})
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/manifest_headers.cmake
deleted file mode 100644
index 1fbc6f2c2b..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "Pointsetinteractionmultispectrum")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "DKFZ")
-set(Plugin-ContactAddress "")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/plugin.xml b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/plugin.xml
deleted file mode 100644
index f36c5593f0..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/plugin.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.pointsetinteractionmultispectrum"
- name="Point Set Interaction Multispectrum"
- class="PointSetInteractionMultispectrum"
- icon="resources/icon.xpm" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/resources/icon.xpm b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/resources/icon.xpm
deleted file mode 100644
index ae3d354bd7..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/resources/icon.xpm
+++ /dev/null
@@ -1,804 +0,0 @@
-/* XPM */
-static char * C:\m\MITK\Plugins\org_mitk_gui_qt_pointsetinteractionmultispectrum\resources\icon_xpm[] = {
-"48 48 753 2",
-" c None",
-". c #C4C3C1",
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-".*+*Q$[.R%) ' R%' ' R%Q$@*#*< $*%*Q$, &*R%R%**' > =*-*Q$) ' 5%' ;*R%, %*y+>*,*'*' )*%*' y+!*' U "};
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.cpp b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.cpp
deleted file mode 100644
index e7bec0d4df..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.cpp
+++ /dev/null
@@ -1,286 +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 "PointSetInteractionMultispectrum.h"
-#include "QmitkPointListWidget.h"
-#include "QmitkRenderWindow.h"
-
-// Qt
-#include <QMessageBox>
-#include <QApplication>
-#include <qwt_plot.h>
-#include <qwt_plot_curve.h>
-#include <qwt_plot_grid.h>
-#include <qwt_symbol.h>
-#include <qwt_legend.h>
-#include <QColor>
-#include <QString>
-
-//mitk image
-#include <mitkImage.h>
-#include <mitkImagePixelReadAccessor.h>
-
-// MITK
-#include "mitkITKImageImport.h"
-#include "mitkProperties.h"
-#include "mitkColorProperty.h"
-#include "mitkImageCast.h"
-#include <mitkVector.h>
-#include <mitkPoint.h>
-#include <mitkImageStatisticsHolder.h>
-// ITK
-#include <itkConnectedThresholdImageFilter.h>
-
-const std::string PointSetInteractionMultispectrum::VIEW_ID =
- "org.mitk.views.pointsetinteractionmultispectrum";
-
-PointSetInteractionMultispectrum::PointSetInteractionMultispectrum() :
- m_PointListWidget(nullptr)
-{
-
-}
-
-void PointSetInteractionMultispectrum::SetFocus()
-{
- m_Controls.buttonPerformImageProcessing->setFocus();
-}
-
-void PointSetInteractionMultispectrum::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()));
-
- //! [cpp-createqtpartcontrol]
- // create a QmitkPointListWidget and add it to the widget created from .ui file
- m_PointListWidget = new QmitkPointListWidget();
- m_Controls.verticalLayout->addWidget(m_PointListWidget, 1);
-
- // retrieve a possibly existing IRenderWindowPart
- if (mitk::IRenderWindowPart* renderWindowPart = GetRenderWindowPart())
- {
- // let the point set widget know about the render window part (crosshair updates)
- RenderWindowPartActivated(renderWindowPart);
- }
-
- // create a new DataNode containing a PointSet with some interaction
- m_PointSet = mitk::PointSet::New();
- mitk::DataNode::Pointer pointSetNode = mitk::DataNode::New();
- pointSetNode->SetData(m_PointSet);
- pointSetNode->SetName("points for displaying reflectance.");
- pointSetNode->SetProperty("helper object", mitk::BoolProperty::New(true));
- pointSetNode->SetProperty("layer", mitk::IntProperty::New(1024));
-
- // add the pointset to the data storage (for rendering and access by other modules)
- GetDataStorage()->Add(pointSetNode);
-
- // tell the GUI widget about the point set
- m_PointListWidget->SetPointSetNode(pointSetNode);
- //! [cpp-createqtpartcontrol]
-
- m_Plot = new QwtPlot();
-}
-
-
-void PointSetInteractionMultispectrum::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 PointSetInteractionMultispectrum::RenderWindowPartActivated(
- mitk::IRenderWindowPart* renderWindowPart)
-{
- // let the point set widget know about the slice navigation controllers
- // in the active render window part (crosshair updates)
- foreach(QmitkRenderWindow* renderWindow, renderWindowPart->GetQmitkRenderWindows().values())
- {
- m_PointListWidget->AddSliceNavigationController(renderWindow->GetSliceNavigationController());
- }
-}
-
-void PointSetInteractionMultispectrum::RenderWindowPartDeactivated(
- mitk::IRenderWindowPart* renderWindowPart)
-{
- foreach(QmitkRenderWindow* renderWindow, renderWindowPart->GetQmitkRenderWindows().values())
- {
- m_PointListWidget->RemoveSliceNavigationController(renderWindow->GetSliceNavigationController());
- }
-}
-
-void PointSetInteractionMultispectrum::DoImageProcessing()
-{
- QList<mitk::DataNode::Pointer> DataManagerNodes =
- this->GetDataManagerSelection();
- if (DataManagerNodes.empty())
- return;
-
- mitk::DataNode* DataManagerNode = DataManagerNodes.front();
-
- if (!DataManagerNode)
- {
- // 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).
- // notice that this is the 'BaseData' type.
-
- mitk::BaseData* data = DataManagerNode->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)
- {
- //! [cpp-doimageprocessing]
- // So we have an image. Let's see if the user has set some seed points already
- if (m_PointSet->GetSize() == 0)
- {
- // no points there. Not good for region growing
- QMessageBox::information( nullptr,
- "Reflectance display functionality",
- "Please set some points inside the image first.\n"
- "(hold Shift key and click left mouse button inside the image.)");
- return;
- }
-
- // plot the reflectances //
- PlotReflectance(m_PointSet, DataManagerNodes);
-
- //! [cpp-doimageprocessing]
- }
- }
-}
-
-
-void PointSetInteractionMultispectrum::PlotReflectance(mitk::PointSet::Pointer m_PointSet, QList<mitk::DataNode::Pointer> dataManagerNodes)
-{
- mitk::PointSet::PointsIterator PtIterator; // The point iterator in the PointSet, which gets access to each point.
- mitk::Point3D Point; // The extracted point. Notice that a point has three components (x, y, z).
- itk::Index<3> index; // The 3D index, which is converted from the world coordinate
- itk::Index<2> index2; // The truncated version of the 3D index, for which only the first two components are extracted.
- itk::VectorImage<double, 2>::Pointer itkImage; // The itk vector image. This is used since the mitk::Image could not handle multi-channel images well.
-
-
- // //////////////// Qwt window configuration /////////////////////////////////////////////
- delete m_Plot;
- m_Plot = new QwtPlot(); // create a new plot //
- m_Plot->setAxisAutoScale(QwtPlot::xBottom); // automatical scale -x //
- m_Plot->setAxisAutoScale(QwtPlot::yLeft); // automatical scale -y //
- m_Plot->setTitle("Multispectral Reflectance"); // set the plot title //
- m_Plot->setCanvasBackground(Qt::white); // set the background color //
- m_Plot->insertLegend(new QwtLegend()); // set the legend //
- QwtPlotGrid* grid = new QwtPlotGrid(); // set the grid //
- grid->attach(m_Plot); // set the grid //
- m_Controls.verticalLayout->addWidget(m_Plot, 1); // put the plot into the workbench //
-
- // the number of the plotted curve
- int curveIdx = 0;
-
- // iterate selected datanodes:
- for (auto node = dataManagerNodes.begin(); node != dataManagerNodes.end(); ++node)
- {
- mitk::BaseData* data = node->GetPointer()->GetData();
-
- // the current number of examined data point:
- int pointIdx = 0;
-
- if (data)
- {
- std::string curveNameString = "";
-
- node->GetPointer()->GetStringProperty("name", curveNameString);
-
- curveNameString += " point ";
-
- // 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)
- {
- // convert the MITK image to the ITK image //
- mitk::CastToItkImage(image, itkImage);
-
-
- ////////////////////////// main loop /////////////////////////////////
- int reflectanceIdx;
- itk::VariableLengthVector<double> reflectance;
- int channels;
-
- // The loop goes through each point in the point set //
- for (PtIterator = m_PointSet->Begin(0); PtIterator != m_PointSet->End(0); PtIterator++)
- {
-
- // extract the reflectance on a given pixel //
- Point = PtIterator.Value();
- image->GetGeometry(0)->WorldToIndex(Point, index);
- index2[0] = index[0];
- index2[1] = index[1];
- reflectance = itkImage->GetPixel(index2);
- channels = reflectance.GetNumberOfElements();
-
- // plot the reflectance dynamically //
- // create colors for each element in pointset.
- // "randomly" select colors for each added point by multiplying with prime.
- QColor curveColor((200 + (41 * curveIdx)) % 255, (89 * curveIdx) % 255,
- (37 * curveIdx) % 255);
-
- QString curveName(curveNameString.c_str());
- curveName.append(QString::number(pointIdx));
-
- QPolygonF qwtPoints;
- QwtPlotCurve* curve = new QwtPlotCurve();
- curve->setTitle(curveName);
- curve->setPen(curveColor, 4);
- curve->setRenderHint(QwtPlotItem::RenderAntialiased, true);
- QwtSymbol *symbol = new QwtSymbol(QwtSymbol::Ellipse,
- QBrush(Qt::yellow), QPen(Qt::black, 2), QSize(10, 10));
-
- for (reflectanceIdx = 0; reflectanceIdx < channels; reflectanceIdx++)
- {
- qwtPoints<< QPointF((double) reflectanceIdx,reflectance.GetElement(reflectanceIdx));
- }
-
- curve->setSamples(qwtPoints);
- curve->setSymbol(symbol);
- curve->attach(m_Plot);
- m_Plot->show();
-
- ++curveIdx;
- ++pointIdx;
- }
- }
- }
- }
-
-}
-
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.h b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.h
deleted file mode 100644
index e43934a39d..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrum.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 PointSetInteractionMultispectrum_h
-#define PointSetInteractionMultispectrum_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-#include <qwt_plot.h>
-#include "ui_PointSetInteractionMultispectrumControls.h"
-
-/////////////added from the regiongrowing plugin//////////////
-#include "mitkPointSet.h" ///////
-#include "mitkIRenderWindowPartListener.h" ///////
-#include <itkImage.h> ///////
-//////////////////////////////////////////////////////////////
-/**
- \brief PointSetInteractionMultispectrum
-
- \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 QmitkPointListWidget;
-
-class PointSetInteractionMultispectrum : public QmitkAbstractView
-{
- Q_OBJECT
-
- public:
-
- static const std::string VIEW_ID;
- PointSetInteractionMultispectrum();
-
-
- protected slots:
-
- /// \brief Called when the user clicks the GUI button
- void DoImageProcessing();
-
- protected:
-
-
- void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart);
- void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart);
-
-
- void CreateQtPartControl(QWidget *parent) override;
-
- void SetFocus() override;
-
- void OnSelectionChanged( berry::IWorkbenchPart::Pointer source,
- const QList<mitk::DataNode::Pointer>& nodes ) override;
-
- Ui::PointSetInteractionMultispectrumControls m_Controls;
-
- private:
-
- void PlotReflectance(mitk::PointSet::Pointer m_PointSet, QList<mitk::DataNode::Pointer> dataManagerNodes);
-
- mitk::PointSet::Pointer m_PointSet;
- QmitkPointListWidget* m_PointListWidget;
- QwtPlot* m_Plot;
-
-};
-
-#endif // PointSetInteractionMultispectrum_h
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrumControls.ui b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrumControls.ui
deleted file mode 100644
index 8434f88266..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/PointSetInteractionMultispectrumControls.ui
+++ /dev/null
@@ -1,64 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>PointSetInteractionMultispectrumControls</class>
- <widget class="QWidget" name="PointSetInteractionMultispectrumControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>222</width>
- <height>161</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="QPushButton" name="buttonPerformImageProcessing">
- <property name="toolTip">
- <string>Do image processing</string>
- </property>
- <property name="text">
- <string>Plot</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.pointsetinteractionmultispectrum/src/internal/org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator.cpp b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator.cpp
deleted file mode 100644
index 316f60f3e1..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/org_mitk_gui_qt_pointsetinteractionmultispectrum_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_pointsetinteractionmultispectrum_Activator.h"
-#include "PointSetInteractionMultispectrum.h"
-
-namespace mitk {
-
-void org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(PointSetInteractionMultispectrum, context)
-}
-
-void org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator::stop(ctkPluginContext* context)
-{
- Q_UNUSED(context)
-}
-
-}
diff --git a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator.h b/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator.h
deleted file mode 100644
index ad19f09da3..0000000000
--- a/Plugins/org.mitk.gui.qt.pointsetinteractionmultispectrum/src/internal/org_mitk_gui_qt_pointsetinteractionmultispectrum_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_pointsetinteractionmultispectrum_Activator_h
-#define org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
-class org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator :
- public QObject, public ctkPluginActivator
-{
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_pointsetinteractionmultispectrum")
- Q_INTERFACES(ctkPluginActivator)
-
-public:
-
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
-}; // org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator
-
-}
-
-#endif // org_mitk_gui_qt_pointsetinteractionmultispectrum_Activator_h
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/CMakeLists.txt b/Plugins/org.mitk.gui.qt.semanticrelations/CMakeLists.txt
deleted file mode 100644
index 970cb000dd..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_semanticrelations)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE MITK_GUI_SEMANTICRELATIONS_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkPersistence MitkSemanticRelationsUI MitkRenderWindowManager MitkMultilabel MitkSegmentationUI
-)
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/files.cmake b/Plugins/org.mitk.gui.qt.semanticrelations/files.cmake
deleted file mode 100644
index 09421a5b1d..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/files.cmake
+++ /dev/null
@@ -1,52 +0,0 @@
-set(INTERNAL_CPP_FILES
- mitkPluginActivator.cpp
- QmitkDataNodeAddToSemanticRelationsAction.cpp
- QmitkDataNodeRemoveFromSemanticRelationsAction.cpp
- QmitkDataNodeUnlinkFromLesionAction.cpp
- QmitkDataNodeSetControlPointAction.cpp
- QmitkDataNodeSetInformationTypeAction.cpp
- QmitkDataSetOpenInAction.cpp
- QmitkFocusOnLesionAction.cpp
- QmitkLabelSetJumpToAction.cpp
- QmitkLesionInfoWidget.cpp
- QmitkSemanticRelationsContextMenu.cpp
- QmitkSemanticRelationsNodeSelectionDialog.cpp
- QmitkSemanticRelationsStatisticsView.cpp
- QmitkSemanticRelationsView.cpp
-)
-
-set(UI_FILES
- src/internal/QmitkLesionInfoWidgetControls.ui
- src/internal/QmitkSemanticRelationsControls.ui
- src/internal/QmitkSemanticRelationsStatisticsControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/mitkPluginActivator.h
- src/internal/QmitkDataNodeAddToSemanticRelationsAction.h
- src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.h
- src/internal/QmitkDataNodeUnlinkFromLesionAction.h
- src/internal/QmitkDataNodeSetControlPointAction.h
- src/internal/QmitkDataNodeSetInformationTypeAction.h
- src/internal/QmitkDataSetOpenInAction.h
- src/internal/QmitkFocusOnLesionAction.h
- src/internal/QmitkLabelSetJumpToAction.h
- src/internal/QmitkLesionInfoWidget.h
- src/internal/QmitkSemanticRelationsContextMenu.h
- src/internal/QmitkSemanticRelationsNodeSelectionDialog.h
- src/internal/QmitkSemanticRelationsStatisticsView.h
- src/internal/QmitkSemanticRelationsView.h
-)
-
-set(CACHED_RESOURCE_FILES
- resources/SemanticRelations_48.png
- resources/SemanticRelationsStatistics_48.png
- plugin.xml
-)
-
-set(QRC_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.semanticrelations/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.semanticrelations/manifest_headers.cmake
deleted file mode 100644
index ed90be50bd..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "MITK Semantic relations")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "DKFZ")
-set(Plugin-ContactAddress "https://www.mitk.org")
-set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.application org.mitk.gui.qt.segmentation)
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/plugin.xml b/Plugins/org.mitk.gui.qt.semanticrelations/plugin.xml
deleted file mode 100644
index 618c2e82f1..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/plugin.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.semanticrelations"
- name="Semantic Relations"
- class="QmitkSemanticRelationsView"
- icon="resources/SemanticRelations_48.png"
- category="Semantic Relations"/>
-
- <view id="org.mitk.views.semanticrelationsstatistics"
- name="Semantic Relations Statistics"
- class="QmitkSemanticRelationsStatisticsView"
- icon="resources/SemanticRelationsStatistics_48.png"
- category="Semantic Relations"/>
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/resources/SemanticRelationsStatistics_48.png b/Plugins/org.mitk.gui.qt.semanticrelations/resources/SemanticRelationsStatistics_48.png
deleted file mode 100644
index 182a722caf..0000000000
Binary files a/Plugins/org.mitk.gui.qt.semanticrelations/resources/SemanticRelationsStatistics_48.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/resources/SemanticRelations_48.png b/Plugins/org.mitk.gui.qt.semanticrelations/resources/SemanticRelations_48.png
deleted file mode 100644
index fc0096e0ac..0000000000
Binary files a/Plugins/org.mitk.gui.qt.semanticrelations/resources/SemanticRelations_48.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.cpp
deleted file mode 100644
index e587cb8cc3..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.cpp
+++ /dev/null
@@ -1,249 +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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkDataNodeAddToSemanticRelationsAction.h"
-#include "QmitkDataNodeRemoveFromSemanticRelationsAction.h"
-
-// semantic relations module
-#include <mitkControlPointManager.h>
-#include <mitkDICOMHelper.h>
-#include <mitkNodePredicates.h>
-#include <mitkSemanticRelationsDataStorageAccess.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkSemanticRelationsIntegration.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkRelationStorage.h>
-#include <mitkUIDGeneratorBoost.h>
-
-// mitk gui common plugin
-#include <mitkDataNodeSelection.h>
-
-// mitk core
-#include <mitkTemporoSpatialStringProperty.h>
-
-// qt
-#include <QMessageBox>
-
-// namespace that contains the concrete action
-namespace AddToSemanticRelationsAction
-{
- void Run(mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode)
- {
- if (nullptr == dataStorage
- || nullptr == dataNode)
- {
- return;
- }
-
- if (mitk::NodePredicates::GetImagePredicate()->CheckNode(dataNode))
- {
- try
- {
- AddImage(dataStorage, dataNode);
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
- else if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode))
- {
- try
- {
- AddSegmentation(dataStorage, dataNode);
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
- }
-
- void AddImage(mitk::DataStorage* dataStorage, const mitk::DataNode* image)
- {
- mitk::SemanticTypes::InformationType informationType;
- mitk::SemanticTypes::ExaminationPeriod examinationPeriod;
- mitk::SemanticRelationsDataStorageAccess::DataNodeVector allSpecificImages;
- try
- {
- mitk::SemanticTypes::CaseID caseID = GetCaseIDFromDataNode(image);
- informationType = GetDICOMModalityFromDataNode(image);
- // see if the examination period - information type cell is already taken
- examinationPeriod = FindFittingExaminationPeriod(image);
- auto semanticRelationsDataStorageAccess = mitk::SemanticRelationsDataStorageAccess(dataStorage);
- try
- {
- allSpecificImages = semanticRelationsDataStorageAccess.GetAllSpecificImages(caseID, informationType, examinationPeriod);
- }
- catch (const mitk::SemanticRelationException&)
- {
- // just continue since an exception means that there is no specific image
- }
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
-
- if (!allSpecificImages.empty())
- {
- // examination period - information type cell is already taken
- // ask if cell should be overwritten
- QMessageBox::StandardButton answerButton =
- QMessageBox::question(nullptr,
- "Specific image already exists.",
- QString::fromStdString("Force overwriting existing image " + informationType + " at " + examinationPeriod.name + "?"),
- QMessageBox::Yes | QMessageBox::No, QMessageBox::Yes);
-
- if (answerButton == QMessageBox::Yes)
- {
- try
- {
- // remove already existent images at specific cell
- for (const auto& specificImage : allSpecificImages)
- {
- RemoveFromSemanticRelationsAction::Run(dataStorage, specificImage);
- }
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- return;
- }
- }
- else
- {
- // else case is: no overwriting
- return;
- }
- }
-
- // specific image does not exist or has been removed; adding the image should work
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- try
- {
- semanticRelationsIntegration.AddImage(image);
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
-
- void AddSegmentation(mitk::DataStorage* dataStorage, const mitk::DataNode* segmentation)
- {
- if (nullptr == segmentation)
- {
- return;
- }
-
- mitk::BaseData* baseData = segmentation->GetData();
- if (nullptr == baseData)
- {
- return;
- }
-
- // continue with valid segmentation data
- // get parent node of the current segmentation node with the node predicate
- mitk::DataStorage::SetOfObjects::ConstPointer parentNodes = dataStorage->GetSources(segmentation, mitk::NodePredicates::GetImagePredicate(), false);
- if (parentNodes->empty())
- {
- // segmentation without corresponding image will not be added
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not add the selected segmentation.",
- "The program wasn't able to correctly add the selected segmentation.\n"
- "Reason: No parent image found");
- msgBox.exec();
- return;
- }
-
- // check for already existing, identifying base properties
- auto caseIDPropertyName = mitk::GetCaseIDDICOMProperty();
- auto nodeIDPropertyName = mitk::GetNodeIDDICOMProperty();
- mitk::BaseProperty* caseIDProperty = baseData->GetProperty(caseIDPropertyName.c_str());
- mitk::BaseProperty* nodeIDProperty = baseData->GetProperty(nodeIDPropertyName.c_str());
- if (nullptr == caseIDProperty || nullptr == nodeIDProperty)
- {
- MITK_INFO << "No DICOM tags for case and node identification found. Transferring DICOM tags from the parent node to the selected segmentation node.";
-
- mitk::SemanticTypes::CaseID caseID;
- mitk::SemanticTypes::ID nodeID;
- try
- {
- caseID = mitk::GetCaseIDFromDataNode(parentNodes->front());
- nodeID = mitk::GetIDFromDataNode(parentNodes->front());
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- return;
- }
-
- // transfer DICOM tags to the segmentation node
- baseData->SetProperty(caseIDPropertyName, mitk::TemporoSpatialStringProperty::New(caseID));
- // add UID to distinguish between different segmentations of the same parent node
- baseData->SetProperty(nodeIDPropertyName, mitk::TemporoSpatialStringProperty::New(nodeID + mitk::UIDGeneratorBoost::GenerateUID()));
- }
-
- // add the parent node if not already existent
- if (!mitk::SemanticRelationsInference::InstanceExists(parentNodes->front()))
- {
- AddImage(dataStorage, parentNodes->front());
- }
-
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- try
- {
- // add the segmentation with its parent image to the semantic relations storage
- semanticRelationsIntegration.AddSegmentation(segmentation, parentNodes->front());
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
-}
-
-QmitkDataNodeAddToSemanticRelationsAction::QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(workbenchPartSite)
-{
- setText(tr("Add to semantic relations"));
- InitializeAction();
-}
-
-QmitkDataNodeAddToSemanticRelationsAction::QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Add to semantic relations"));
- InitializeAction();
-}
-
-void QmitkDataNodeAddToSemanticRelationsAction::InitializeAction()
-{
- connect(this, &QAction::triggered, this, &QmitkDataNodeAddToSemanticRelationsAction::OnActionTriggered);
-}
-
-void QmitkDataNodeAddToSemanticRelationsAction::OnActionTriggered(bool /*checked*/)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- auto dataNode = GetSelectedNode();
- AddToSemanticRelationsAction::Run(dataStorage, dataNode);
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h
deleted file mode 100644
index 9fbf842373..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeAddToSemanticRelationsAction.h
+++ /dev/null
@@ -1,69 +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 QmitkDataNodeAddToSemanticRelationsAction_h
-#define QmitkDataNodeAddToSemanticRelationsAction_h
-
-#include <org_mitk_gui_qt_semanticrelations_Export.h>
-
-// mitk gui qt application plugin
-#include <QmitkAbstractDataNodeAction.h>
-
-// qt
-#include <QAction>
-
-namespace AddToSemanticRelationsAction
-{
- /**
- * @brief The function checks whether the given node is an image or a segmentation and calls the corresponding add function.
- * The corresponding add functions will add the data node to the semantic relations storage.
- * If an image is added, the 'AddImage' function will check if another image at the fitting control-point - information type cell
- * already exists. If so, the user is prompted to overwrite the existing image or abort the process.
- * If the user wants to overwrite the existing image, the image and it's corresponding segmentation nodes will be removed from the semantic relations storage.
- * If a segmentation is added, the parent image node will also be to the semantic relations storage. If the segmentation does not contain the required DICOM information,
- * the DICOM information of the parent data will be transferred to the segmentation data.
- *
- * @pre The given dataStorage has to be valid (!nullptr).
- * @pre The given dataNode has to be valid (!nullptr).
- * The function simply returns if the preconditions are not met.
- *
- * @throw SemanticRelationException re-thrown.
- *
- * @param dataStorage The data storage to use for to remove the existing image and to check for the parent image node of a segmentation.
- * @param dataNode The data node to add.
- */
- MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(mitk::DataStorage* dataStorage, const mitk::DataNode* image);
-
- void AddImage(mitk::DataStorage* dataStorage, const mitk::DataNode* image);
- void AddSegmentation(mitk::DataStorage* dataStorage, const mitk::DataNode* segmentation);
-}
-
-class MITK_GUI_SEMANTICRELATIONS_EXPORT QmitkDataNodeAddToSemanticRelationsAction : public QAction, public QmitkAbstractDataNodeAction
-{
- Q_OBJECT
-
-public:
-
- QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkDataNodeAddToSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
-private Q_SLOTS:
-
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.cpp
deleted file mode 100644
index e7b33a31a6..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkDataNodeRemoveFromSemanticRelationsAction.h"
-
-// semantic relations module
-#include <mitkNodePredicates.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsIntegration.h>
-
-// mitk gui common plugin
-#include <mitkDataNodeSelection.h>
-
-// qt
-#include <QMessageBox>
-
-// namespace that contains the concrete action
-namespace RemoveFromSemanticRelationsAction
-{
- void Run(mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode)
- {
- if (nullptr == dataStorage
- || nullptr == dataNode)
- {
- return;
- }
-
- if (mitk::NodePredicates::GetImagePredicate()->CheckNode(dataNode))
- {
- try
- {
- RemoveImage(dataStorage, dataNode);
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
- else if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode))
- {
- try
- {
- RemoveSegmentation(dataNode);
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
- }
-
- void RemoveImage(mitk::DataStorage* dataStorage, const mitk::DataNode* image)
- {
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- try
- {
- // remove each corresponding segmentation from the semantic relations storage
- mitk::DataStorage::SetOfObjects::ConstPointer childNodes = dataStorage->GetDerivations(image, mitk::NodePredicates::GetSegmentationPredicate(), false);
- for (auto it = childNodes->Begin(); it != childNodes->End(); ++it)
- {
- RemoveSegmentation(it->Value());
- }
- // remove the image from the semantic relations storage
- semanticRelationsIntegration.RemoveImage(image);
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
-
- void RemoveSegmentation(const mitk::DataNode* segmentation)
- {
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- try
- {
- // remove the segmentation from the semantic relations storage
- semanticRelationsIntegration.RemoveSegmentation(segmentation);
- }
- catch (mitk::SemanticRelationException& e)
- {
- mitkReThrow(e);
- }
- }
-}
-
-QmitkDataNodeRemoveFromSemanticRelationsAction::QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(workbenchPartSite)
-{
- setText(tr("Remove from semantic relations"));
- InitializeAction();
-}
-
-QmitkDataNodeRemoveFromSemanticRelationsAction::QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Remove from semantic relations"));
- InitializeAction();
-}
-
-void QmitkDataNodeRemoveFromSemanticRelationsAction::InitializeAction()
-{
- connect(this, &QAction::triggered, this, &QmitkDataNodeRemoveFromSemanticRelationsAction::OnActionTriggered);
-}
-
-void QmitkDataNodeRemoveFromSemanticRelationsAction::OnActionTriggered(bool /*checked*/)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- auto dataNode = GetSelectedNode();
- RemoveFromSemanticRelationsAction::Run(dataStorage, dataNode);
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.h
deleted file mode 100644
index 590449473a..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeRemoveFromSemanticRelationsAction.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 QmitkDataNodeRemoveFromSemanticRelationsAction_h
-#define QmitkDataNodeRemoveFromSemanticRelationsAction_h
-
-#include <org_mitk_gui_qt_semanticrelations_Export.h>
-
-// mitk gui qt application plugin
-#include <QmitkAbstractDataNodeAction.h>
-
-// qt
-#include <QAction>
-
-namespace RemoveFromSemanticRelationsAction
-{
- /**
- * @brief The function checks whether the given node is an image or a segmentation and calls the corresponding remove function.
- * The corresponding remove functions will remove the data node from the semantic relations storage.
- * If an image is removed, the child segmentation nodes will also be removed from the semantic relations storage.
- *
- * @pre The given dataStorage has to be valid (!nullptr).
- * @pre The given dataNode has to be valid (!nullptr).
- * The function simply returns if the preconditions are not met.
- *
- * @throw SemanticRelationException re-thrown.
- *
- * @param dataStorage The data storage to use to check for the child segmentation nodes of an image.
- * @param dataNode The data node to remove.
- */
- MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(mitk::DataStorage* dataStorage, const mitk::DataNode* dataNode);
-
- void RemoveImage(mitk::DataStorage* dataStorage, const mitk::DataNode* image);
- void RemoveSegmentation(const mitk::DataNode* segmentation);
-}
-
-class MITK_GUI_SEMANTICRELATIONS_EXPORT QmitkDataNodeRemoveFromSemanticRelationsAction : public QAction, public QmitkAbstractDataNodeAction
-{
- Q_OBJECT
-
-public:
-
- QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkDataNodeRemoveFromSemanticRelationsAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
-private Q_SLOTS:
-
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetControlPointAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetControlPointAction.cpp
deleted file mode 100644
index 58a8521275..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetControlPointAction.cpp
+++ /dev/null
@@ -1,170 +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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkDataNodeSetControlPointAction.h"
-#include "QmitkDataNodeRemoveFromSemanticRelationsAction.h"
-
-// semantic relations module
-#include <mitkControlPointManager.h>
-#include <mitkDICOMHelper.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsDataStorageAccess.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkSemanticRelationsIntegration.h>
-#include <mitkUIDGeneratorBoost.h>
-
-// semantic relations UI module
-#include "QmitkControlPointDialog.h"
-
-// qt
-#include <QInputDialog>
-#include <QMessageBox>
-
-QmitkDataNodeSetControlPointAction::QmitkDataNodeSetControlPointAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(workbenchPartSite)
-{
- setText(tr("Set control point"));
- m_Parent = parent;
- InitializeAction();
-}
-
-QmitkDataNodeSetControlPointAction::QmitkDataNodeSetControlPointAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Set control point"));
- m_Parent = parent;
- InitializeAction();
-}
-
-void QmitkDataNodeSetControlPointAction::InitializeAction()
-{
- connect(this, &QAction::triggered, this, &QmitkDataNodeSetControlPointAction::OnActionTriggered);
-}
-
-void QmitkDataNodeSetControlPointAction::OnActionTriggered(bool /*checked*/)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- auto dataNode = GetSelectedNode();
- if (dataNode.IsNull())
- {
- return;
- }
-
- QmitkControlPointDialog* inputDialog = new QmitkControlPointDialog(m_Parent);
- inputDialog->setWindowTitle("Set control point");
- inputDialog->SetCurrentDate(mitk::SemanticRelationsInference::GetControlPointOfImage(dataNode));
-
- int dialogReturnValue = inputDialog->exec();
- if (QDialog::Rejected == dialogReturnValue)
- {
- return;
- }
-
- const QDate& userSelectedDate = inputDialog->GetCurrentDate();
- mitk::SemanticTypes::ControlPoint controlPoint;
- controlPoint.UID = mitk::UIDGeneratorBoost::GenerateUID();
- controlPoint.date = boost::gregorian::date(userSelectedDate.year(),
- userSelectedDate.month(),
- userSelectedDate.day());
-
- mitk::SemanticTypes::InformationType informationType;
- mitk::SemanticTypes::ExaminationPeriod examinationPeriod;
- mitk::SemanticRelationsDataStorageAccess::DataNodeVector allSpecificImages;
- try
- {
- mitk::SemanticTypes::CaseID caseID = mitk::GetCaseIDFromDataNode(dataNode);
- informationType = mitk::SemanticRelationsInference::GetInformationTypeOfImage(dataNode);
- // see if the examination period - information type cell is already taken
- examinationPeriod = mitk::FindFittingExaminationPeriod(caseID, controlPoint);
- auto semanticRelationsDataStorageAccess = mitk::SemanticRelationsDataStorageAccess(dataStorage);
- try
- {
- allSpecificImages = semanticRelationsDataStorageAccess.GetAllSpecificImages(caseID, informationType, examinationPeriod);
- }
- catch (const mitk::SemanticRelationException&)
- {
- // just continue since an exception means that there is no specific image
- }
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not set the control point.",
- "The program wasn't able to correctly set the control point.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
-
- if (!allSpecificImages.empty())
- {
- // examination period - information type cell is already taken
- // ask if cell should be overwritten
- QMessageBox::StandardButton answerButton =
- QMessageBox::question(nullptr,
- "Specific image already exists.",
- QString::fromStdString("Force overwriting existing image " + informationType + " at " + examinationPeriod.name + "?"),
- QMessageBox::Yes | QMessageBox::No, QMessageBox::Yes);
-
- if (answerButton == QMessageBox::Yes)
- {
- try
- {
- // remove already existent images at specific cell
- for (const auto& specificImage : allSpecificImages)
- {
- RemoveFromSemanticRelationsAction::Run(dataStorage, specificImage);
- }
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not set the control point.",
- "The program wasn't able to correctly set the control point.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
- }
- else
- {
- // else case is: no overwriting
- return;
- }
- }
-
- // specific image does not exist or has been removed; setting the control point should work
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- try
- {
- semanticRelationsIntegration.UnlinkImageFromControlPoint(dataNode);
- semanticRelationsIntegration.SetControlPointOfImage(dataNode, controlPoint);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not set the control point.",
- "The program wasn't able to correctly set the control point.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetControlPointAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetControlPointAction.h
deleted file mode 100644
index edb0a0ec3c..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetControlPointAction.h
+++ /dev/null
@@ -1,43 +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 QmitkDataNodeSetControlPointAction_h
-#define QmitkDataNodeSetControlPointAction_h
-
-// mitk gui qt application plugin
-#include <QmitkAbstractDataNodeAction.h>
-
-// qt
-#include <QAction>
-
-class QmitkDataNodeSetControlPointAction : public QAction, public QmitkAbstractDataNodeAction
-{
- Q_OBJECT
-
-public:
-
- QmitkDataNodeSetControlPointAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkDataNodeSetControlPointAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
-private Q_SLOTS:
-
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-
- QWidget* m_Parent;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetInformationTypeAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetInformationTypeAction.cpp
deleted file mode 100644
index 079475afee..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetInformationTypeAction.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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkDataNodeSetInformationTypeAction.h"
-#include "QmitkDataNodeRemoveFromSemanticRelationsAction.h"
-
-// semantic relations module
-#include <mitkControlPointManager.h>
-#include <mitkDICOMHelper.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsDataStorageAccess.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkSemanticRelationsIntegration.h>
-
-// qt
-#include <QInputDialog>
-#include <QMessageBox>
-
-QmitkDataNodeSetInformationTypeAction::QmitkDataNodeSetInformationTypeAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(workbenchPartSite)
-{
- setText(tr("Set information type"));
- m_Parent = parent;
- InitializeAction();
-}
-
-QmitkDataNodeSetInformationTypeAction::QmitkDataNodeSetInformationTypeAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Set information type"));
- m_Parent = parent;
- InitializeAction();
-}
-
-void QmitkDataNodeSetInformationTypeAction::InitializeAction()
-{
- connect(this, &QAction::triggered, this, &QmitkDataNodeSetInformationTypeAction::OnActionTriggered);
-}
-
-void QmitkDataNodeSetInformationTypeAction::OnActionTriggered(bool /*checked*/)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- auto dataNode = GetSelectedNode();
- if (dataNode.IsNull())
- {
- return;
- }
-
- QInputDialog* inputDialog = new QInputDialog(m_Parent);
- inputDialog->setWindowTitle(tr("Set information type of selected node"));
- inputDialog->setLabelText(tr("Information type:"));
- inputDialog->setTextValue(QString::fromStdString(mitk::SemanticRelationsInference::GetInformationTypeOfImage(dataNode)));
- inputDialog->setMinimumSize(250, 100);
-
- int dialogReturnValue = inputDialog->exec();
- if (QDialog::Rejected == dialogReturnValue)
- {
- return;
- }
-
- mitk::SemanticTypes::InformationType informationType = inputDialog->textValue().toStdString();
-
- mitk::SemanticTypes::ExaminationPeriod examinationPeriod;
- mitk::SemanticTypes::ControlPoint controlPoint;
- mitk::SemanticRelationsDataStorageAccess::DataNodeVector allSpecificImages;
- try
- {
- mitk::SemanticTypes::CaseID caseID = mitk::GetCaseIDFromDataNode(dataNode);
- controlPoint = mitk::SemanticRelationsInference::GetControlPointOfImage(dataNode);
- // see if the examination period - information type cell is already taken
- examinationPeriod = mitk::FindFittingExaminationPeriod(caseID, controlPoint);
- auto semanticRelationsDataStorageAccess = mitk::SemanticRelationsDataStorageAccess(dataStorage);
- try
- {
- allSpecificImages = semanticRelationsDataStorageAccess.GetAllSpecificImages(caseID, informationType, examinationPeriod);
- }
- catch (const mitk::SemanticRelationException&)
- {
- // just continue since an exception means that there is no specific image
- }
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not set the information type.",
- "The program wasn't able to correctly set the information type.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
-
- if (!allSpecificImages.empty())
- {
- // examination period - information type cell is already taken
- // ask if cell should be overwritten
- QMessageBox::StandardButton answerButton =
- QMessageBox::question(nullptr,
- "Specific image already exists.",
- QString::fromStdString("Force overwriting existing image " + informationType + " at " + examinationPeriod.name + "?"),
- QMessageBox::Yes | QMessageBox::No, QMessageBox::Yes);
-
- if (answerButton == QMessageBox::Yes)
- {
- try
- {
- // remove already existent images at specific cell
- for (const auto& specificImage : allSpecificImages)
- {
- RemoveFromSemanticRelationsAction::Run(dataStorage, specificImage);
- }
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not set the information type.",
- "The program wasn't able to correctly set the information type.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
- }
- else
- {
- // else case is: no overwriting
- return;
- }
- }
-
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- try
- {
- semanticRelationsIntegration.SetInformationType(dataNode, informationType);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not set the information type.",
- "The program wasn't able to correctly set the information type.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetInformationTypeAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetInformationTypeAction.h
deleted file mode 100644
index 63bba50eb4..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeSetInformationTypeAction.h
+++ /dev/null
@@ -1,43 +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 QmitkDataNodeSetInformationTypeAction_h
-#define QmitkDataNodeSetInformationTypeAction_h
-
-// mitk gui qt application plugin
-#include <QmitkAbstractDataNodeAction.h>
-
-// qt
-#include <QAction>
-
-class QmitkDataNodeSetInformationTypeAction : public QAction, public QmitkAbstractDataNodeAction
-{
- Q_OBJECT
-
-public:
-
- QmitkDataNodeSetInformationTypeAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkDataNodeSetInformationTypeAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
-private Q_SLOTS:
-
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-
- QWidget* m_Parent;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeUnlinkFromLesionAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeUnlinkFromLesionAction.cpp
deleted file mode 100644
index 5cd80458f0..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeUnlinkFromLesionAction.cpp
+++ /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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkDataNodeUnlinkFromLesionAction.h"
-
-// semantic relations module
-#include <mitkNodePredicates.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsIntegration.h>
-#include <mitkUIDGeneratorBoost.h>
-
-// mitk gui common plugin
-#include <mitkDataNodeSelection.h>
-
-// qt
-#include <QMessageBox>
-
-// namespace that contains the concrete action
-namespace UnlinkFromLesionAction
-{
- void Run(const mitk::DataNode* dataNode)
- {
- if (nullptr == dataNode)
- {
- return;
- }
-
- if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode))
- {
- mitk::SemanticRelationsIntegration semanticRelationsIntegration;
- try
- {
- semanticRelationsIntegration.UnlinkSegmentationFromLesion(dataNode);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not unlink the selected segmentation.",
- "The program wasn't able to correctly unlink the selected segmentation.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str()));
- msgBox.exec();
- }
- }
- else
- {
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not unlink the selected data node.",
- "Please chose a valid segmentation to unlink from its represented lesion!");
- msgBox.exec();
- }
- }
-}
-
-QmitkDataNodeUnlinkFromLesionAction::QmitkDataNodeUnlinkFromLesionAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(workbenchPartSite)
-{
- setText(tr("Unlink from lesion"));
- InitializeAction();
-}
-
-QmitkDataNodeUnlinkFromLesionAction::QmitkDataNodeUnlinkFromLesionAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Unlink from lesion"));
- InitializeAction();
-}
-
-void QmitkDataNodeUnlinkFromLesionAction::InitializeAction()
-{
- connect(this, &QAction::triggered, this, &QmitkDataNodeUnlinkFromLesionAction::OnActionTriggered);
-}
-
-void QmitkDataNodeUnlinkFromLesionAction::OnActionTriggered(bool /*checked*/)
-{
- auto dataNode = GetSelectedNode();
- UnlinkFromLesionAction::Run(dataNode);
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeUnlinkFromLesionAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeUnlinkFromLesionAction.h
deleted file mode 100644
index 35b89deba2..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataNodeUnlinkFromLesionAction.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 QmitkDataNodeUnlinkFromLesionAction_h
-#define QmitkDataNodeUnlinkFromLesionAction_h
-
-#include <org_mitk_gui_qt_semanticrelations_Export.h>
-
-// mitk gui qt application plugin
-#include <QmitkAbstractDataNodeAction.h>
-
-// qt
-#include <QAction>
-
-namespace UnlinkFromLesionAction
-{
- MITK_GUI_SEMANTICRELATIONS_EXPORT void Run(const mitk::DataNode* dataNode);
-}
-
-class MITK_GUI_SEMANTICRELATIONS_EXPORT QmitkDataNodeUnlinkFromLesionAction : public QAction, public QmitkAbstractDataNodeAction
-{
- Q_OBJECT
-
-public:
-
- QmitkDataNodeUnlinkFromLesionAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkDataNodeUnlinkFromLesionAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
-private Q_SLOTS:
-
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataSetOpenInAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataSetOpenInAction.cpp
deleted file mode 100644
index 73ac1edd38..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataSetOpenInAction.cpp
+++ /dev/null
@@ -1,156 +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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkDataSetOpenInAction.h"
-
-// mitk core
-#include <mitkImage.h>
-#include <mitkRenderingManager.h>
-
-// render window manager module
-#include <mitkRenderWindowLayerController.h>
-#include <mitkRenderWindowLayerUtilities.h>
-
-// semantic relations module
-#include "mitkNodePredicates.h"
-
-// mitk gui qt application plugin
-#include <QmitkDataNodeReinitAction.h>
-
-// qt
-#include <QMessageBox>
-#include <QMenu>
-
-namespace OpenInAction
-{
- void Run(mitk::DataStorage::Pointer dataStorage, mitk::DataNode::Pointer imageNode, mitk::BaseRenderer* renderer /*= nullptr*/)
- {
- if (dataStorage.IsNull())
- {
- return;
- }
-
- if (imageNode.IsNull())
- {
- return;
- }
-
- auto renderWindowLayerController = std::make_unique<mitk::RenderWindowLayerController>();
- renderWindowLayerController->SetDataStorage(dataStorage);
-
- // get current layer stack of the specified renderer
- // remove them from the specified renderer
- auto layerStack = mitk::RenderWindowLayerUtilities::GetLayerStack(dataStorage, renderer);
- for (auto& layerNode : layerStack)
- {
- // hide all nodes of the specified renderer
- layerNode.second->SetVisibility(false, renderer);
- layerNode.second->Modified();
- }
-
- // make the selected data node visible
- imageNode->SetVisibility(true, renderer);
- imageNode->Modified();
- // move node to front, which also request a render update
- renderWindowLayerController->MoveNodeToFront(imageNode, renderer);
-
- QList<mitk::DataNode::Pointer> visibleNodes;
- visibleNodes.push_back(imageNode);
- // get all corresponding segmentations of this node
- mitk::DataStorage::SetOfObjects::ConstPointer segmentationNodes = dataStorage->GetDerivations(imageNode, mitk::NodePredicates::GetSegmentationPredicate(), false);
- for (auto it = segmentationNodes->Begin(); it != segmentationNodes->End(); ++it)
- {
- auto segmentation = it->Value();
- segmentation->SetVisibility(true, renderer);
- // move node to front, which also request a render update
- renderWindowLayerController->MoveNodeToFront(segmentation, renderer);
- visibleNodes.push_back(segmentation);
- }
-
- ReinitAction::Run(berry::IWorkbenchPartSite::Pointer(), dataStorage, visibleNodes, renderer);
- }
-}
-
-QmitkDataSetOpenInAction::QmitkDataSetOpenInAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QmitkDataNodeOpenInAction(parent, workbenchPartSite)
-{
- setText(tr("Open in"));
- InitializeAction();
-}
-
-QmitkDataSetOpenInAction::QmitkDataSetOpenInAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QmitkDataNodeOpenInAction(parent, berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Open in"));
- InitializeAction();
-}
-
-void QmitkDataSetOpenInAction::InitializeAction()
-{
- setCheckable(true);
-
- setMenu(new QMenu);
- connect(menu(), &QMenu::aboutToShow, this, &QmitkDataSetOpenInAction::OnMenuAboutToShow);
-
- SetControlledRenderer();
-}
-
-void QmitkDataSetOpenInAction::OnMenuAboutToShow()
-{
- menu()->clear();
- QAction* action;
-
- QStringList rendererNames;
- for (const auto& renderer : m_ControlledRenderer)
- {
- rendererNames.append(renderer->GetName());
- }
-
- rendererNames.sort();
- for (const auto& rendererName : rendererNames)
- {
- action = menu()->addAction(rendererName);
- connect(action, &QAction::triggered, this, &QmitkDataSetOpenInAction::OnActionTriggered);
- }
-}
-
-void QmitkDataSetOpenInAction::OnActionTriggered(bool /*checked*/)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- auto dataNode = GetSelectedNode();
- if (dataNode.IsNull())
- {
- return;
- }
-
- QAction* senderAction = qobject_cast<QAction*>(QObject::sender());
- if (nullptr == senderAction)
- {
- return;
- }
-
- std::string selectedRenderer = senderAction->text().toStdString();
- mitk::BaseRenderer* renderer = mitk::BaseRenderer::GetByName(selectedRenderer);
- if (nullptr == renderer)
- {
- return;
- }
-
- OpenInAction::Run(dataStorage, dataNode, renderer);
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataSetOpenInAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataSetOpenInAction.h
deleted file mode 100644
index cabfb865db..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkDataSetOpenInAction.h
+++ /dev/null
@@ -1,44 +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 QmitkDataSetOpenInAction_h
-#define QmitkDataSetOpenInAction_h
-
-#include "QmitkDataNodeOpenInAction.h"
-
-namespace OpenInAction
-{
- void Run(mitk::DataStorage::Pointer dataStorage,
- mitk::DataNode::Pointer imageNode,
- mitk::BaseRenderer* renderer = nullptr);
-}
-
-class QmitkDataSetOpenInAction : public QmitkDataNodeOpenInAction
-{
- Q_OBJECT
-
-public:
-
- QmitkDataSetOpenInAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkDataSetOpenInAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
-private Q_SLOTS:
-
- void OnMenuAboutToShow();
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkFocusOnLesionAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkFocusOnLesionAction.cpp
deleted file mode 100644
index d54629da0c..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkFocusOnLesionAction.cpp
+++ /dev/null
@@ -1,125 +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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkFocusOnLesionAction.h"
-#include "QmitkLabelSetJumpToAction.h"
-
-// mitk core
-#include <mitkImage.h>
-#include <mitkRenderingManager.h>
-
-// render window manager module
-#include <mitkRenderWindowLayerController.h>
-#include <mitkRenderWindowLayerUtilities.h>
-
-// semantic relations module
-#include <mitkDICOMHelper.h>
-#include <mitkSemanticRelationsInference.h>
-
-// qt
-#include <QMessageBox>
-#include <QMenu>
-
-QmitkFocusOnLesionAction::QmitkFocusOnLesionAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(workbenchPartSite)
-{
- setText(tr("Focus on lesion"));
- InitializeAction();
-}
-
-QmitkFocusOnLesionAction::QmitkFocusOnLesionAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Focus on lesion"));
- InitializeAction();
-}
-
-void QmitkFocusOnLesionAction::SetSelectedLesion(mitk::SemanticTypes::Lesion selectedLesion)
-{
- m_Lesion = selectedLesion;
-}
-
-void QmitkFocusOnLesionAction::InitializeAction()
-{
- setCheckable(true);
- connect(this, &QAction::triggered, this, &QmitkFocusOnLesionAction::OnActionTriggered);
-
- SetControlledRenderer();
-}
-
-void QmitkFocusOnLesionAction::OnActionTriggered(bool /*checked*/)
-{
- auto workbenchPartSite = m_WorkbenchPartSite.Lock();
-
- if (workbenchPartSite.IsNull())
- {
- return;
- }
-
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- auto renderWindowLayerController = std::make_unique<mitk::RenderWindowLayerController>();
- renderWindowLayerController->SetDataStorage(dataStorage);
- // check each renderer to see if it contains a segmentation represented by the currently selected lesion
- for (const auto& renderer : m_ControlledRenderer)
- {
- // get currently fixed layer nodes of the specified renderer
- auto layerStack = mitk::RenderWindowLayerUtilities::GetLayerStack(dataStorage, renderer, true);
- // check each node to see if it is a segmentation represented by the currently selected lesion
- for (const auto& layer : layerStack)
- {
- auto dataNode = layer.second;
- bool isVisible = false;
- if (dataNode.IsNotNull())
- {
- dataNode->GetBoolProperty("visible", isVisible, renderer);
- }
-
- // only focus in renderer where the segmentation is visible
- if (!isVisible)
- {
- continue;
- }
-
- auto currentLesion = mitk::SemanticRelationsInference::GetLesionOfSegmentation(dataNode);
- if (currentLesion.UID == m_Lesion.UID)
- {
- // jump to this lesion in the specified renderer
- LabelSetJumpToAction::Run(workbenchPartSite, dataNode, renderer);
- }
- }
- }
-}
-
-void QmitkFocusOnLesionAction::SetControlledRenderer()
-{
- const mitk::RenderingManager::RenderWindowVector allRegisteredRenderWindows =
- mitk::RenderingManager::GetInstance()->GetAllRegisteredRenderWindows();
- mitk::BaseRenderer *baseRenderer = nullptr;
- m_ControlledRenderer.clear();
- for (const auto& renderWindow : allRegisteredRenderWindows)
- {
- baseRenderer = mitk::BaseRenderer::GetInstance(renderWindow);
- if (nullptr != baseRenderer)
- {
- m_ControlledRenderer.push_back(baseRenderer);
- }
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkFocusOnLesionAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkFocusOnLesionAction.h
deleted file mode 100644
index c5b8988164..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkFocusOnLesionAction.h
+++ /dev/null
@@ -1,52 +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 QmitkFocusOnLesionAction_h
-#define QmitkFocusOnLesionAction_h
-
-// mitk gui qt application plugin
-#include <QmitkAbstractDataNodeAction.h>
-
-// semantic relations module
-#include <mitkSemanticTypes.h>
-
-// qt
-#include <QAction>
-
-class QmitkFocusOnLesionAction : public QAction, public QmitkAbstractDataNodeAction
-{
- Q_OBJECT
-
-public:
-
- typedef std::vector<mitk::BaseRenderer*> RendererVector;
-
- QmitkFocusOnLesionAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkFocusOnLesionAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
- void SetSelectedLesion(mitk::SemanticTypes::Lesion selectedLesion);
-
-private Q_SLOTS:
-
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-
- void SetControlledRenderer();
-
- RendererVector m_ControlledRenderer;
- mitk::SemanticTypes::Lesion m_Lesion;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLabelSetJumpToAction.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLabelSetJumpToAction.cpp
deleted file mode 100644
index 3585dfc626..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLabelSetJumpToAction.cpp
+++ /dev/null
@@ -1,121 +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.
-
-============================================================================*/
-
-// mitk gui qt application plugin
-#include "QmitkLabelSetJumpToAction.h"
-
-// mitk core
-#include <mitkImage.h>
-#include <mitkRenderingManager.h>
-#include <mitkWorkbenchUtil.h>
-
-// mitk multi label module
-#include <mitkLabelSetImage.h>
-
-// qt
-#include <QMessageBox>
-#include <QMenu>
-
-namespace LabelSetJumpToAction
-{
- void Run(berry::IWorkbenchPartSite::Pointer workbenchPartSite, const mitk::DataNode* dataNode, mitk::BaseRenderer* baseRenderer /*= nullptr*/)
- {
- if (workbenchPartSite.IsNull())
- {
- return;
- }
-
- if (nullptr == dataNode)
- {
- return;
- }
-
- mitk::LabelSetImage* labelSetImage = dynamic_cast<mitk::LabelSetImage*>(dataNode->GetData());
- if (nullptr == labelSetImage)
- {
- return;
- }
-
- unsigned int activeLayer = labelSetImage->GetActiveLayer();
- mitk::Label* activeLabel = labelSetImage->GetActiveLabel(activeLayer);
- labelSetImage->UpdateCenterOfMass(activeLabel->GetValue(), activeLayer);
- const mitk::Point3D& centerPosition = activeLabel->GetCenterOfMassCoordinates();
- if (centerPosition.GetVnlVector().max_value() > 0.0)
- {
- auto renderWindowPart = mitk::WorkbenchUtil::GetRenderWindowPart(workbenchPartSite->GetPage(), mitk::WorkbenchUtil::NONE);
- if (nullptr == renderWindowPart)
- {
- renderWindowPart = mitk::WorkbenchUtil::OpenRenderWindowPart(workbenchPartSite->GetPage(), false);
- if (nullptr == renderWindowPart)
- {
- // no render window available
- return;
- }
- }
-
- auto segmentation = dynamic_cast<mitk::LabelSetImage*>(dataNode->GetData());
- if (nullptr != segmentation)
- {
- if (nullptr == baseRenderer)
- {
- renderWindowPart->SetSelectedPosition(centerPosition);
- mitk::RenderingManager::GetInstance()->InitializeViews(segmentation->GetTimeGeometry());
- }
- else
- {
- renderWindowPart->SetSelectedPosition(centerPosition, baseRenderer->GetName());
- mitk::RenderingManager::GetInstance()->InitializeView(baseRenderer->GetRenderWindow(), segmentation->GetTimeGeometry());
- }
- }
- }
- }
-}
-
-QmitkLabelSetJumpToAction::QmitkLabelSetJumpToAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(workbenchPartSite)
-{
- setText(tr("Jump to"));
- InitializeAction();
-}
-
-QmitkLabelSetJumpToAction::QmitkLabelSetJumpToAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite)
- : QAction(parent)
- , QmitkAbstractDataNodeAction(berry::IWorkbenchPartSite::Pointer(workbenchPartSite))
-{
- setText(tr("Jump to"));
- InitializeAction();
-}
-
-void QmitkLabelSetJumpToAction::InitializeAction()
-{
- connect(this, &QAction::triggered, this, &QmitkLabelSetJumpToAction::OnActionTriggered);
-}
-
-void QmitkLabelSetJumpToAction::OnActionTriggered(bool /*checked*/)
-{
- auto workbenchPartSite = m_WorkbenchPartSite.Lock();
-
- if (workbenchPartSite.IsNull())
- {
- return;
- }
-
- auto dataNode = GetSelectedNode();
- if (dataNode.IsNull())
- {
- return;
- }
-
- mitk::BaseRenderer::Pointer baseRenderer = GetBaseRenderer();
- LabelSetJumpToAction::Run(workbenchPartSite, dataNode, baseRenderer);
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLabelSetJumpToAction.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLabelSetJumpToAction.h
deleted file mode 100644
index 9bb3405dca..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLabelSetJumpToAction.h
+++ /dev/null
@@ -1,46 +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 QmitkLabelSetJumpToAction_h
-#define QmitkLabelSetJumpToAction_h
-
-#include "QmitkAbstractDataNodeAction.h"
-
-// qt
-#include <QAction>
-
-namespace LabelSetJumpToAction
-{
- void Run(berry::IWorkbenchPartSite::Pointer workbenchPartSite,
- const mitk::DataNode* dataNode,
- mitk::BaseRenderer* baseRenderer = nullptr);
-}
-
-class QmitkLabelSetJumpToAction : public QAction, public QmitkAbstractDataNodeAction
-{
- Q_OBJECT
-
-public:
-
- QmitkLabelSetJumpToAction(QWidget* parent, berry::IWorkbenchPartSite::Pointer workbenchPartSite);
- QmitkLabelSetJumpToAction(QWidget* parent, berry::IWorkbenchPartSite* workbenchPartSite);
-
-private Q_SLOTS:
-
- void OnActionTriggered(bool);
-
-protected:
-
- void InitializeAction() override;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp
deleted file mode 100644
index 4570a97efb..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp
+++ /dev/null
@@ -1,495 +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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkLesionInfoWidget.h"
-#include "QmitkDataNodeAddToSemanticRelationsAction.h"
-#include "QmitkFocusOnLesionAction.h"
-#include "QmitkSemanticRelationsNodeSelectionDialog.h"
-
-// semantic relations UI module
-#include <QmitkLesionTextDialog.h>
-
-// semantic relations module
-#include <mitkLesionManager.h>
-#include <mitkNodePredicates.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkRelationStorage.h>
-
-// segmentation
-#include <mitkLabelSetImage.h>
-#include <QmitkNewSegmentationDialog.h>
-
-// qt
-#include <QCompleter>
-#include <QListWidget>
-#include <QMenu>
-#include <QMessageBox>
-#include <QString>
-
-QmitkLesionInfoWidget::QmitkLesionInfoWidget(mitk::DataStorage* dataStorage,
- berry::IWorkbenchPartSite::Pointer workbenchPartSite,
- QWidget* parent /*= nullptr*/)
- : QWidget(parent)
- , m_DataStorage(dataStorage)
- , m_WorkbenchPartSite(workbenchPartSite)
- , m_SemanticRelationsDataStorageAccess(std::make_unique<mitk::SemanticRelationsDataStorageAccess>(dataStorage))
- , m_SemanticRelationsIntegration(std::make_unique<mitk::SemanticRelationsIntegration>())
-{
- Initialize();
-}
-
-void QmitkLesionInfoWidget::Initialize()
-{
- m_Controls.setupUi(this);
-
- m_Controls.lesionTreeView->setAlternatingRowColors(true);
- m_Controls.lesionTreeView->setSelectionMode(QAbstractItemView::SingleSelection);
- m_Controls.lesionTreeView->setSelectionBehavior(QAbstractItemView::SelectRows);
- m_Controls.lesionTreeView->setContextMenuPolicy(Qt::CustomContextMenu);
-
- m_StorageModel = new QmitkLesionTreeModel(m_Controls.lesionTreeView);
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- m_StorageModel->SetDataStorage(dataStorage);
- m_Controls.lesionTreeView->setModel(m_StorageModel);
-
- SetUpConnections();
-}
-
-void QmitkLesionInfoWidget::SetUpConnections()
-{
- connect(m_StorageModel, &QmitkLesionTreeModel::ModelUpdated, this, &QmitkLesionInfoWidget::OnModelUpdated);
- connect(m_Controls.addLesionPushButton, &QPushButton::clicked, this, &QmitkLesionInfoWidget::OnAddLesionButtonClicked);
- connect(m_Controls.lesionTreeView->selectionModel(), &QItemSelectionModel::currentChanged, this, &QmitkLesionInfoWidget::OnSelectionChanged);
- connect(m_Controls.lesionTreeView, &QTreeView::customContextMenuRequested, this, &QmitkLesionInfoWidget::OnLesionListContextMenuRequested);
-}
-
-void QmitkLesionInfoWidget::SetCaseID(const mitk::SemanticTypes::CaseID& caseID)
-{
- m_CaseID = caseID;
- m_StorageModel->SetCaseID(caseID);
-}
-
-void QmitkLesionInfoWidget::SetDataNodeSelection(const QList<mitk::DataNode::Pointer>& dataNodeSelection)
-{
- m_StorageModel->SetDataNodeSelection(dataNodeSelection);
-}
-
-//////////////////////////////////////////////////////////////////////////
-// Implementation of the QT_SLOTS
-//////////////////////////////////////////////////////////////////////////
-void QmitkLesionInfoWidget::OnModelUpdated()
-{
- m_Controls.lesionTreeView->expandAll();
- int columns = m_Controls.lesionTreeView->model()->columnCount();
- for (int i = 0; i < columns; ++i)
- {
- m_Controls.lesionTreeView->resizeColumnToContents(i);
- }
-}
-
-void QmitkLesionInfoWidget::OnAddLesionButtonClicked()
-{
- if (m_CaseID.empty())
- {
- QMessageBox msgBox(QMessageBox::Warning,
- "No case ID set.",
- "In order to add a lesion, please specify the current case / patient.");
- msgBox.exec();
- return;
- }
-
- mitk::SemanticTypes::Lesion newLesion = mitk::GenerateNewLesion();
- try
- {
- m_SemanticRelationsIntegration->AddLesion(m_CaseID, newLesion);
- }
- catch (mitk::SemanticRelationException& e)
- {
- MITK_INFO << "Could not add a new lesion. " << e;
- }
-}
-
-void QmitkLesionInfoWidget::OnSelectionChanged(const QModelIndex& current, const QModelIndex& /*previous*/)
-{
- // only the UID is needed to identify a representing lesion
- QVariant data = m_StorageModel->data(current, Qt::UserRole);
- if (!data.canConvert<QmitkLesionTreeItem*>())
- {
- return;
- }
-
- auto lesion = data.value<QmitkLesionTreeItem*>()->GetData().GetLesion();
- if (false == mitk::SemanticRelationsInference::InstanceExists(m_CaseID, lesion))
- {
- // no UID of a existing lesion found; cannot create a lesion
- return;
- }
-
- // if selected data nodes are set, reset to empty list to
- // hide "selected data nodes presence background highlighting" in the model
- if (!m_StorageModel->GetSelectedDataNodes().isEmpty())
- {
- m_StorageModel->SetDataNodeSelection(QList<mitk::DataNode::Pointer>());
- }
-
- emit LesionSelectionChanged(lesion);
-}
-
-void QmitkLesionInfoWidget::OnLesionListContextMenuRequested(const QPoint& pos)
-{
- if (nullptr == m_SemanticRelationsIntegration)
- {
- return;
- }
-
- if (m_CaseID.empty())
- {
- QMessageBox msgBox(QMessageBox::Warning,
- "No case ID set.",
- "In order to access the context menu entries a case ID has to be set.");
- msgBox.exec();
- return;
- }
-
- QModelIndex index = m_Controls.lesionTreeView->indexAt(pos);
- if (!index.isValid())
- {
- // no item clicked; cannot retrieve the current lesion
- return;
- }
-
- QVariant data = m_StorageModel->data(index, Qt::UserRole);
- mitk::SemanticTypes::Lesion selectedLesion;
- if (data.canConvert<QmitkLesionTreeItem*>())
- {
- selectedLesion = data.value<QmitkLesionTreeItem*>()->GetData().GetLesion();
- }
- else
- {
- return;
- }
-
- QMenu* menu = new QMenu(m_Controls.lesionTreeView);
-
- QAction* linkToSegmentation = new QAction("Link to segmentation", this);
- linkToSegmentation->setEnabled(true);
- connect(linkToSegmentation, &QAction::triggered, [this, selectedLesion] { OnLinkToSegmentation(selectedLesion); });
- menu->addAction(linkToSegmentation);
-
- QAction* setLesionName = new QAction("Set lesion name", this);
- setLesionName->setEnabled(true);
- connect(setLesionName, &QAction::triggered, [this, selectedLesion] { OnSetLesionName(selectedLesion); });
- menu->addAction(setLesionName);
-
- QAction* setLesionClass = new QAction("Set lesion class", this);
- setLesionClass->setEnabled(true);
- connect(setLesionClass, &QAction::triggered, [this, selectedLesion] { OnSetLesionClass(selectedLesion); });
- menu->addAction(setLesionClass);
-
- QAction* createNewSegmentation = new QAction("Create new lesion", this);
- createNewSegmentation->setEnabled(true);
- connect(createNewSegmentation, &QAction::triggered, [this, selectedLesion] { OnCreateNewSegmentation(selectedLesion); });
- menu->addAction(createNewSegmentation);
-
- QAction* removeLesion = new QAction("Remove lesion", this);
- removeLesion->setEnabled(true);
- connect(removeLesion, &QAction::triggered, [this, selectedLesion] { OnRemoveLesion(selectedLesion); });
- menu->addAction(removeLesion);
-
- auto workbenchPartSite = m_WorkbenchPartSite.Lock();
-
- if (workbenchPartSite.IsNotNull())
- {
- QmitkFocusOnLesionAction* focusOnLesion = new QmitkFocusOnLesionAction(this, workbenchPartSite);
- focusOnLesion->SetDataStorage(m_DataStorage.Lock());
- focusOnLesion->SetSelectedLesion(selectedLesion);
- menu->addAction(focusOnLesion);
- }
-
- menu->popup(QCursor::pos());
-}
-
-void QmitkLesionInfoWidget::OnLinkToSegmentation(mitk::SemanticTypes::Lesion selectedLesion)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- QmitkSemanticRelationsNodeSelectionDialog* dialog = new QmitkSemanticRelationsNodeSelectionDialog(this, "Select segmentation to link to the selected lesion.", "");
- dialog->setWindowTitle("Select segmentation node");
- dialog->SetDataStorage(dataStorage);
- dialog->SetNodePredicate(mitk::NodePredicates::GetSegmentationPredicate());
- dialog->SetSelectOnlyVisibleNodes(true);
- dialog->SetCaseID(m_CaseID);
- // set the last added segmentation node as pre-selected data node
- const mitk::DataNode* lastSegmentation = m_StorageModel->GetLastSegmentation();
- QList<mitk::DataNode::Pointer> selectedDataNodes;
- if (nullptr != lastSegmentation)
- {
- selectedDataNodes.push_back(const_cast<mitk::DataNode*>(lastSegmentation));
- dialog->SetCurrentSelection(selectedDataNodes);
- }
-
- int dialogReturnValue = dialog->exec();
- if (QDialog::Rejected == dialogReturnValue)
- {
- return;
- }
-
- mitk::DataNode::Pointer selectedDataNode = nullptr;
- selectedDataNodes = dialog->GetSelectedNodes();
- if (!selectedDataNodes.isEmpty())
- {
- // only single selection allowed
- selectedDataNode = selectedDataNodes.front();
- }
-
- if (nullptr == selectedDataNode
- || false == mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(selectedDataNode))
- {
- QMessageBox msgBox(QMessageBox::Warning,
- "No valid segmentation node selected.",
- "In order to link the selected lesion to a segmentation, please specify a valid segmentation node.");
- msgBox.exec();
- return;
- }
-
- mitk::BaseData* baseData = selectedDataNode->GetData();
- if (nullptr == baseData)
- {
- QMessageBox msgBox(QMessageBox::Warning,
- "No valid base data.",
- "In order to link the selected lesion to a segmentation, please specify a valid segmentation node.");
- msgBox.exec();
- return;
- }
-
- LinkSegmentationToLesion(selectedDataNode, selectedLesion);
-}
-
-void QmitkLesionInfoWidget::OnSetLesionName(mitk::SemanticTypes::Lesion selectedLesion)
-{
- // use the lesion information to set the input text for the dialog
- QmitkLesionTextDialog* inputDialog = new QmitkLesionTextDialog(this);
- inputDialog->setWindowTitle("Set lesion name");
- inputDialog->SetLineEditText(selectedLesion.name);
-
- int dialogReturnValue = inputDialog->exec();
- if (QDialog::Rejected == dialogReturnValue)
- {
- return;
- }
-
- selectedLesion.name = inputDialog->GetLineEditText().toStdString();
- m_SemanticRelationsIntegration->OverwriteLesion(m_CaseID, selectedLesion);
-}
-
-void QmitkLesionInfoWidget::OnSetLesionClass(mitk::SemanticTypes::Lesion selectedLesion)
-{
- // use the lesion information to set the input text for the dialog
- QmitkLesionTextDialog* inputDialog = new QmitkLesionTextDialog(this);
- inputDialog->setWindowTitle("Set lesion class");
- inputDialog->SetLineEditText(selectedLesion.lesionClass.classType);
-
- // prepare the completer for the dialogs input text field
- mitk::LesionClassVector allLesionClasses = mitk::SemanticRelationsInference::GetAllLesionClassesOfCase(m_CaseID);
-
- QStringList wordList;
- for (const auto& lesionClass : allLesionClasses)
- {
- wordList << QString::fromStdString(lesionClass.classType);
- }
- QCompleter* completer = new QCompleter(wordList, this);
- completer->setCaseSensitivity(Qt::CaseInsensitive);
- inputDialog->GetLineEdit()->setCompleter(completer);
-
- int dialogReturnValue = inputDialog->exec();
- if (QDialog::Rejected == dialogReturnValue)
- {
- return;
- }
-
- // retrieve the new input lesion class type and check for an already existing lesion class types
- std::string newLesionClassType = inputDialog->GetLineEditText().toStdString();
- mitk::SemanticTypes::LesionClass existingLesionClass = mitk::FindExistingLesionClass(m_CaseID, newLesionClassType);
- if (existingLesionClass.UID.empty())
- {
- // could not find lesion class information for the new lesion class type
- // create a new lesion class for the selected lesion
- existingLesionClass = mitk::GenerateNewLesionClass(newLesionClassType);
- }
-
- selectedLesion.lesionClass = existingLesionClass;
- m_SemanticRelationsIntegration->OverwriteLesion(m_CaseID, selectedLesion);
-}
-
-void QmitkLesionInfoWidget::OnCreateNewSegmentation(mitk::SemanticTypes::Lesion selectedLesion)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- QmitkSemanticRelationsNodeSelectionDialog* dialog = new QmitkSemanticRelationsNodeSelectionDialog(this, "Select image to segment lesion on.", "");
- dialog->setWindowTitle("Select image node");
- dialog->SetDataStorage(dataStorage);
- dialog->SetNodePredicate(mitk::NodePredicates::GetImagePredicate());
- dialog->SetSelectOnlyVisibleNodes(true);
- dialog->SetCaseID(m_CaseID);
- dialog->SetLesion(selectedLesion);
-
- int dialogReturnValue = dialog->exec();
- if (QDialog::Rejected == dialogReturnValue)
- {
- return;
- }
-
- auto nodes = dialog->GetSelectedNodes();
- mitk::DataNode::Pointer selectedDataNode = nullptr;
- if (!nodes.isEmpty())
- {
- // only single selection allowed
- selectedDataNode = nodes.front();
- }
-
- if (nullptr == selectedDataNode
- || false == mitk::NodePredicates::GetImagePredicate()->CheckNode(selectedDataNode))
- {
- QMessageBox msgBox(QMessageBox::Warning,
- "No valid image node selected.",
- "In order to create a new segmentation, please specify a valid image node.");
- msgBox.exec();
- return;
- }
-
- mitk::Image* selectedImage = dynamic_cast<mitk::Image*>(selectedDataNode->GetData());
- if (nullptr == selectedImage)
- {
- QMessageBox msgBox(QMessageBox::Warning,
- "No valid image.",
- "In order to create a new segmentation, please specify a valid image node.");
- msgBox.exec();
- return;
- }
-
- mitk::LabelSetImage::Pointer segmentation = mitk::LabelSetImage::New();
- try
- {
- segmentation->Initialize(selectedImage);
- }
- catch (mitk::Exception& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not initialize segmentation.",
- "The segmentation could not be correctly initialized with the selected image geometry.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str()));
- msgBox.exec();
- return;
- }
-
- auto segmentationDialog = new QmitkNewSegmentationDialog(this);
- segmentationDialog->setWindowTitle("New lesion segmentation");
-
- dialogReturnValue = segmentationDialog->exec();
- if (dialogReturnValue == QDialog::Rejected)
- {
- return;
- }
-
- QString segmentatioName = segmentationDialog->GetName();
- if (segmentatioName.isEmpty())
- {
- segmentatioName = "Unnamed";
- }
- segmentation->GetActiveLabelSet()->AddLabel(segmentatioName.toStdString(), segmentationDialog->GetColor());
-
- mitk::DataNode::Pointer segmentationNode = mitk::DataNode::New();
- segmentationNode->SetData(segmentation);
- segmentationNode->SetName(segmentatioName.toStdString());
- dataStorage->Add(segmentationNode, selectedDataNode);
-
- LinkSegmentationToLesion(segmentationNode, selectedLesion);
-}
-
-void QmitkLesionInfoWidget::OnRemoveLesion(mitk::SemanticTypes::Lesion selectedLesion)
-{
- try
- {
- m_SemanticRelationsIntegration->RemoveLesion(m_CaseID, selectedLesion);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not remove the selected lesion.",
- "The program wasn't able to correctly remove the selected lesion from the semantic relations model.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str()));
- msgBox.exec();
- }
-}
-
-void QmitkLesionInfoWidget::LinkSegmentationToLesion(const mitk::DataNode* selectedDataNode, mitk::SemanticTypes::Lesion selectedLesion)
-{
- auto dataStorage = m_DataStorage.Lock();
-
- if (dataStorage.IsNull())
- {
- return;
- }
-
- // if the segmentation is not contained in the semantic relations, add it
- if (!mitk::SemanticRelationsInference::InstanceExists(selectedDataNode))
- {
- try
- {
- AddToSemanticRelationsAction::Run(dataStorage, selectedDataNode);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not link the selected lesion.",
- "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
- }
-
- // link the segmentation
- try
- {
- m_SemanticRelationsIntegration->LinkSegmentationToLesion(selectedDataNode, selectedLesion);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not link the selected lesion.",
- "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str()));
- msgBox.exec();
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.h
deleted file mode 100644
index 7c7a123326..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.h
+++ /dev/null
@@ -1,103 +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 QmitkLesionInfoWidget_h
-#define QmitkLesionInfoWidget_h
-
-// semantic relations plugin
-#include <ui_QmitkLesionInfoWidgetControls.h>
-
-// semantic relations UI module
-#include <QmitkLesionTreeModel.h>
-
-// semantic relations module
-#include <mitkSemanticRelationsDataStorageAccess.h>
-#include <mitkSemanticRelationsIntegration.h>
-
-// mitk
-#include <mitkDataStorage.h>
-
-// berry
-#include <berryIWorkbenchPartSite.h>
-
-// qt
-#include <QWidget>
-
-/*
-* @brief The QmitkLesionInfoWidget is a widget that shows and modifies the currently available lesion data of the semantic relations model.
-*
-* The widget provides a dialogs to add nodes from the data storage to the semantic relations model.
-* It provides functionality to create new lesions and link them with segmentation nodes.
-*
-* The QmitkLesionInfoWidget provides three QListWidgets, that show the lesion data and the referenced segmentation data, as
-* well as the connected image data, depending on the selected lesion.
-*/
-class QmitkLesionInfoWidget : public QWidget
-{
- Q_OBJECT
-
-public:
-
- static const QBrush DEFAULT_BACKGROUND_COLOR;
- static const QBrush SELECTED_BACKGROUND_COLOR;
- static const QBrush CONNECTED_BACKGROUND_COLOR;
-
- QmitkLesionInfoWidget(mitk::DataStorage* dataStorage, berry::IWorkbenchPartSite::Pointer workbenchPartSite, QWidget* parent = nullptr);
-
- void SetCaseID(const mitk::SemanticTypes::CaseID& caseID);
-
- void SetDataNodeSelection(const QList<mitk::DataNode::Pointer>& dataNodeSelection);
-
-Q_SIGNALS:
-
- void LesionSelectionChanged(const mitk::SemanticTypes::Lesion&);
-
-private Q_SLOTS:
-
- void OnModelUpdated();
- /*
- * @brief Generates a new, empty lesion to add to the semantic relations model for the current case ID.
- */
- void OnAddLesionButtonClicked();
-
- // slots for the mouse click events of tree view's selection model
- void OnSelectionChanged(const QModelIndex& current, const QModelIndex& previous);
-
- void OnLesionListContextMenuRequested(const QPoint&);
-
- // slots for the context menu actions of the lesion list widget
- void OnLinkToSegmentation(mitk::SemanticTypes::Lesion);
- void OnSetLesionName(mitk::SemanticTypes::Lesion);
- void OnSetLesionClass(mitk::SemanticTypes::Lesion);
- void OnCreateNewSegmentation(mitk::SemanticTypes::Lesion);
- void OnRemoveLesion(mitk::SemanticTypes::Lesion);
-
-private:
-
- void Initialize();
- void SetUpConnections();
-
- void LinkSegmentationToLesion(const mitk::DataNode* selectedDataNode, mitk::SemanticTypes::Lesion selectedLesion);
-
- Ui::QmitkLesionInfoWidgetControls m_Controls;
- QmitkLesionTreeModel* m_StorageModel;
-
- mitk::SemanticTypes::CaseID m_CaseID;
-
- mitk::WeakPointer<mitk::DataStorage> m_DataStorage;
- berry::IWorkbenchPartSite::WeakPtr m_WorkbenchPartSite;
- std::unique_ptr<mitk::SemanticRelationsDataStorageAccess> m_SemanticRelationsDataStorageAccess;
- std::unique_ptr<mitk::SemanticRelationsIntegration> m_SemanticRelationsIntegration;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidgetControls.ui b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidgetControls.ui
deleted file mode 100644
index 35ace22701..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidgetControls.ui
+++ /dev/null
@@ -1,50 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkLesionInfoWidgetControls</class>
- <widget class="QWidget" name="QmitkLesionInfoWidgetControls">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>350</width>
- <height>300</height>
- </rect>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <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 row="0" column="0">
- <widget class="QLabel" name="lesionInfoWidgetLabel">
- <property name="text">
- <string>Available lesions:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0" rowspan="2">
- <widget class="QTreeView" name="lesionTreeView"/>
- </item>
- <item row="1" column="1">
- <widget class="QPushButton" name="addLesionPushButton">
- <property name="text">
- <string>Add new lesion</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsContextMenu.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsContextMenu.cpp
deleted file mode 100644
index a05a72cfc4..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsContextMenu.cpp
+++ /dev/null
@@ -1,69 +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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkSemanticRelationsContextMenu.h"
-
-QmitkSemanticRelationsContextMenu::QmitkSemanticRelationsContextMenu(berry::IWorkbenchPartSite::Pointer workbenchPartSite, QWidget* parent)
- : QMenu(parent)
- , m_Parent(parent)
- , m_WorkbenchPartSite(workbenchPartSite)
-{
- InitDefaultActions();
-}
-
-void QmitkSemanticRelationsContextMenu::SetDataStorage(mitk::DataStorage* dataStorage)
-{
- if (m_DataStorage != dataStorage)
- {
- // set the new data storage - also for all actions
- m_DataStorage = dataStorage;
- m_ControlPointAction->SetDataStorage(m_DataStorage.Lock());
- m_InformationTypeAction->SetDataStorage(m_DataStorage.Lock());
- m_RemoveFromSemanticRelationsAction->SetDataStorage(m_DataStorage.Lock());
- m_DataSetOpenInAction->SetDataStorage(m_DataStorage.Lock());
- m_UnlinkFromLesionAction->SetDataStorage(m_DataStorage.Lock());
- }
-}
-
-void QmitkSemanticRelationsContextMenu::SetControlledRenderer(mitk::RenderWindowLayerUtilities::RendererVector controlledRenderer)
-{
- if (m_ControlledRenderer != controlledRenderer)
- {
- // set the new set of controlled renderer
- m_ControlledRenderer = controlledRenderer;
- m_DataSetOpenInAction->SetControlledRenderer(m_ControlledRenderer);
- }
-}
-
-void QmitkSemanticRelationsContextMenu::OnContextMenuRequested(const QPoint& /*pos*/)
-{
- popup(QCursor::pos());
-}
-
-void QmitkSemanticRelationsContextMenu::InitDefaultActions()
-{
- m_ControlPointAction = new QmitkDataNodeSetControlPointAction(m_Parent, m_WorkbenchPartSite.Lock());
- addAction(m_ControlPointAction);
-
- m_InformationTypeAction = new QmitkDataNodeSetInformationTypeAction(m_Parent, m_WorkbenchPartSite.Lock());
- addAction(m_InformationTypeAction);
-
- m_UnlinkFromLesionAction = new QmitkDataNodeUnlinkFromLesionAction(m_Parent, m_WorkbenchPartSite.Lock());
- addAction(m_UnlinkFromLesionAction);
-
- m_RemoveFromSemanticRelationsAction = new QmitkDataNodeRemoveFromSemanticRelationsAction(m_Parent, m_WorkbenchPartSite.Lock());
- addAction(m_RemoveFromSemanticRelationsAction);
-
- m_DataSetOpenInAction = new QmitkDataSetOpenInAction(m_Parent, m_WorkbenchPartSite.Lock());
- addAction(m_DataSetOpenInAction);
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsContextMenu.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsContextMenu.h
deleted file mode 100644
index 9f7f456136..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsContextMenu.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 QmitkSemanticRelationsContextMenu_h
-#define QmitkSemanticRelationsContextMenu_h
-
-// semantic relations plugin
-#include "QmitkDataNodeSetControlPointAction.h"
-#include "QmitkDataNodeSetInformationTypeAction.h"
-#include "QmitkDataNodeUnlinkFromLesionAction.h"
-#include "QmitkDataNodeRemoveFromSemanticRelationsAction.h"
-#include "QmitkDataSetOpenInAction.h"
-
-// mitk core
-#include <mitkDataStorage.h>
-#include <mitkWeakPointer.h>
-
-// mitk render window manager module
-#include <mitkRenderWindowLayerUtilities.h>
-
-// blueberry ui qt plugin
-#include <berryIWorkbenchPartSite.h>
-
-//qt
-#include <QMenu>
-
-class QmitkSemanticRelationsContextMenu : public QMenu
-{
- Q_OBJECT
-
-public:
-
- QmitkSemanticRelationsContextMenu(berry::IWorkbenchPartSite::Pointer workbenchPartSite, QWidget* parent = nullptr);
-
- void SetDataStorage(mitk::DataStorage* dataStorage);
- void SetControlledRenderer(mitk::RenderWindowLayerUtilities::RendererVector controlledRenderer);
-
-public Q_SLOTS:
-
- void OnContextMenuRequested(const QPoint&);
-
-private:
-
- void InitDefaultActions();
-
- QWidget* m_Parent;
- berry::IWorkbenchPartSite::WeakPtr m_WorkbenchPartSite;
- mitk::WeakPointer<mitk::DataStorage> m_DataStorage;
- mitk::RenderWindowLayerUtilities::RendererVector m_ControlledRenderer;
-
- QmitkDataNodeSetControlPointAction* m_ControlPointAction;
- QmitkDataNodeSetInformationTypeAction* m_InformationTypeAction;
- QmitkDataNodeUnlinkFromLesionAction* m_UnlinkFromLesionAction;
- QmitkDataNodeRemoveFromSemanticRelationsAction* m_RemoveFromSemanticRelationsAction;
- QmitkDataSetOpenInAction* m_DataSetOpenInAction;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsControls.ui b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsControls.ui
deleted file mode 100644
index bb178d3af5..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsControls.ui
+++ /dev/null
@@ -1,37 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkSemanticRelationsControls</class>
- <widget class="QWidget" name="QmitkSemanticRelationsControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>350</width>
- <height>300</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Semantic relations plugin</string>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="0" column="0">
- <widget class="QLabel" name="caseIDLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Maximum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Currently selected patient:</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QComboBox" name="caseIDComboBox"/>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsNodeSelectionDialog.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsNodeSelectionDialog.cpp
deleted file mode 100644
index a49589c656..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsNodeSelectionDialog.cpp
+++ /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.
-
-============================================================================*/
-
-#include "QmitkSemanticRelationsNodeSelectionDialog.h"
-
-// semantic relations ui module
-#include <QmitkAbstractSemanticRelationsStorageInspector.h>
-
-// semantic relations ui module
-#include <QmitkPatientTableInspector.h>
-
-QmitkSemanticRelationsNodeSelectionDialog::QmitkSemanticRelationsNodeSelectionDialog(QWidget* parent, QString title, QString hint)
- : QmitkNodeSelectionDialog(parent, title, hint)
-{
- // nothing here
-}
-
-void QmitkSemanticRelationsNodeSelectionDialog::SetCaseID(const mitk::SemanticTypes::CaseID& caseID)
-{
- for (auto panel : m_Panels)
- {
- QmitkAbstractSemanticRelationsStorageInspector* semanticRelationsStorageInspector = dynamic_cast<QmitkAbstractSemanticRelationsStorageInspector*>(panel);
- if (nullptr != semanticRelationsStorageInspector)
- {
- semanticRelationsStorageInspector->SetCaseID(caseID);
- }
- }
-}
-
-void QmitkSemanticRelationsNodeSelectionDialog::SetLesion(const mitk::SemanticTypes::Lesion& lesion)
-{
- for (auto panel : m_Panels)
- {
- QmitkAbstractSemanticRelationsStorageInspector* semanticRelationsStorageInspector = dynamic_cast<QmitkAbstractSemanticRelationsStorageInspector*>(panel);
- if (nullptr != semanticRelationsStorageInspector)
- {
- semanticRelationsStorageInspector->SetLesion(lesion);
- }
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsNodeSelectionDialog.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsNodeSelectionDialog.h
deleted file mode 100644
index a767f61ed5..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsNodeSelectionDialog.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 QmitkSemanticRelationsNodeSelectionDialog_h
-#define QmitkSemanticRelationsNodeSelectionDialog_h
-
-// semantic relations module
-#include <mitkSemanticTypes.h>
-
-// org.mitk.gui.qt.common plugin
-#include <QmitkNodeSelectionDialog.h>
-
-/*
-* @brief The QmitkSemanticRelationsNodeSelectionDialog extends the QmitkNodeSelectionDialog so that a case ID and a lesion
-* can be set for each known panel that is of type 'QmitkSemanticRelationsStorageInspector'.
-*/
-class QmitkSemanticRelationsNodeSelectionDialog : public QmitkNodeSelectionDialog
-{
- Q_OBJECT
-
-public:
-
- explicit QmitkSemanticRelationsNodeSelectionDialog(QWidget* parent = nullptr, QString caption = "", QString hint = "");
- /**
- * @brief Extends the base class to allow setting the current case ID which is needed to access the
- * semantic relations storage. The function sets the case ID of each 'QmitkSemanticRelationsStorageInspector'.
- *
- * @param caseID A case ID as string
- */
- virtual void SetCaseID(const mitk::SemanticTypes::CaseID& caseID);
- /**
- * @brief Extends the base class to allow setting the current lesion which can be used to show on which images
- * the lesion is visible. The function sets the lesion of each 'QmitkSemanticRelationsStorageInspector'.
- *
- * @param lesion The selected lesion
- */
- virtual void SetLesion(const mitk::SemanticTypes::Lesion& lesion);
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsControls.ui b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsControls.ui
deleted file mode 100644
index 330e1d12c1..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsControls.ui
+++ /dev/null
@@ -1,40 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkSemanticRelationsStatisticsControls</class>
- <widget class="QWidget" name="QmitkSemanticRelationsStatisticsControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>350</width>
- <height>300</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Semantic relations plugin</string>
- </property>
- <layout class="QGridLayout" name="gridLayout">
- <item row="1" column="0">
- <widget class="QComboBox" name="caseIDComboBox"/>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="caseIDLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Maximum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>Currently selected patient:</string>
- </property>
- </widget>
- </item>
- <item row="2" column="0">
- <widget class="QTreeView" name="statisticsTreeView"/>
- </item>
- </layout>
- </widget>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsView.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsView.cpp
deleted file mode 100644
index 9862b39146..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsView.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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkSemanticRelationsStatisticsView.h"
-
-// semantic relations module
-#include <mitkSemanticRelationsIntegration.h>
-#include <mitkRelationStorage.h>
-
-const std::string QmitkSemanticRelationsStatisticsView::VIEW_ID = "org.mitk.views.semanticrelationsstatistics";
-
-QmitkSemanticRelationsStatisticsView::~QmitkSemanticRelationsStatisticsView()
-{
- auto semanticRelationsIntegration = std::make_unique<mitk::SemanticRelationsIntegration>();
- semanticRelationsIntegration->RemoveObserver(this);
-}
-
-void QmitkSemanticRelationsStatisticsView::Update(const mitk::SemanticTypes::CaseID& caseID)
-{
- AddToComboBox(caseID);
-}
-
-void QmitkSemanticRelationsStatisticsView::SetFocus()
-{
- // nothing here
-}
-
-void QmitkSemanticRelationsStatisticsView::CreateQtPartControl(QWidget* parent)
-{
- // create GUI elements
- m_Controls.setupUi(parent);
-
- m_StatisticsTreeModel = new QmitkStatisticsTreeModel(parent);
- m_StatisticsTreeModel->SetDataStorage(GetDataStorage());
- m_Controls.statisticsTreeView->setModel(m_StatisticsTreeModel);
-
- auto semanticRelationsIntegration = std::make_unique<mitk::SemanticRelationsIntegration>();
- semanticRelationsIntegration->AddObserver(this);
-
- SetUpConnections();
- const auto& allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- for (const auto& caseID : allCaseIDs)
- {
- AddToComboBox(caseID);
- }
-}
-
-void QmitkSemanticRelationsStatisticsView::SetUpConnections()
-{
- connect(m_Controls.caseIDComboBox, static_cast<void (QComboBox::*)(const QString&)>(&QComboBox::currentIndexChanged), this, &QmitkSemanticRelationsStatisticsView::OnCaseIDSelectionChanged);
- connect(m_StatisticsTreeModel, &QmitkStatisticsTreeModel::ModelUpdated, this, &QmitkSemanticRelationsStatisticsView::OnModelUpdated);
-}
-
-void QmitkSemanticRelationsStatisticsView::OnCaseIDSelectionChanged(const QString& caseID)
-{
- m_StatisticsTreeModel->SetCaseID(caseID.toStdString());
-}
-
-void QmitkSemanticRelationsStatisticsView::OnModelUpdated()
-{
- m_Controls.statisticsTreeView->expandAll();
- int columns = m_Controls.statisticsTreeView->model()->columnCount();
- for (int i = 0; i < columns; ++i)
- {
- m_Controls.statisticsTreeView->resizeColumnToContents(i);
- }
-}
-
-void QmitkSemanticRelationsStatisticsView::AddToComboBox(const mitk::SemanticTypes::CaseID& caseID)
-{
- int foundIndex = m_Controls.caseIDComboBox->findText(QString::fromStdString(caseID));
- if (-1 == foundIndex)
- {
- // add the caseID to the combo box, as it is not already contained
- m_Controls.caseIDComboBox->addItem(QString::fromStdString(caseID));
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsView.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsView.h
deleted file mode 100644
index 5fcafd7996..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsStatisticsView.h
+++ /dev/null
@@ -1,74 +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 QmitkSemanticRelationsStatisticsView_h
-#define QmitkSemanticRelationsStatisticsView_h
-
-// semantic relations plugin
-#include "ui_QmitkSemanticRelationsStatisticsControls.h"
-
-// semantic relations module
-#include <mitkSemanticTypes.h>
-
-// semantic relations ui module
-#include "QmitkStatisticsTreeModel.h"
-
-// mitk qt gui common plugin
-#include <QmitkAbstractView.h>
-
-/*
-* @brief The QmitkSemanticRelationsStatisticsView is an MITK view to combine and show the statistics tree view of the 'SemanticRelationsUI'-module.
-* It observes the semantic relations storage and displays the currently available case IDs in a combo box.
-* A 'QmitkStatisticsTreeModel' is created and set as the model of a QTreeView.
-*/
-class QmitkSemanticRelationsStatisticsView : public QmitkAbstractView, public mitk::ISemanticRelationsObserver
-{
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- ~QmitkSemanticRelationsStatisticsView() override;
-
- /*
- * @brief Update the view with the data from the semantic relations.
- *
- * Overridden from 'ISemanticRelationsObserver'.
- * In order for the Update-function to be called, this view has to be added as an observer of SemanticRelation
- * (e.g. m_SemanticRelations->AddObserver(this);)
- *
- * @par caseID The current case ID to identify the currently active patient / case.
- */
- void Update(const mitk::SemanticTypes::CaseID& caseID) override;
-
-protected:
-
- void SetFocus() override;
- void CreateQtPartControl(QWidget* parent) override;
-
-private Q_SLOTS:
-
- void OnCaseIDSelectionChanged(const QString&);
- void OnModelUpdated();
-
-private:
-
- void SetUpConnections();
- void AddToComboBox(const mitk::SemanticTypes::CaseID& caseID);
-
- Ui::QmitkSemanticRelationsStatisticsControls m_Controls;
-
- QmitkStatisticsTreeModel* m_StatisticsTreeModel;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.cpp
deleted file mode 100644
index b6e9ce7db4..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.cpp
+++ /dev/null
@@ -1,281 +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.
-
-============================================================================*/
-
-// semantic relations plugin
-#include "QmitkSemanticRelationsView.h"
-#include "QmitkDataNodeAddToSemanticRelationsAction.h"
-#include "QmitkDataNodeRemoveFromSemanticRelationsAction.h"
-#include "QmitkLabelSetJumpToAction.h"
-
-// semantic relations module
-#include <mitkDICOMHelper.h>
-#include <mitkNodePredicates.h>
-#include <mitkSemanticRelationException.h>
-#include <mitkSemanticRelationsInference.h>
-#include <mitkRelationStorage.h>
-
-// mitk core
-#include <mitkImage.h>
-
-// mitk qt widgets module
-#include <QmitkDnDDataNodeWidget.h>
-#include <QmitkRenderWindow.h>
-
-// berry
-#include <berryISelectionService.h>
-#include <berryIWorkbenchWindow.h>
-
-// qt
-#include <QMenu>
-#include <QMessageBox>
-#include <QTreeView>
-
-const std::string QmitkSemanticRelationsView::VIEW_ID = "org.mitk.views.semanticrelations";
-
-void QmitkSemanticRelationsView::SetFocus()
-{
- // nothing here
-}
-
-void QmitkSemanticRelationsView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart)
-{
- if (m_RenderWindowPart != renderWindowPart)
- {
- m_RenderWindowPart = renderWindowPart;
- SetControlledRenderer();
- }
-}
-
-void QmitkSemanticRelationsView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart)
-{
- if (m_RenderWindowPart == renderWindowPart)
- {
- m_RenderWindowPart = nullptr;
- SetControlledRenderer();
- }
-}
-
-void QmitkSemanticRelationsView::RenderWindowPartInputChanged(mitk::IRenderWindowPart* renderWindowPart)
-{
- if (m_RenderWindowPart == renderWindowPart)
- {
- SetControlledRenderer();
- }
-}
-
-void QmitkSemanticRelationsView::CreateQtPartControl(QWidget* parent)
-{
- // create GUI widgets
- m_Controls.setupUi(parent);
-
- m_LesionInfoWidget = new QmitkLesionInfoWidget(GetDataStorage(), GetSite(), parent);
- m_Controls.gridLayout->addWidget(m_LesionInfoWidget);
-
- m_PatientTableInspector = new QmitkPatientTableInspector(parent);
- m_PatientTableInspector->SetDataStorage(GetDataStorage());
- m_Controls.gridLayout->addWidget(m_PatientTableInspector);
-
- QGridLayout* dndDataNodeWidgetLayout = new QGridLayout;
- dndDataNodeWidgetLayout->addWidget(m_PatientTableInspector, 0, 0);
- dndDataNodeWidgetLayout->setContentsMargins(0, 0, 0, 0);
-
- m_DnDDataNodeWidget = new QmitkDnDDataNodeWidget(parent);
- m_DnDDataNodeWidget->setLayout(dndDataNodeWidgetLayout);
-
- m_Controls.gridLayout->addWidget(m_DnDDataNodeWidget);
-
- m_ContextMenu = new QmitkSemanticRelationsContextMenu(GetSite(), m_PatientTableInspector);
- m_ContextMenu->SetDataStorage(GetDataStorage());
-
- mitk::IRenderWindowPart* renderWindowPart = GetRenderWindowPart();
- if (nullptr != renderWindowPart)
- {
- RenderWindowPartActivated(renderWindowPart);
- }
-
- SetUpConnections();
-
- const auto& allCaseIDs = mitk::RelationStorage::GetAllCaseIDs();
- for (const auto& caseID : allCaseIDs)
- {
- AddToComboBox(caseID);
- }
-}
-
-void QmitkSemanticRelationsView::SetUpConnections()
-{
- connect(m_Controls.caseIDComboBox, static_cast<void (QComboBox::*)(const QString&)>(&QComboBox::currentIndexChanged), this, &QmitkSemanticRelationsView::OnCaseIDSelectionChanged);
- connect(m_LesionInfoWidget, &QmitkLesionInfoWidget::LesionSelectionChanged, this, &QmitkSemanticRelationsView::OnLesionSelectionChanged);
- connect(m_PatientTableInspector, &QmitkPatientTableInspector::CurrentSelectionChanged, this, &QmitkSemanticRelationsView::OnDataNodeSelectionChanged);
- connect(m_PatientTableInspector, &QmitkPatientTableInspector::DataNodeDoubleClicked, this, &QmitkSemanticRelationsView::OnDataNodeDoubleClicked);
- connect(m_DnDDataNodeWidget, &QmitkDnDDataNodeWidget::NodesDropped, this, &QmitkSemanticRelationsView::OnNodesAdded);
-
- connect(m_PatientTableInspector, &QmitkPatientTableInspector::OnContextMenuRequested, m_ContextMenu, &QmitkSemanticRelationsContextMenu::OnContextMenuRequested);
- connect(m_PatientTableInspector, &QmitkPatientTableInspector::OnNodeRemoved, this, &QmitkSemanticRelationsView::NodeRemoved);
-}
-
-QItemSelectionModel* QmitkSemanticRelationsView::GetDataNodeSelectionModel() const
-{
- return m_PatientTableInspector->GetSelectionModel();
-}
-
-void QmitkSemanticRelationsView::NodeRemoved(const mitk::DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- return;
- }
-
- if (mitk::SemanticRelationsInference::InstanceExists(dataNode))
- {
- try
- {
- RemoveFromSemanticRelationsAction::Run(GetDataStorage(), dataNode);
- mitk::SemanticTypes::CaseID caseID = mitk::GetCaseIDFromDataNode(dataNode);
- RemoveFromComboBox(caseID);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not remove the data node(s).",
- "The program wasn't able to correctly remove the selected data node(s).\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
- }
-}
-
-void QmitkSemanticRelationsView::OnLesionSelectionChanged(const mitk::SemanticTypes::Lesion& lesion)
-{
- m_PatientTableInspector->SetLesion(lesion);
-}
-
-void QmitkSemanticRelationsView::OnDataNodeSelectionChanged(const QList<mitk::DataNode::Pointer>& dataNodeSelection)
-{
- m_LesionInfoWidget->SetDataNodeSelection(dataNodeSelection);
-}
-
-void QmitkSemanticRelationsView::OnDataNodeDoubleClicked(const mitk::DataNode* dataNode)
-{
- if (nullptr == dataNode)
- {
- return;
- }
-
- if (mitk::NodePredicates::GetImagePredicate()->CheckNode(dataNode))
- {
- OpenInEditor(dataNode);
- }
- else if (mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(dataNode))
- {
- LabelSetJumpToAction::Run(GetSite(), dataNode);
- }
-}
-
-void QmitkSemanticRelationsView::OnCaseIDSelectionChanged(const QString& caseID)
-{
- m_LesionInfoWidget->SetCaseID(caseID.toStdString());
- m_PatientTableInspector->SetCaseID(caseID.toStdString());
-}
-
-void QmitkSemanticRelationsView::OnNodesAdded(std::vector<mitk::DataNode*> nodes)
-{
- mitk::SemanticTypes::CaseID caseID = "";
- for (mitk::DataNode* dataNode : nodes)
- {
- try
- {
- AddToSemanticRelationsAction::Run(GetDataStorage(), dataNode);
- caseID = mitk::GetCaseIDFromDataNode(dataNode);
- AddToComboBox(caseID);
- }
- catch (const mitk::SemanticRelationException& e)
- {
- std::stringstream exceptionMessage; exceptionMessage << e;
- QMessageBox msgBox(QMessageBox::Warning,
- "Could not add the data node(s).",
- "The program wasn't able to correctly add the selected data node(s).\n"
- "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n"));
- msgBox.exec();
- }
- }
-}
-
-void QmitkSemanticRelationsView::OnNodeRemoved(const mitk::DataNode* dataNode)
-{
- NodeRemoved(dataNode);
-}
-
-void QmitkSemanticRelationsView::AddToComboBox(const mitk::SemanticTypes::CaseID& caseID)
-{
- int foundIndex = m_Controls.caseIDComboBox->findText(QString::fromStdString(caseID));
- if (-1 == foundIndex)
- {
- // add the caseID to the combo box, as it is not already contained
- m_Controls.caseIDComboBox->addItem(QString::fromStdString(caseID));
- }
-}
-
-void QmitkSemanticRelationsView::RemoveFromComboBox(const mitk::SemanticTypes::CaseID& caseID)
-{
- std::vector<mitk::SemanticTypes::ControlPoint> allControlPoints = mitk::RelationStorage::GetAllControlPointsOfCase(caseID);
- int foundIndex = m_Controls.caseIDComboBox->findText(QString::fromStdString(caseID));
- if (allControlPoints.empty() && -1 != foundIndex)
- {
- // caseID does not contain any control points and therefore no data
- // remove the caseID, if it is still contained
- m_Controls.caseIDComboBox->removeItem(foundIndex);
- }
-}
-
-void QmitkSemanticRelationsView::OpenInEditor(const mitk::DataNode* dataNode)
-{
- auto renderWindowPart = GetRenderWindowPart();
- if (nullptr == renderWindowPart)
- {
- renderWindowPart = GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::BRING_TO_FRONT | mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN);
- if (nullptr == renderWindowPart)
- {
- // no render window available
- return;
- }
- }
-
- auto image = dynamic_cast<mitk::Image*>(dataNode->GetData());
- if (nullptr != image)
- {
- mitk::RenderingManager::GetInstance()->InitializeViews(image->GetTimeGeometry());
- }
-}
-
-void QmitkSemanticRelationsView::SetControlledRenderer()
-{
- QHash<QString, QmitkRenderWindow*> renderWindows;
- if (m_RenderWindowPart != nullptr)
- {
- renderWindows = m_RenderWindowPart->GetQmitkRenderWindows();
- }
-
- mitk::RenderWindowLayerUtilities::RendererVector controlledRenderer;
- mitk::BaseRenderer* baseRenderer = nullptr;
- for (const auto& renderWindow : renderWindows.values())
- {
- baseRenderer = mitk::BaseRenderer::GetInstance(renderWindow->GetVtkRenderWindow());
- if (nullptr != baseRenderer)
- {
- controlledRenderer.push_back(baseRenderer);
- }
- }
-
- m_ContextMenu->SetControlledRenderer(controlledRenderer);
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.h
deleted file mode 100644
index 639d04c265..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkSemanticRelationsView.h
+++ /dev/null
@@ -1,106 +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 QmitkSemanticRelationsView_h
-#define QmitkSemanticRelationsView_h
-
-// semantic relations plugin
-#include "ui_QmitkSemanticRelationsControls.h"
-#include "QmitkLesionInfoWidget.h"
-#include "QmitkSemanticRelationsContextMenu.h"
-
-// semantic relations module
-#include <mitkSemanticTypes.h>
-
-// semantic relations UI module
-#include <QmitkPatientTableInspector.h>
-
-// mitk gui common plugin
-#include <mitkIRenderWindowPartListener.h>
-
-// berry
-#include <berryISelectionListener.h>
-
-// mitk qt gui common plugin
-#include <QmitkAbstractView.h>
-
-class QmitkDnDDataNodeWidget;
-class QMenu;
-
-/*
-* @brief The QmitkSemanticRelationsView is an MITK view to combine and show the widgets of the 'SemanticRelationsUI'-module and this semantic relations plugin.
-*
-* It allows the MITK user to see and modify the content of the SemanticRelations-session.
-* A combo box is used to select and show the current patient.
-*/
-class QmitkSemanticRelationsView : public QmitkAbstractView, public mitk::IRenderWindowPartListener
-{
- Q_OBJECT
-
-public:
-
- static const std::string VIEW_ID;
-
- void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override;
- void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override;
- void RenderWindowPartInputChanged(mitk::IRenderWindowPart* renderWindowPart) override;
-
-protected:
-
- void SetFocus() override;
- void CreateQtPartControl(QWidget* parent) override;
-
-private Q_SLOTS:
-
- void OnLesionSelectionChanged(const mitk::SemanticTypes::Lesion&);
- void OnDataNodeSelectionChanged(const QList<mitk::DataNode::Pointer>&);
- void OnDataNodeDoubleClicked(const mitk::DataNode*);
- void OnCaseIDSelectionChanged(const QString&);
-
- void OnNodesAdded(std::vector<mitk::DataNode*>);
- void OnNodeRemoved(const mitk::DataNode*);
-
-private:
-
- void SetUpConnections();
- /**
- * @brief Provide a QItemSelectionModel, which supports the data role 'QmitkDataNodeRole' (\see QmitkRenderWindowDataModel).
- *
- * The provided QItemSelectionModel is used in the QmitkAbstractView-base class as the selection model of
- * the selection provider (\see QmitkAbstractView::SetSelectionProvider()).
- * The default selection provider is a QmitkDataNodeSelectionProvider. Each time a selection in the provided
- * QItemSelectionModel is changed, a selection changed event is fired. All plugins (views), that subclass the
- * QmitkAbstractView will be informed about the selection changed via the OnSelectionChanged-function.
- */
- QItemSelectionModel* GetDataNodeSelectionModel() const override;
-
- void NodeRemoved(const mitk::DataNode* dataNode) override;
-
- void AddToComboBox(const mitk::SemanticTypes::CaseID& caseID);
- void RemoveFromComboBox(const mitk::SemanticTypes::CaseID& caseID);
-
- void OpenInEditor(const mitk::DataNode* dataNode);
-
- void SetControlledRenderer();
-
- Ui::QmitkSemanticRelationsControls m_Controls;
-
- mitk::IRenderWindowPart* m_RenderWindowPart;
-
- QmitkLesionInfoWidget* m_LesionInfoWidget;
- QmitkPatientTableInspector* m_PatientTableInspector;
- QmitkDnDDataNodeWidget* m_DnDDataNodeWidget;
-
- QmitkSemanticRelationsContextMenu* m_ContextMenu;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/mitkPluginActivator.cpp
deleted file mode 100644
index 883a0f8650..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/mitkPluginActivator.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 "mitkPluginActivator.h"
-#include "QmitkSemanticRelationsStatisticsView.h"
-#include "QmitkSemanticRelationsView.h"
-
-#include <mitkPersistenceService.h>
-
-namespace mitk
-{
- void SemanticRelationsActivator::start(ctkPluginContext *context)
- {
- mitk::PersistenceService::LoadModule();
-
- BERRY_REGISTER_EXTENSION_CLASS(QmitkSemanticRelationsView, context)
- BERRY_REGISTER_EXTENSION_CLASS(QmitkSemanticRelationsStatisticsView, context)
- }
-
- void SemanticRelationsActivator::stop(ctkPluginContext *context) { Q_UNUSED(context) }
-}
diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/mitkPluginActivator.h
deleted file mode 100644
index e1bc611bd3..0000000000
--- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/mitkPluginActivator.h
+++ /dev/null
@@ -1,33 +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 mitkPluginActivator_h
-#define mitkPluginActivator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk
-{
- class SemanticRelationsActivator : public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_semanticrelations")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
- };
-}
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/CMakeLists.txt b/Plugins/org.mitk.gui.qt.tubegraph/CMakeLists.txt
deleted file mode 100644
index cb85bf6f41..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-PROJECT(org_mitk_gui_qt_tubegraph)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE TUBEGRAPH_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkTubeGraph MitkQtWidgetsExt #QmitkExt MitkSegmentationUI
-)
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/files.cmake b/Plugins/org.mitk.gui.qt.tubegraph/files.cmake
deleted file mode 100644
index 53d078307a..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/files.cmake
+++ /dev/null
@@ -1,47 +0,0 @@
-SET(SRC_CPP_FILES
-
-)
-
-SET(INTERNAL_CPP_FILES
- mitkPluginActivator.cpp
- mitkTubeGraphDefaultLabelGroups.cpp
- QmitkTubeGraphView.cpp
- QmitkTubeGraphLabelWidget.cpp
- QmitkTubeGraphLabelGroupWidget.cpp
- QmitkTubeGraphDeleteLabelGroupDialog.cpp
- QmitkTubeGraphNewLabelGroupDialog.cpp
- QmitkTubeGraphNewAnnotationDialog.cpp
-)
-SET(UI_FILES
- src/internal/QmitkTubeGraphViewControls.ui
-)
-
-SET(MOC_H_FILES
- src/internal/mitkPluginActivator.h
- src/internal/QmitkTubeGraphView.h
- src/internal/QmitkTubeGraphLabelWidget.h
- src/internal/QmitkTubeGraphLabelGroupWidget.h
- src/internal/QmitkTubeGraphDeleteLabelGroupDialog.h
- src/internal/QmitkTubeGraphNewLabelGroupDialog.h
- src/internal/QmitkTubeGraphNewAnnotationDialog.h
-)
-
-SET(CACHED_RESOURCE_FILES
- resources/tubeGraph.png
- resources/icon_seedpoint.png
- 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.tubegraph/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.tubegraph/manifest_headers.cmake
deleted file mode 100644
index 2b6a1b533c..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "MITK Tube Graph")
-set(Plugin-Version "1.0.0")
-set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
-set(Plugin-ContactAddress "https://www.mitk.org")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/plugin.xml b/Plugins/org.mitk.gui.qt.tubegraph/plugin.xml
deleted file mode 100644
index 91761a43b2..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/plugin.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?BlueBerry version="0.1"?>
-<plugin>
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.tubegraph"
- name="Tube Graph"
- icon="resources/tubeGraph.png"
- class="QmitkTubeGraphView" />
- </extension>
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/resources/icon_seedpoint.png b/Plugins/org.mitk.gui.qt.tubegraph/resources/icon_seedpoint.png
deleted file mode 100644
index 6175c379fe..0000000000
Binary files a/Plugins/org.mitk.gui.qt.tubegraph/resources/icon_seedpoint.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/resources/tubeGraph.png b/Plugins/org.mitk.gui.qt.tubegraph/resources/tubeGraph.png
deleted file mode 100644
index 71ba043c1b..0000000000
Binary files a/Plugins/org.mitk.gui.qt.tubegraph/resources/tubeGraph.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.cpp
deleted file mode 100644
index 5f3dfc2b33..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.cpp
+++ /dev/null
@@ -1,89 +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 "QmitkTubeGraphDeleteLabelGroupDialog.h"
-
-#include <QAbstractItemView>
-#include <QPushButton>
-#include <QLayout>
-#include <QLabel>
-#include <QListWidget>
-
-
-
-QmitkTubeGraphDeleteLabelGroupDialog::QmitkTubeGraphDeleteLabelGroupDialog(QWidget* parent)
-:QDialog(parent)
-{
-
- QDialog::setFixedSize(400, 400);
-
- auto layout = new QVBoxLayout(this);
- layout->setContentsMargins(QMargins(5, 5, 5, 5));
- layout->setSpacing(5);
-
- descriptionLabel = new QLabel("Which Label Group should be removed?", this);
- layout->addWidget(descriptionLabel);
-
- labelGroupListWidget = new QListWidget(this);
- labelGroupListWidget->setSelectionMode(QAbstractItemView::MultiSelection);
- layout->addWidget(labelGroupListWidget);
-
- auto buttonLayout = new QHBoxLayout();
-
- deleteButton = new QPushButton("Delete", this);
- buttonLayout->addWidget(deleteButton);
- connect( deleteButton, SIGNAL(clicked()), this, SLOT(OnDeleteLabelGroupClicked()) );
-
- cancleButton = new QPushButton("Cancel", this);
- buttonLayout->addWidget(cancleButton);
- connect( cancleButton, SIGNAL(clicked()), this, SLOT(reject()) );
-
- layout->addLayout(buttonLayout);
-
- deleteButton->setFocus();
-
-}
-
-QmitkTubeGraphDeleteLabelGroupDialog::~QmitkTubeGraphDeleteLabelGroupDialog()
-{
- delete descriptionLabel;
- delete labelGroupListWidget;
- delete deleteButton;
- delete cancleButton;
-}
-
-void QmitkTubeGraphDeleteLabelGroupDialog::OnDeleteLabelGroupClicked()
-{
- //get selected items and save it in vector
- m_LabelGroupList.clear();
- for (int i =0; i < labelGroupListWidget->count(); i++)
- {
- QListWidgetItem* newItem= labelGroupListWidget->item(i);
- if(newItem->isSelected()) //For all checked items
- {
- m_LabelGroupList.push_back(newItem->text());
- }
- }
-
- this->accept();
-}
-
-QStringList QmitkTubeGraphDeleteLabelGroupDialog::GetSelectedLabelGroups()
-{
- return m_LabelGroupList;
-}
-
-void QmitkTubeGraphDeleteLabelGroupDialog::SetLabelGroups(const QStringList &labelGroups)
-{
- for (const auto &labelGroup : labelGroups)
- labelGroupListWidget->addItem(labelGroup);
-}
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.h
deleted file mode 100644
index 5b86428900..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphDeleteLabelGroupDialog.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 QmitkTubeGraphDeleteLabelGroupDialog_h
-#define QmitkTubeGraphDeleteLabelGroupDialog_h
-
-
-#include <QDialog>
-
-class QPushButton;
-class QListWidget;
-class QLabel;
-class QWidget;
-
-class QmitkTubeGraphDeleteLabelGroupDialog : public QDialog
-{
- Q_OBJECT
-
-public:
-
- QmitkTubeGraphDeleteLabelGroupDialog(QWidget* parent = nullptr);
- ~QmitkTubeGraphDeleteLabelGroupDialog() override;
-
- QStringList GetSelectedLabelGroups();
- void SetLabelGroups(const QStringList &labelGroups);
-
-
- protected slots:
- void OnDeleteLabelGroupClicked();
-
-protected:
- QLabel* descriptionLabel;
- QListWidget* labelGroupListWidget;
- QPushButton* deleteButton;
- QPushButton* cancleButton;
-
- QStringList m_LabelGroupList;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelGroupWidget.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelGroupWidget.cpp
deleted file mode 100644
index 3498ecff66..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelGroupWidget.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 "QmitkTubeGraphLabelGroupWidget.h"
-
-#include "QmitkTubeGraphLabelWidget.h"
-
-QmitkTubeGraphLabelGroupWidget::QmitkTubeGraphLabelGroupWidget(QWidget* parent, const char* name)
-:QWidget(parent)
-{
- m_GroupLayout = new QVBoxLayout();
- this->SetGroupName(QString(name));
- this->setLayout(m_GroupLayout);
-}
-
-QmitkTubeGraphLabelGroupWidget::~QmitkTubeGraphLabelGroupWidget()
-{
- //m_Labels.clear();
- delete m_GroupLayout;
-}
-
-void QmitkTubeGraphLabelGroupWidget::AddLabel(QString name, mitk::Color color)
-{
- auto label = new QmitkTubeGraphLabelWidget(this);
- label->SetLabelName(name);
- label->SetLabelColor(&color);
-
- m_GroupLayout->addWidget(label);
-
- connect(label, SIGNAL(SignalLabelVisibilityToggled(bool, QString)), this, SLOT(OnVisibilityToggled(bool, QString)));
- connect(label, SIGNAL(SignalLabelButtonClicked(QString)), this, SLOT(OnLabelButtonClicked(QString)));
- connect(label, SIGNAL(SignalLabelColorChanged(mitk::Color, QString)), this, SLOT(OnColoringButtonClicked(mitk::Color, QString)));
-}
-
-void QmitkTubeGraphLabelGroupWidget::SetGroupName(QString name)
-{
- m_GroupName = name;
-}
-
-QString QmitkTubeGraphLabelGroupWidget::GetGroupName()
-{
- return m_GroupName;
-}
-
-void QmitkTubeGraphLabelGroupWidget::OnVisibilityToggled(bool isVisible, QString labelName)
-{
- emit SignalLabelVisibilityInGroupToggled(isVisible, labelName, this->GetGroupName());
-}
-
-void QmitkTubeGraphLabelGroupWidget::OnLabelButtonClicked(QString labelName)
-{
- emit SignalLabelButtonInGroupClicked(labelName, this->GetGroupName());
-}
-
-void QmitkTubeGraphLabelGroupWidget::OnColoringButtonClicked(mitk::Color color, QString labelName)
-{
- emit SignalLabelColorInGroupChanged(color, labelName, this->GetGroupName());
-}
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelGroupWidget.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelGroupWidget.h
deleted file mode 100644
index 116fdd1d26..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelGroupWidget.h
+++ /dev/null
@@ -1,53 +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 QmitkTubeGraphLabelGroupWidget_h
-#define QmitkTubeGraphLabelGroupWidget_h
-
-#include "mitkColorProperty.h"
-
-#include <QVector>
-#include <QVBoxLayout>
-#include <QWidget>
-
-class QmitkTubeGraphLabelGroupWidget : public QWidget
-{
- Q_OBJECT
-
-public:
- QmitkTubeGraphLabelGroupWidget(QWidget *parent = nullptr, const char* name = nullptr);
- ~QmitkTubeGraphLabelGroupWidget() override;
-
- void SetGroupName(QString name);
- QString GetGroupName();
- void AddLabel(QString name, mitk::Color color);
-
-signals:
- void SignalLabelVisibilityInGroupToggled(bool, QString, QString);
- void SignalLabelButtonInGroupClicked(QString, QString);
- void SignalLabelColorInGroupChanged(mitk::Color, QString, QString);
-
- protected slots:
-
- void OnVisibilityToggled(bool isVisible, QString labelName);
- void OnLabelButtonClicked(QString labelName);
- void OnColoringButtonClicked(mitk::Color color, QString labelName);
-
-private:
-
- QString m_GroupName;
- QVBoxLayout* m_GroupLayout;
- //QVector<QmitkTubeGraphLabelWidget*> m_Labels;
-
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelWidget.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelWidget.cpp
deleted file mode 100644
index ca5289bc97..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelWidget.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 "QmitkTubeGraphLabelWidget.h"
-
-#include <QHBoxLayout>
-#include <QColorDialog>
-
-QmitkTubeGraphLabelWidget::QmitkTubeGraphLabelWidget(QWidget* parent)
-:QWidget(parent)
-{
- this->InitWidget();
-}
-
-QmitkTubeGraphLabelWidget::~QmitkTubeGraphLabelWidget()
-{
- delete m_VisibilityCheckBox;
- delete m_LabelPushButton;
- delete m_ColoringPushButton;
-}
-
-void QmitkTubeGraphLabelWidget::InitWidget()
-{
-
- m_VisibilityCheckBox = new QCheckBox("", this);
- m_VisibilityCheckBox->setChecked(true);
- m_VisibilityCheckBox->setSizePolicy(QSizePolicy::Fixed, QSizePolicy::Fixed);
-
- m_LabelPushButton = new QPushButton("", this);
- //m_LabelPushButton->setCheckable(true);
- //m_LabelPushButton->setAutoExclusive(true);
-
- m_ColoringPushButton = new QPushButton(this);
- m_ColoringPushButton->setStyleSheet( QString("* { background-color: rgb(0,0,0)}"));
- m_ColoringPushButton->setSizePolicy(QSizePolicy::Fixed, QSizePolicy::Fixed);
-
- auto layout = new QHBoxLayout;
-
- layout->addWidget(m_VisibilityCheckBox);
- layout->addWidget(m_LabelPushButton);
- layout->addWidget(m_ColoringPushButton);
-
- this->setLayout(layout);
-
- connect(m_VisibilityCheckBox, SIGNAL(toggled(bool)), this, SLOT(OnVisibilityToggled(bool)));
- connect(m_LabelPushButton, SIGNAL(clicked()), this, SLOT(OnLabelButtonClicked()));
-
- connect(m_ColoringPushButton, SIGNAL(clicked()), this, SLOT(OnColoringButtonClicked()));
- //connect(m_ColoringPushButton, SIGNAL(clicked()), this, SIGNAL(SignalLabelColorChanged(this->GetLabelName())));
-}
-
-void QmitkTubeGraphLabelWidget::SetLabelName(QString name)
-{
- m_LabelPushButton->setText(name);
-}
-
-QString QmitkTubeGraphLabelWidget::GetLabelName()
-{
- return m_LabelPushButton->text();
-}
-
-void QmitkTubeGraphLabelWidget::SetLabelColor(mitk::Color* color)
-{
- m_ColoringPushButton->setStyleSheet( QString("* { background-color: rgb(%1,%2,%3)}").arg(color->GetRed()).arg(color->GetGreen()).arg(color->GetBlue()) );
-}
-
-mitk::Color* QmitkTubeGraphLabelWidget::GetLabelColor()
-{
- //return the background color of the button
- const QColor color = m_ColoringPushButton->palette().color(QPalette::Button);
- auto rgb = new mitk::Color();
- rgb->Set(color.red(), color.green(), color.blue());
- return rgb;
-}
-
-void QmitkTubeGraphLabelWidget::OnVisibilityToggled(bool isVisible)
-{
- emit SignalLabelVisibilityToggled(isVisible, this->GetLabelName());
-}
-
-void QmitkTubeGraphLabelWidget::OnLabelButtonClicked()
-{
- emit SignalLabelButtonClicked(this->GetLabelName());
-}
-
-void QmitkTubeGraphLabelWidget::OnColoringButtonClicked()
-{
- QColor usersChoice = QColorDialog::getColor();
- mitk::Color color;
-
- if (usersChoice.spec() != 0)
- {
- color[0] = usersChoice.red();
- color[1] = usersChoice.green();
- color[2] = usersChoice.blue();
-
- this->SetLabelColor(&color);
- emit SignalLabelColorChanged(color, this->GetLabelName());
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelWidget.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelWidget.h
deleted file mode 100644
index 3953c3655b..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphLabelWidget.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 QmitkTubeGraphLabelWidget_h
-#define QmitkTubeGraphLabelWidget_h
-
-#include "mitkColorProperty.h"
-
-#include <QCheckBox>
-#include <QPushButton>
-
-class QmitkTubeGraphLabelWidget : public QWidget
-{
- Q_OBJECT
-
-public:
-
- QmitkTubeGraphLabelWidget(QWidget* parent = nullptr);
- //QmitkTubeGraphLabelWidget(QWidget* parent = 0, const char* name = 0, mitk::Color* color = 0 /*TODO*/);
- ~QmitkTubeGraphLabelWidget() override;
-
- void SetLabelName(QString name);
- QString GetLabelName();
- void SetLabelColor(mitk::Color* color);
- mitk::Color* GetLabelColor();
-
-signals:
-
- void SignalLabelVisibilityToggled(bool, QString);
- void SignalLabelButtonClicked(QString);
- void SignalLabelColorChanged(mitk::Color, QString);
-
- protected slots:
-
- void OnVisibilityToggled(bool isVisible);
- void OnLabelButtonClicked();
- void OnColoringButtonClicked();
-
-
-private:
-
- void InitWidget();
-
- QCheckBox* m_VisibilityCheckBox;
- QPushButton* m_LabelPushButton;
- QPushButton* m_ColoringPushButton;
-
-};
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.cpp
deleted file mode 100644
index 07f4761203..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.cpp
+++ /dev/null
@@ -1,95 +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 "QmitkTubeGraphNewAnnotationDialog.h"
-
-#include <qpushbutton.h>
-#include <qlayout.h>
-#include <qlineedit.h>
-#include <qlabel.h>
-#include <qlistwidget.h>
-
-
-QmitkTubeGraphNewAnnotationDialog::QmitkTubeGraphNewAnnotationDialog(QWidget* parent)
-:QDialog(parent)
-{
- QDialog::setFixedSize(200, 200);
-
- layout = new QVBoxLayout(this);
- layout->setContentsMargins(QMargins(5, 5, 5, 5));
- layout->setSpacing(5);
-
- annotationNameLabel = new QLabel("Enter the name of the annotation!", this);
- layout->addWidget(annotationNameLabel);
-
- annotationNameLineEdit = new QLineEdit(this);
- layout->addWidget(annotationNameLineEdit);
-
- annotationDescriptionLabel = new QLabel("Enter a description!", this);
- layout->addWidget(annotationDescriptionLabel);
-
- annotationDescriptionLineEdit = new QLineEdit(this);
- layout->addWidget(annotationDescriptionLineEdit);
-
- buttonLayout = new QHBoxLayout();
-
- okButton = new QPushButton("Ok", this);
- buttonLayout->addWidget(okButton, 0, Qt::AlignRight);
- connect( okButton, SIGNAL(clicked()), this, SLOT(OnAddingAnnotation()) );
-
- cancleButton = new QPushButton("Cancel", this);
- buttonLayout->addWidget(cancleButton, 0, Qt::AlignRight);
- connect( cancleButton, SIGNAL(clicked()), this, SLOT(reject()) );
-
- layout->addLayout(buttonLayout);
-
- annotationNameLineEdit->setFocus();
-}
-
-void QmitkTubeGraphNewAnnotationDialog::OnAddingAnnotation()
-{
- if (annotationNameLineEdit->text().isEmpty())
- {
- annotationNameLineEdit->setStyleSheet("border: 1px solid red");
- return;
- }
-
- m_NewAnnotationName = annotationNameLineEdit->text();
- m_NewAnnotationDescription = annotationDescriptionLineEdit->text();
-
- this->accept();
-}
-
-QmitkTubeGraphNewAnnotationDialog::~QmitkTubeGraphNewAnnotationDialog()
-{
- delete layout;
-
- delete okButton;
- delete cancleButton;
- // delete buttonLayout;
-
- delete annotationNameLabel;
- delete annotationNameLineEdit;
-
- delete annotationDescriptionLabel;
- delete annotationDescriptionLineEdit;
-}
-
-QString QmitkTubeGraphNewAnnotationDialog::GetAnnotationName()
-{
- return m_NewAnnotationName;
-}
-
-QString QmitkTubeGraphNewAnnotationDialog::GetAnnotationDescription()
-{
- return m_NewAnnotationDescription;
-}
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.h
deleted file mode 100644
index f9ff4fe7ed..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewAnnotationDialog.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 QmitkTubeGraphNewAnnotationDialog_h
-#define QmitkTubeGraphNewAnnotationDialog_h
-
-#include <qdialog.h>
-
-class QPushButton;
-class QVBoxLayout;
-class QHBoxLayout;
-class QLineEdit;
-class QLabel;
-
-class QmitkTubeGraphNewAnnotationDialog : public QDialog
-{
- Q_OBJECT
-
-public:
-
- QmitkTubeGraphNewAnnotationDialog(QWidget* parent = nullptr);
- ~QmitkTubeGraphNewAnnotationDialog() override;
-
- QString GetAnnotationName();
- QString GetAnnotationDescription();
-
-protected slots:
-
-void OnAddingAnnotation();
-
-protected:
-
- QVBoxLayout* layout;
- QHBoxLayout* buttonLayout;
-
- QPushButton* okButton;
- QPushButton* cancleButton;
-
- QLabel* annotationNameLabel;
- QLineEdit* annotationNameLineEdit;
-
- QLabel* annotationDescriptionLabel;
- QLineEdit* annotationDescriptionLineEdit;
-
- QString m_NewAnnotationName;
- QString m_NewAnnotationDescription;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.cpp
deleted file mode 100644
index 4b785f1bf8..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.cpp
+++ /dev/null
@@ -1,270 +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 "QmitkTubeGraphNewLabelGroupDialog.h"
-
-#include <qpushbutton.h>
-#include <qlayout.h>
-#include <qlineedit.h>
-#include <qlabel.h>
-#include <qlistwidget.h>
-#include <qtreewidget.h>
-#include <qheaderview.h>
-
-#include "mitkTubeGraphDefaultLabelGroups.h"
-
-
-QmitkTubeGraphNewLabelGroupDialog::QmitkTubeGraphNewLabelGroupDialog(QWidget* parent)
-:QDialog(parent)
-,m_NewLabelGroup()
-{
- QDialog::setFixedSize(200, 200);
-
- layout = new QVBoxLayout(this);
- layout->setContentsMargins(QMargins(5, 5, 5, 5));
- layout->setSpacing(5);
-
- newLabelGroupButton = new QPushButton("Create new label group", this);
- layout->addWidget(newLabelGroupButton, 0, Qt::AlignHCenter);
- connect( newLabelGroupButton, SIGNAL(clicked()), this, SLOT(OnCreateNewLabelGroup()) );
-
- standardLabelGroupButton = new QPushButton("Add standard label group", this);
- layout->addWidget(standardLabelGroupButton, 0, Qt::AlignHCenter);
- connect( standardLabelGroupButton, SIGNAL(clicked()), this, SLOT(OnAddStandardLabelGroup()) );
-
- spacer = new QSpacerItem( 20, 40, QSizePolicy::Minimum, QSizePolicy::Minimum );
- layout->addSpacerItem(spacer);
-
- buttonLayout = new QHBoxLayout();
-
- okButton = new QPushButton("Ok", this);
- buttonLayout->addWidget(okButton, 0, Qt::AlignRight);
- okButton->setVisible(false);
-
- cancleButton = new QPushButton("Cancel", this);
- buttonLayout->addWidget(cancleButton, 0, Qt::AlignRight);
- connect( cancleButton, SIGNAL(clicked()), this, SLOT(reject()) );
-
- layout->addLayout(buttonLayout);
-
- newLabelGroupButton->setFocus();
-
-}
-
-QmitkTubeGraphNewLabelGroupDialog::~QmitkTubeGraphNewLabelGroupDialog()
-{
- //delete layout;
- ////delete buttonLayout;
- //delete spacer;
- //delete okButton;
- //delete cancleButton;
-
- //delete labelGroupDescriptionLabel;
- /* delete labelGroupLineEdit;
-
- delete labelDescriptionLabel;
- delete labelLineEdit;
- delete addLabelButton;
- delete labelListWidget; */
- //delete labelGroupTreeWidget;
-}
-
-void QmitkTubeGraphNewLabelGroupDialog::OnCreateNewLabelGroup()
-{
- QDialog::setFixedSize(400, 200);
-
- layout->removeWidget(newLabelGroupButton);
- delete newLabelGroupButton;
-
- layout->removeWidget(standardLabelGroupButton);
- delete standardLabelGroupButton;
-
- layout->removeWidget(okButton);
- layout->removeWidget(cancleButton);
-
- layout->removeItem(spacer);
- layout->removeItem(buttonLayout);
-
- labelGroupDescriptionLabel = new QLabel("Enter the label group name!", this);
- layout->addWidget(labelGroupDescriptionLabel);
-
- labelGroupLineEdit = new QLineEdit(this);
- layout->addWidget(labelGroupLineEdit);
-
- labelDescriptionLabel = new QLabel("Enter a label name!", this);
- layout->addWidget(labelDescriptionLabel);
-
-
- auto labelLayout = new QHBoxLayout();
-
- labelLineEdit = new QLineEdit(this);
- labelLayout->addWidget(labelLineEdit);
-
- addLabelButton = new QPushButton("+", this);
- labelLayout->addWidget(addLabelButton);
- connect( addLabelButton, SIGNAL(clicked()), this, SLOT(OnAddingLabel()) );
-
- layout->addLayout(labelLayout);
-
- labelListWidget = new QListWidget(this);
- labelListWidget->setDragDropMode(QAbstractItemView::InternalMove);
- labelListWidget->addItem("Undefined");
- layout->addWidget(labelListWidget);
-
- layout->addLayout(buttonLayout);
- connect( okButton, SIGNAL(clicked()), this, SLOT(OnAddingNewLabelGroup()) );
-
- okButton->setVisible(true);
-}
-
-void QmitkTubeGraphNewLabelGroupDialog::OnAddStandardLabelGroup()
-{
- QDialog::setFixedSize(400, 200);
-
- layout->removeWidget(newLabelGroupButton);
- delete newLabelGroupButton;
-
- layout->removeWidget(standardLabelGroupButton);
- delete standardLabelGroupButton;
-
- layout->removeWidget(okButton);
- layout->removeWidget(cancleButton);
-
- layout->removeItem(spacer);
- layout->removeItem(buttonLayout);
-
- labelGroupDescriptionLabel = new QLabel("Choose one of the standard label group!", this);
- layout->addWidget(labelGroupDescriptionLabel);
-
- labelGroupTreeWidget = new QTreeWidget(this);
- labelGroupTreeWidget->header()->close();
-
-
- auto defaultLabelGroups = new mitk::TubeGraphDefaultLabelGroups();
-
- m_LabelGroupsLiver = defaultLabelGroups->GetLabelGroupForLiver();
- m_LabelGroupsLung = defaultLabelGroups->GetLabelGroupForLung();
-
- auto liverItem = new QTreeWidgetItem(labelGroupTreeWidget);
- liverItem->setText(0, tr("Liver"));
- QTreeWidgetItem* liverChildItem;
- for (unsigned int k = 0; k < m_LabelGroupsLiver.size(); k++)
- {
- liverChildItem = new QTreeWidgetItem(liverItem);
- liverChildItem->setText(0, QString::fromStdString(m_LabelGroupsLiver.at(k)->labelGroupName));
- }
- liverItem->setExpanded(true);
-
- auto lungItem = new QTreeWidgetItem(labelGroupTreeWidget);
- lungItem->setText(0, tr("Lung"));
- QTreeWidgetItem* lungChildItem;
- for (unsigned int k = 0; k < m_LabelGroupsLung.size(); k++)
- {
- lungChildItem = new QTreeWidgetItem(lungItem);
- lungChildItem->setText(0, QString::fromStdString(m_LabelGroupsLung.at(k)->labelGroupName));
- }
- lungItem->setExpanded(true);
-
-
- labelGroupTreeWidget->insertTopLevelItem(1,lungItem);
-
- delete defaultLabelGroups;
-
- layout->addWidget(labelGroupTreeWidget);
-
- layout->addLayout(buttonLayout);
- connect( okButton, SIGNAL(clicked()), this, SLOT(OnAddingStandardLabelGroup()) );
-
- okButton->setVisible(true);
-
-}
-
-void QmitkTubeGraphNewLabelGroupDialog::OnAddingLabel()
-{
- if (labelLineEdit->text().isEmpty())
- {
- labelLineEdit->setStyleSheet("border: 1px solid red");
- return;
- }
-
- labelListWidget->addItem(labelLineEdit->text());
- labelLineEdit->clear();
-}
-
-void QmitkTubeGraphNewLabelGroupDialog::OnAddingNewLabelGroup()
-{
- if (labelGroupLineEdit->text().isEmpty())
- {
- labelGroupLineEdit->setStyleSheet("border: 1px solid red");
- return;
- }
- m_NewLabelGroup = new LabelGroupType();
- m_NewLabelGroup->labelGroupName = (labelGroupLineEdit->text()).toStdString();
-
- for (int i =0; i < labelListWidget->count(); i++)
- {
- auto label = new LabelType();
- label->labelName = (labelListWidget->item(i)->text()).toStdString();
- mitk::Color color;
-
- if(label->labelName.compare("Undefined") == 0)
- {
- color[0] = 170; color[1] = 170; color[2] = 169;
- }
- else
- {
- color[0] = rand() % 255; color[1] = rand() % 255; color[2] = rand() % 255;
- }
- label->labelColor = color;
- label->isVisible = true;
- m_NewLabelGroup->labels.push_back(label);
- }
-
- this->accept();
-}
-
-void QmitkTubeGraphNewLabelGroupDialog::OnAddingStandardLabelGroup()
-{
- if (labelGroupTreeWidget->selectedItems().isEmpty())
- {
- labelGroupDescriptionLabel->setStyleSheet("border: 1px solid red");
- return;
- }
-
- if(labelGroupTreeWidget->selectedItems().at(0)->parent()->text(0) == "Lung")
- {
- for (unsigned int k = 0; k < m_LabelGroupsLung.size(); k++)
- {
- if(m_LabelGroupsLung.at(k)->labelGroupName == (labelGroupTreeWidget->selectedItems().at(0)->text(0)).toStdString())
- m_NewLabelGroup = m_LabelGroupsLung.at(k);
- }
- }
- else
- {
- for (unsigned int k = 0; k < m_LabelGroupsLiver.size(); k++)
- {
- if(m_LabelGroupsLiver.at(k)->labelGroupName == (labelGroupTreeWidget->selectedItems().at(0)->text(0)).toStdString())
- m_NewLabelGroup = m_LabelGroupsLiver.at(k);
- }
- }
- if (m_NewLabelGroup == nullptr)
- return;
-
-
- this->accept();
-
-}
-
-QmitkTubeGraphNewLabelGroupDialog::LabelGroupType* QmitkTubeGraphNewLabelGroupDialog::GetLabelGroup()
-{
- return m_NewLabelGroup;
-}
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.h
deleted file mode 100644
index 9f0a43f7df..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphNewLabelGroupDialog.h
+++ /dev/null
@@ -1,78 +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 QmitkTubeGraphNewLabelGroupDialog_h
-#define QmitkTubeGraphNewLabelGroupDialog_h
-
-#include <qdialog.h>
-#include <vector>
-#include "mitkTubeGraphProperty.h"
-
-class QSpacerItem;
-class QPushButton;
-class QVBoxLayout;
-class QHBoxLayout;
-class QLineEdit;
-class QLabel;
-class QListWidget;
-class QTreeWidget;
-
-class QmitkTubeGraphNewLabelGroupDialog : public QDialog
-{
- Q_OBJECT
-
- typedef mitk::TubeGraphProperty::LabelGroup LabelGroupType;
- typedef LabelGroupType::Label LabelType;
-
-public:
-
- QmitkTubeGraphNewLabelGroupDialog(QWidget* parent = nullptr);
- ~QmitkTubeGraphNewLabelGroupDialog() override;
-
- mitk::TubeGraphProperty::LabelGroup* GetLabelGroup();
-
- protected slots:
-
- void OnCreateNewLabelGroup();
- void OnAddStandardLabelGroup();
- void OnAddingNewLabelGroup();
- void OnAddingStandardLabelGroup();
- void OnAddingLabel();
-
-protected:
-
- QVBoxLayout* layout;
- QHBoxLayout* buttonLayout;
- QSpacerItem* spacer;
-
- QPushButton* newLabelGroupButton;
- QPushButton* standardLabelGroupButton;
-
- QPushButton* okButton;
- QPushButton* cancleButton;
-
- QLabel* labelGroupDescriptionLabel;
- QLineEdit* labelGroupLineEdit;
-
- QLabel* labelDescriptionLabel;
- QLineEdit* labelLineEdit;
- QPushButton* addLabelButton;
- QListWidget* labelListWidget;
-
- QTreeWidget* labelGroupTreeWidget;
-
- LabelGroupType* m_NewLabelGroup;
- std::vector<LabelGroupType*> m_LabelGroupsLiver;
- std::vector<LabelGroupType*> m_LabelGroupsLung;
-};
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphView.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphView.cpp
deleted file mode 100644
index 10ede762da..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphView.cpp
+++ /dev/null
@@ -1,621 +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 "QmitkTubeGraphView.h"
-
-#include "mitkDataStorage.h"
-#include "mitkRenderingManager.h"
-#include "mitkNodePredicateDataType.h"
-#include "usModuleRegistry.h"
-#include "QmitkTubeGraphLabelGroupWidget.h"
-#include "QmitkTubeGraphDeleteLabelGroupDialog.h"
-#include "QmitkTubeGraphNewLabelGroupDialog.h"
-#include "QmitkTubeGraphNewAnnotationDialog.h"
-
-const std::string QmitkTubeGraphView::VIEW_ID = "org.mitk.views.tubegraph";
-
-QmitkTubeGraphView::QmitkTubeGraphView()
- :QmitkAbstractView(),
- m_ActiveTubeGraph(),
- m_ActiveProperty(),
- m_ActivationMode(mitk::TubeGraphDataInteractor::None)
-{
-}
-
-QmitkTubeGraphView::~QmitkTubeGraphView()
-{
- //m_ActivationMode.mitk::TubeGraphDataInteractor::ActivationMode::~ActivationMode();
-
- //remove observer
- //if (m_ActiveInteractor.IsNotNull())
- //m_ActiveInteractor->RemoveObserver(m_InformationChangedObserverTag);
-
-}
-
-void QmitkTubeGraphView::SetFocus()
-{
- m_Controls.activeNodeGroupBox->setFocus();
-}
-
-void QmitkTubeGraphView::CreateQtPartControl(QWidget *parent)
-{
- // create GUI widgets
- m_Parent = parent;
- m_Controls.setupUi(parent);
- this->CreateConnections();
-}
-
-void QmitkTubeGraphView::NodeRemoved(const mitk::DataNode* /*node*/)
-{
-
-}
-
-void QmitkTubeGraphView::CreateConnections()
-{
- mitk::NodePredicateDataType::Pointer tubeGraphPred = mitk::NodePredicateDataType::New("TubeGraph");
- m_Controls.activeGraphComboBox->SetDataStorage(this->GetDataStorage());
- m_Controls.activeGraphComboBox->SetPredicate(tubeGraphPred);
-
- //activation mode
- connect( m_Controls.activeGraphComboBox, SIGNAL(currentIndexChanged (int)), this, SLOT(OnActiveGraphChanged(int)) );
- connect( m_Controls.noneModeRadioButton, SIGNAL(clicked()), this, SLOT(OnActivationModeChanged()));
- connect( m_Controls.singleModeRadioButton, SIGNAL(clicked()), this, SLOT(OnActivationModeChanged()));
- connect( m_Controls.multipleModeRadioButton, SIGNAL(clicked()), this, SLOT(OnActivationModeChanged()));
- connect( m_Controls.peripheryModeRadioButton, SIGNAL(clicked()), this, SLOT(OnActivationModeChanged()));
- connect( m_Controls.rootModeRadioButton, SIGNAL(clicked()), this, SLOT(OnActivationModeChanged()));
- connect( m_Controls.pointModeRadioButton, SIGNAL(clicked()), this, SLOT(OnActivationModeChanged()));
- connect( m_Controls.setRootButton, SIGNAL(toggled(bool)), this, SLOT(OnSetRootToggled(bool)));
-
- //deselect tubes
- connect( m_Controls.deselectAllButton, SIGNAL(clicked()), this, SLOT(OnDeselectAllTubes()));
-
- // tab switch
- connect( m_Controls.tubeGraphTabWidget, SIGNAL(currentChanged(int)), this, SLOT(OnTabSwitched(int)));
-
- //attributation tab
- connect( m_Controls.addLabelGroupButton, SIGNAL(clicked()), this, SLOT(OnAddingLabelGroup()));
- connect( m_Controls.removeLabelGroupButton, SIGNAL(clicked()), this, SLOT(OnRemoveLabelGroup()));
-
- //annotation tab
- connect( m_Controls.addAnnotationButton, SIGNAL(clicked()), this, SLOT(OnAddingAnnotation()));
- connect( m_Controls.deleteAnnotationButton, SIGNAL(clicked()), this, SLOT(OnRemoveAnnotation()));
-
- //edit tab
- connect( m_Controls.editSelectionNewButton, SIGNAL(clicked()), this, SLOT(OnAddTubeBetweenSelection()));
- connect( m_Controls.editSelectionSeperateButton, SIGNAL(clicked()), this, SLOT(OnSeperateSelection()));
- connect( m_Controls.editSelectionDeleteButton, SIGNAL(clicked()), this, SLOT(OnDeleteSelection()));
-
-
- this->SetTabsEnable(false);
-}
-
-void QmitkTubeGraphView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList<mitk::DataNode::Pointer>& nodes)
-{
- for (mitk::DataNode::Pointer node: nodes)
- {
- if( node.IsNotNull() && dynamic_cast< mitk::TubeGraph* >(node->GetData()) )
- {
- m_Controls.activeGraphComboBox->SetSelectedNode(node);
- m_ActiveTubeGraph = dynamic_cast< mitk::TubeGraph* >(node->GetData());
-
- m_ActiveProperty = dynamic_cast<mitk::TubeGraphProperty*>(m_ActiveTubeGraph->GetProperty( "Tube Graph.Visualization Information" ).GetPointer());
-
- this->UpdateActiveTubeGraphInInteractors();
- this->UpdateLabelGroups();
- this->UpdateAnnotation();
- }
- }
-}
-
-void QmitkTubeGraphView::OnActiveGraphChanged(int)
-{
- mitk::DataNode::Pointer selectedNode = m_Controls.activeGraphComboBox->GetSelectedNode();
-
- if(selectedNode.IsNotNull())
- {
- m_ActiveTubeGraph = dynamic_cast <mitk::TubeGraph* >( selectedNode->GetData() );
-
- m_ActiveProperty = dynamic_cast<mitk::TubeGraphProperty*>(m_ActiveTubeGraph->GetProperty("Tube Graph.Visualization Information" ).GetPointer());
- this->SetTabsEnable(true);
- this->UpdateGraphInformation();
- }
- else
- {
- m_ActiveTubeGraph = nullptr;
- m_ActiveProperty = nullptr;
- this->SetTabsEnable(false);
-
- }
- this->UpdateActiveTubeGraphInInteractors();
- this->UpdateLabelGroups();
- this->UpdateAnnotation();
-}
-
-void QmitkTubeGraphView::UpdateActiveTubeGraphInInteractors()
-{
- //
- // traverse all tube graphs and check, and add an interactor if needed...
- //
- mitk::NodePredicateDataType::Pointer tubeGraphPred = mitk::NodePredicateDataType::New("TubeGraph");
- mitk::DataStorage::SetOfObjects::ConstPointer tubeGraphs = this->GetDataStorage()->GetSubset(tubeGraphPred);
- for(mitk::DataStorage::SetOfObjects::ConstIterator it = tubeGraphs->Begin();
- it != tubeGraphs->End();
- ++it)
- {
- mitk::DataNode::Pointer node = it.Value().GetPointer();
- if ( node->GetDataInteractor().IsNull() )
- {
- mitk::TubeGraphDataInteractor::Pointer tubeGraphInteractor = mitk::TubeGraphDataInteractor::New();
- tubeGraphInteractor->LoadStateMachine("TubeGraphInteraction.xml", us::ModuleRegistry::GetModule("MitkTubeGraph"));
- tubeGraphInteractor->SetEventConfig("TubeGraphConfig.xml", us::ModuleRegistry::GetModule("MitkTubeGraph"));
- tubeGraphInteractor->SetActivationMode(m_ActivationMode);
- tubeGraphInteractor->SetDataNode(node);
- }
- }
-
- if (m_ActiveTubeGraph.IsNotNull())
- {
- //remove old observer
- // if (m_ActiveInteractor.IsNotNull())
- // m_ActiveInteractor->RemoveObserver(m_InformationChangedObserverTag);
-
- mitk::DataNode::Pointer node = m_Controls.activeGraphComboBox->GetSelectedNode();
- //set active interactor to interactor from selected node
- m_ActiveInteractor = dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer());
-
- m_ActiveInteractor->SetActivationMode(m_ActivationMode);
-
- //add observer to activeInteractor
- typedef itk::SimpleMemberCommand< QmitkTubeGraphView > SimpleCommandType;
- SimpleCommandType::Pointer changeInformationCommand = SimpleCommandType::New();
- changeInformationCommand->SetCallbackFunction(this, &QmitkTubeGraphView::SelectionInformationChanged);
- //m_InformationChangedObserverTag = m_ActiveInteractor->AddObserver(mitk::SelectionChangedTubeGraphEvent(), changeInformationCommand);
-
- ////Add selected node to all tube graph interactors as current node
- //mitk::TubeGraphDataInteractor::SetCurrentSelectedDataNode( node );
-
- if (m_ActiveProperty.IsNull())
- {
- mitk::TubeGraphProperty::Pointer newProperty = mitk::TubeGraphProperty::New();
- m_ActiveTubeGraph->SetProperty("Tube Graph.Visualization Information",newProperty);
- m_ActiveProperty = newProperty;
- }
- }
-}
-
-void QmitkTubeGraphView::UpdateLabelGroups()
-{
- for(int i = m_Controls.toolBox->count()- 1; i >= 0 ; i--)
- m_Controls.toolBox->removeItem(i);
-
- if (m_ActiveProperty.IsNotNull())
- {
- if(m_ActiveProperty->GetNumberOfLabelGroups()!= 0)
- {
- std::vector<LabelGroupType*> labelGroups = m_ActiveProperty->GetLabelGroups();
-
- for (unsigned int k = 0; k < labelGroups.size(); k++)
- this->CreateLabelGroupWidget(labelGroups.at(k));
- }
- }
-}
-
-void QmitkTubeGraphView::OnActivationModeChanged()
-{
- if (m_Controls.noneModeRadioButton->isChecked())
- m_ActivationMode = mitk::TubeGraphDataInteractor::None;
- else if (m_Controls.singleModeRadioButton->isChecked())
- m_ActivationMode = mitk::TubeGraphDataInteractor::Single;
- else if (m_Controls.multipleModeRadioButton->isChecked())
- m_ActivationMode = mitk::TubeGraphDataInteractor::Multiple;
- else if (m_Controls.rootModeRadioButton->isChecked())
- m_ActivationMode = mitk::TubeGraphDataInteractor::ToRoot;
- else if (m_Controls.peripheryModeRadioButton->isChecked())
- m_ActivationMode = mitk::TubeGraphDataInteractor::ToPeriphery;
- else if (m_Controls.pointModeRadioButton->isChecked())
- m_ActivationMode = mitk::TubeGraphDataInteractor::Points;
- else //normally not possible, but.... set to single mode
- m_ActivationMode = mitk::TubeGraphDataInteractor::Single;
-
- mitk::DataNode::Pointer node = m_Controls.activeGraphComboBox->GetSelectedNode();
- if(node.IsNotNull() && m_ActiveProperty.IsNotNull())
- {
- dynamic_cast< mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->SetActivationMode(m_ActivationMode);
-
- //m_ActiveTubeGraph->Modified();
- // render new selection
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
- }
-}
-
-mitk::TubeGraphDataInteractor::ActivationMode QmitkTubeGraphView::GetActivationMode ()
-{
- return m_ActivationMode;
-}
-
-void QmitkTubeGraphView::OnSetRootToggled(bool enable)
-{
- this->SetTabsEnable(!enable);
- if (m_ActiveTubeGraph.IsNotNull())
- {
- mitk::DataNode::Pointer node = m_Controls.activeGraphComboBox->GetSelectedNode();
- if(node.IsNotNull())
- {
- if (enable)
- dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->SetActionMode(mitk::TubeGraphDataInteractor::RootMode);
- else
- dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->SetActionMode(mitk::TubeGraphDataInteractor::AttributationMode);
- }
- }
-}
-
-void QmitkTubeGraphView::OnDeselectAllTubes()
-{
- mitk::DataNode::Pointer node = m_Controls.activeGraphComboBox->GetSelectedNode();
- if(node.IsNotNull())
- dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->ResetPickedTubes();
-
- if (m_ActiveProperty.IsNull())
- {
- MITK_ERROR << "Oho!No Property..mhhhh";
- return;
- }
- m_ActiveProperty->DeactivateAllTubes();
- m_ActiveTubeGraph->Modified();
- // render new selection
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void QmitkTubeGraphView::OnTabSwitched(int tabIndex)
-{
- mitk::DataNode::Pointer node = m_Controls.activeGraphComboBox->GetSelectedNode();
- if(node.IsNotNull())
- {
- if (dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer()) == nullptr)
- {
- this->UpdateActiveTubeGraphInInteractors();
- /* if (dynamic_cast<mitk::TubeGraphDataInteractor::Pointer>(node->GetDataInteractor().GetPointer()).IsNull());*/
- return;
- }
-
- switch(tabIndex)
- {
- case 0:
- dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->SetActionMode(mitk::TubeGraphDataInteractor::AttributationMode);
- m_Controls.noneModeRadioButton->setEnabled(true);
- m_Controls.singleModeRadioButton->setEnabled(true);
- m_Controls.multipleModeRadioButton->setEnabled(true);
- m_Controls.peripheryModeRadioButton->setEnabled(true);
- m_Controls.rootModeRadioButton->setEnabled(true);
- m_Controls.pointModeRadioButton->setEnabled(true);
- break;
- case 1:
- dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->SetActionMode(mitk::TubeGraphDataInteractor::AnnotationMode);
- m_ActiveProperty->DeactivateAllTubes();
- m_Controls.noneModeRadioButton->setEnabled(true);
- m_Controls.singleModeRadioButton->setEnabled(true);
- m_Controls.multipleModeRadioButton->setEnabled(false);
- m_Controls.peripheryModeRadioButton->setEnabled(false);
- m_Controls.rootModeRadioButton->setEnabled(false);
- m_Controls.pointModeRadioButton->setEnabled(false);
- break;
- case 2:
- dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->SetActionMode(mitk::TubeGraphDataInteractor::EditMode);
- m_Controls.noneModeRadioButton->setEnabled(true);
- m_Controls.singleModeRadioButton->setEnabled(true);
- m_Controls.multipleModeRadioButton->setEnabled(true);
- m_Controls.peripheryModeRadioButton->setEnabled(true);
- m_Controls.rootModeRadioButton->setEnabled(true);
- m_Controls.pointModeRadioButton->setEnabled(true);
- break;
- case 3:
- dynamic_cast<mitk::TubeGraphDataInteractor*>(node->GetDataInteractor().GetPointer())->SetActionMode(mitk::TubeGraphDataInteractor::InformationMode);
- m_Controls.noneModeRadioButton->setEnabled(false);
- m_Controls.singleModeRadioButton->setEnabled(false);
- m_Controls.multipleModeRadioButton->setEnabled(false);
- m_Controls.peripheryModeRadioButton->setEnabled(false);
- m_Controls.rootModeRadioButton->setEnabled(false);
- m_Controls.pointModeRadioButton->setEnabled(false);
- this->UpdateGraphInformation();
- break;
- default:
- break;
- }
- }
-}
-
-void QmitkTubeGraphView::OnAddingLabelGroup()
-{
- QmitkTubeGraphNewLabelGroupDialog* dialog = new QmitkTubeGraphNewLabelGroupDialog( m_Parent );
-
- int dialogReturnValue = dialog->exec();
-
- LabelGroupType* newLabelGroup = dialog->GetLabelGroup();
- delete dialog;
-
- if ( dialogReturnValue != QDialog::Rejected ) // user doesn't clicked cancel or pressed Esc or something similar
- {
- m_ActiveProperty->AddLabelGroup(newLabelGroup, m_ActiveProperty->GetNumberOfLabelGroups());
- this->UpdateLabelGroups();
- }
-}
-
-void QmitkTubeGraphView::CreateLabelGroupWidget(LabelGroupType* labelGroup)
-{
- QmitkTubeGraphLabelGroupWidget* labelGroupWidget = new QmitkTubeGraphLabelGroupWidget(m_Controls.toolBox, (labelGroup->labelGroupName).c_str());
-
- for (std::vector<LabelType*>::iterator it = labelGroup->labels.begin(); it != labelGroup->labels.end(); it++)
- {
- labelGroupWidget->AddLabel(QString::fromStdString((*it)->labelName), (*it)->labelColor);
- }
-
- m_Controls.toolBox->addItem(labelGroupWidget, QString::fromStdString(labelGroup->labelGroupName));
-
- connect(labelGroupWidget, SIGNAL(SignalLabelVisibilityInGroupToggled(bool, QString, QString)), this, SLOT(OnLabelVisibilityChanged(bool, QString, QString)));
- connect(labelGroupWidget, SIGNAL(SignalLabelButtonInGroupClicked(QString, QString)), this, SLOT(OnLabelChanged(QString, QString)));
- connect(labelGroupWidget, SIGNAL(SignalLabelColorInGroupChanged(mitk::Color, QString, QString)), this, SLOT(OnLabelColorChanged(mitk::Color, QString, QString)));
-}
-
-void QmitkTubeGraphView::OnRemoveLabelGroup()
-{
- QStringList allLabelGroups;
- std::vector<LabelGroupType*> labelGroups = m_ActiveProperty->GetLabelGroups();
- for (unsigned int i = 0; i < labelGroups.size(); i++)
- allLabelGroups.push_back(QString::fromStdString(labelGroups.at(i)->labelGroupName));
-
- QmitkTubeGraphDeleteLabelGroupDialog* dialog = new QmitkTubeGraphDeleteLabelGroupDialog( m_Parent );
- dialog->SetLabelGroups(allLabelGroups);
-
- int dialogReturnValue = dialog->exec();
-
- QList<QString> toDeleteItemsList = dialog->GetSelectedLabelGroups();
-
- delete dialog;
-
- if ( dialogReturnValue != QDialog::Rejected ) // user clicked cancel or pressed Esc or something similar
- {
- for (QList<QString>::iterator it = toDeleteItemsList.begin(); it != toDeleteItemsList.end(); it++ )
- {
- std::string labelGroupName = (*it).toStdString();
- LabelGroupType* labelGroup = m_ActiveProperty->GetLabelGroupByName(labelGroupName);
- m_ActiveProperty->RemoveLabelGroup(labelGroup);
- }
- this->UpdateLabelGroups();
- }
-}
-
-void QmitkTubeGraphView::OnAddingAnnotation()
-{
- std::vector <mitk::TubeGraph::TubeDescriptorType> activeTubes = m_ActiveProperty->GetActiveTubes();
- if (activeTubes.size()!= 0)
- {
- QmitkTubeGraphNewAnnotationDialog* dialog = new QmitkTubeGraphNewAnnotationDialog( m_Parent );
-
- int dialogReturnValue = dialog->exec();
-
- QString newAnnotationName = dialog->GetAnnotationName();
- QString newDescription = dialog->GetAnnotationDescription();
- QString tubeString = QString("[%1,%2]").arg(activeTubes.begin()->first).arg(activeTubes.begin()->second);
-
- delete dialog;
-
- if ( dialogReturnValue != QDialog::Rejected ) // user doesn't clicked cancel or pressed Esc or something similar
- {
-
- mitk::TubeGraphProperty::Annotation* annotation = new mitk::TubeGraphProperty::Annotation();
- annotation->name = newAnnotationName.toStdString();
- annotation->description = newDescription.toStdString();
- annotation->tube = (*activeTubes.begin());
-
- m_ActiveProperty->AddAnnotation(annotation);
- this->UpdateAnnotation();
- }
- }
- else
- {
- MITK_INFO<< "No Tube select for annotation";
- }
-}
-
-void QmitkTubeGraphView::UpdateAnnotation()
-{
- m_Controls.annotationsTableWidget->clear();
- m_Controls.annotationsTableWidget->setRowCount(0);
- if (m_ActiveProperty.IsNotNull())
- {
- std::vector<mitk::TubeGraphProperty::Annotation*> annotations = m_ActiveProperty->GetAnnotations();
-
- if (annotations.size() != 0)
- {
- for (unsigned int k = 0; k < annotations.size(); k++)
- {
- m_Controls.annotationsTableWidget->setRowCount(k+1); // add one row
-
- QTableWidgetItem* annotationNameItem = new QTableWidgetItem(QString::fromStdString(annotations[k]->name));
- QTableWidgetItem* annotationDescriptionItem = new QTableWidgetItem(QString::fromStdString(annotations[k]->description));
- QString tubeString = QString("[%1,%2]").arg(annotations[k]->tube.first).arg(annotations[k]->tube.second);
- QTableWidgetItem* annotationTubeItem = new QTableWidgetItem(tubeString);
-
- m_Controls.annotationsTableWidget->setItem(k, 0, annotationNameItem);
- m_Controls.annotationsTableWidget->setItem(k, 1, annotationDescriptionItem);
- m_Controls.annotationsTableWidget->setItem(k, 2, annotationTubeItem);
- }
- }
- }
-}
-
-
-void QmitkTubeGraphView::OnRemoveAnnotation()
-{
- //m_Controls.annotationsTableWidget->removeRow(m_Controls.annotationsTableWidget->currentRow());
- int row = m_Controls.annotationsTableWidget->currentRow();
-
- if (row >= 0)
- {
- std::string name = m_Controls.annotationsTableWidget->item(row, 0)->text().toStdString();
-
- mitk::TubeGraphProperty::Annotation* annotation = m_ActiveProperty->GetAnnotationByName(name);
- m_ActiveProperty->RemoveAnnotation(annotation);
- this->UpdateAnnotation();
- }
-
-}
-
-
-void QmitkTubeGraphView::OnAddTubeBetweenSelection()
-{
-}
-
-void QmitkTubeGraphView::OnSeperateSelection()
-{
- std::vector <mitk::TubeGraph::TubeDescriptorType> activeTubes = m_ActiveProperty->GetActiveTubes();
- if (activeTubes.size()!= 0)
- {
- mitk::TubeGraph::Pointer subGraph = m_ActiveTubeGraph->CreateSubGraph(activeTubes);
-
- mitk::DataNode::Pointer originGraphNode = m_Controls.activeGraphComboBox->GetSelectedNode();
-
- mitk::DataNode::Pointer newGraphNode = mitk::DataNode::New();
- newGraphNode->SetData(subGraph);
- newGraphNode->SetName(originGraphNode->GetName() + "-SubGraph");
-
- mitk::TubeGraphDataInteractor::Pointer tubeGraphInteractor = mitk::TubeGraphDataInteractor::New();
- tubeGraphInteractor->LoadStateMachine("TubeGraphInteraction.xml", us::ModuleRegistry::GetModule("TubeGraph"));
- tubeGraphInteractor->SetEventConfig("TubeGraphConfig.xml", us::ModuleRegistry::GetModule("TubeGraph"));
- tubeGraphInteractor->SetDataNode(newGraphNode);
-
- mitk::TubeGraphProperty::Pointer newProperty = mitk::TubeGraphProperty::New();
- subGraph->SetProperty("Tube Graph.Visualization Information",newProperty);
-
- this->GetDataStorage()->Add(newGraphNode, originGraphNode);
- }
-}
-
-void QmitkTubeGraphView::OnDeleteSelection()
-{ //TODO Action for Interactor + undo/redo
-
- std::vector <mitk::TubeGraph::TubeDescriptorType> activeTubes = m_ActiveProperty->GetActiveTubes();
- m_ActiveTubeGraph->RemoveSubGraph(m_ActiveProperty->GetActiveTubes());
-}
-
-void QmitkTubeGraphView::OnLabelVisibilityChanged(bool isVisible, QString labelName, QString labelGroupName)
-{
- if (m_ActiveProperty.IsNull())
- {
- MITK_ERROR << "Oho!No Property..mhhhh";
- return;
- }
- LabelGroupType* labelGroup = m_ActiveProperty->GetLabelGroupByName(labelGroupName.toStdString());
- LabelType* label = m_ActiveProperty->GetLabelByName(labelGroup, labelName.toStdString());
-
- if(labelGroup == nullptr || label == nullptr )
- {
- MITK_ERROR << "This label group or label doesn't exist!";
- return;
- }
-
- m_ActiveProperty->SetLabelVisibility(label, isVisible);
- m_ActiveTubeGraph->Modified();
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void QmitkTubeGraphView::OnLabelChanged(QString labelName, QString labelGroupName)
-{
- if (m_ActiveProperty.IsNull())
- {
- MITK_ERROR << "Oho!No Property..mhhhh";
- return;
- }
- LabelGroupType* labelGroup = m_ActiveProperty->GetLabelGroupByName(labelGroupName.toStdString());
- LabelType* label = m_ActiveProperty->GetLabelByName(labelGroup, labelName.toStdString());
- if(labelGroup == nullptr || label == nullptr )
- {
- MITK_ERROR << "This label group or label doesn't exist!";
- return;
- }
-
- m_ActiveProperty->SetLabelForActivatedTubes(labelGroup, label);
- m_ActiveTubeGraph->Modified();
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void QmitkTubeGraphView::OnLabelColorChanged (mitk::Color color, QString labelName, QString labelGroupName)
-{
- if (m_ActiveProperty.IsNull())
- {
- MITK_ERROR << "Oho!No Property..mhhhh";
- return;
- }
-
- LabelGroupType* labelGroup = m_ActiveProperty->GetLabelGroupByName(labelGroupName.toStdString());
- LabelType* label = m_ActiveProperty->GetLabelByName(labelGroup, labelName.toStdString());
-
- if(labelGroup == nullptr || label == nullptr )
- {
- MITK_ERROR << "This label group or label doesn't exist!";
- return;
- }
-
- m_ActiveProperty->SetLabelColor(label, color);
- m_ActiveTubeGraph->Modified();
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-
-void QmitkTubeGraphView::SetTabsEnable(bool enable)
-{
- m_Controls.tubeGraphTabWidget->setTabEnabled(0, enable); //attributationTab
- m_Controls.tubeGraphTabWidget->setTabEnabled(1, enable);//annotationTab
- m_Controls.tubeGraphTabWidget->setTabEnabled(2, enable);//editTab
- m_Controls.tubeGraphTabWidget->setTabEnabled(3, enable);//informationTab
-}
-
-void QmitkTubeGraphView::UpdateGraphInformation()
-{
- mitk::TubeGraph::TubeDescriptorType root = m_ActiveTubeGraph->GetRootTube();
- mitk::BaseGeometry::Pointer geometry = m_ActiveTubeGraph->GetGeometry();
- mitk::Point3D origin = geometry->GetOrigin();
- mitk::Vector3D spacing = geometry->GetSpacing();
- QString information;
- information.append(QString("Number of Vertices: %1\n").arg(m_ActiveTubeGraph->GetNumberOfVertices()));
- information.append(QString("Number of Edges: %1\n").arg(m_ActiveTubeGraph->GetNumberOfEdges()));
- information.append(QString("Root Id: [%1,%2]\n\n").arg(root.first).arg(root.second));
- information.append(QString("Origin: [%1,%2,%3]\n").arg(origin[0]).arg(origin[1]).arg(origin[2]));
- information.append(QString("Spacing: [%1,%2,%3]").arg(spacing[0]).arg(spacing[1]).arg(spacing[2]));
-
- m_Controls.informationLabel->setText(information);
-}
-
-void QmitkTubeGraphView::SelectionInformationChanged()
-{
- std::vector <mitk::TubeGraph::TubeDescriptorType> activeTubes = m_ActiveProperty->GetActiveTubes();
- if(activeTubes.size()==0)
- m_Controls.shortInformationLabel->setText("");
- else
- {
- mitk::TubeGraph::TubeDescriptorType root = m_ActiveTubeGraph->GetRootTube();
- /*double averageDiameter;
- for (int i = 0; i < activeTubes.size(); i++)
- {
- mitk::TubeGraph::EdgeDescriptorType edgeDescriptor = m_ActiveTubeGraph->GetEdgeDescriptorByVerices(activeTubes.at(i).first, activeTubes.at(i).second);
- mitk::TubeGraphEdge edge = m_ActiveTubeGraph->GetEdge(edgeDescriptor);
- averageDiameter += edge.GetEdgeAverageDiameter(m_ActiveTubeGraph->GetVertex(activeTubes.at(i).first), m_ActiveTubeGraph->GetVertex(activeTubes.at(i).second));
- }
- averageDiameter = averageDiameter/activeTubes.size();*/
-
- QString information;
- information.append(QString("Number of Selected Tubes: %1\n").arg(activeTubes.size()));
- //information.append(QString("Average diameter\n").arg(averageDiameter));
- information.append(QString("Root Id: [%1,%2]").arg(root.first).arg(root.second));
- m_Controls.shortInformationLabel->setText(information);
- }
-}
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphView.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphView.h
deleted file mode 100644
index 4dcd6a76c0..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphView.h
+++ /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.
-
-============================================================================*/
-
-#ifndef QmitkTubeGraphView_h
-#define QmitkTubeGraphView_h
-
-#include "ui_QmitkTubeGraphViewControls.h"
-
-#include <QmitkAbstractView.h>
-
-#include "mitkColorProperty.h"
-#include "mitkTubeGraph.h"
-#include "mitkTubeGraphProperty.h"
-#include "mitkTubeGraphDataInteractor.h"
-
-#include <QCheckBox>
-#include <QSignalMapper>
-
-
-/*!
-*
-* \brief QmitkTubeGraphConverterView
-*
-*/
-class QmitkTubeGraphView: public QmitkAbstractView
-{
- // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject)
- Q_OBJECT
-
- typedef mitk::TubeGraphProperty::LabelGroup LabelGroupType;
- typedef LabelGroupType::Label LabelType;
-
-public:
-
- static const std::string VIEW_ID;
- /**
- * @brief Constructor.
- **/
- QmitkTubeGraphView();
-
- /**
- * @brief Destructor.
- */
- ~QmitkTubeGraphView() override;
-
- void CreateQtPartControl(QWidget *parent) override;
-
- /** \brief Method to create the connections for the component. This Method is obligatory even if no connections is needed*/
- virtual void CreateConnections();
-
- protected slots:
- //active tube graph
- void OnActiveGraphChanged(int);
-
- //activation mode
- void OnActivationModeChanged();
- void OnDeselectAllTubes();
- void OnSetRootToggled(bool);
-
- void OnTabSwitched(int);
-
- //attributation tab
- void OnAddingLabelGroup();
- void OnRemoveLabelGroup();
-
- //annotation tab
- void OnAddingAnnotation();
- void OnRemoveAnnotation();
-
- //edit tab
- void OnAddTubeBetweenSelection();
- void OnSeperateSelection();
- void OnDeleteSelection();
-
- //label group
- void OnLabelVisibilityChanged(bool, QString labelName, QString labelGroupName);
- void OnLabelChanged(QString labelName, QString labelGroupName);
- void OnLabelColorChanged(mitk::Color color, QString labelName, QString labelGroupName);
-
-protected:
-
- mitk::TubeGraphDataInteractor::ActivationMode GetActivationMode();
- void SetFocus() override;
- void NodeRemoved(const mitk::DataNode*) override;
- /// \brief called by QmitkAbstractView when DataManager's selection has changed
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,const QList<mitk::DataNode::Pointer>& nodes) override;
-
- Ui::QmitkTubeGraphViewControls m_Controls;
- // the Qt parent of our GUI (NOT of this object)
- QWidget* m_Parent;
-
-private:
- void UpdateActiveTubeGraphInInteractors();
- void CreateLabelGroupWidget(LabelGroupType* labelGroup);
- void InitializeLabelGroups();
- void SetTabsEnable(bool enable);
- void UpdateLabelGroups();
- void UpdateAnnotation();
- void SelectionInformationChanged();
- void UpdateGraphInformation();
-
- mitk::TubeGraph::Pointer m_ActiveTubeGraph;
- mitk::TubeGraphProperty::Pointer m_ActiveProperty;
- mitk::TubeGraphDataInteractor::Pointer m_ActiveInteractor;
- mitk::TubeGraphDataInteractor::ActivationMode m_ActivationMode;
-
- /* std::vector<QString> m_LabelGroupName;
- std::vector<QString> m_LabelName;*/
-
- unsigned int m_InformationChangedObserverTag;
-
-};
-
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphViewControls.ui b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphViewControls.ui
deleted file mode 100644
index c1b48b36a4..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/QmitkTubeGraphViewControls.ui
+++ /dev/null
@@ -1,559 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkTubeGraphViewControls</class>
- <widget class="QWidget" name="QmitkTubeGraphViewControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>385</width>
- <height>739</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string/>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_5">
- <item>
- <widget class="QGroupBox" name="activeNodeGroupBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="title">
- <string>Active Tube Graph</string>
- </property>
- <property name="flat">
- <bool>false</bool>
- </property>
- <property name="checkable">
- <bool>false</bool>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <property name="sizeConstraint">
- <enum>QLayout::SetDefaultConstraint</enum>
- </property>
- <item>
- <widget class="QmitkDataStorageComboBox" name="activeGraphComboBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QGroupBox" name="activationGroupBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="title">
- <string>Activation Mode</string>
- </property>
- <layout class="QHBoxLayout" name="horizontalLayout_3">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout_4">
- <item>
- <widget class="QGroupBox" name="activationModeGroupBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="title">
- <string/>
- </property>
- <property name="checkable">
- <bool>false</bool>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <widget class="QRadioButton" name="noneModeRadioButton">
- <property name="text">
- <string>None</string>
- </property>
- <property name="checked">
- <bool>true</bool>
- </property>
- <attribute name="buttonGroup">
- <string>buttonGroup</string>
- </attribute>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="singleModeRadioButton">
- <property name="text">
- <string>Single</string>
- </property>
- <attribute name="buttonGroup">
- <string>buttonGroup</string>
- </attribute>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="multipleModeRadioButton">
- <property name="text">
- <string>Multiple</string>
- </property>
- <attribute name="buttonGroup">
- <string>buttonGroup</string>
- </attribute>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="peripheryModeRadioButton">
- <property name="text">
- <string>Periphery</string>
- </property>
- <attribute name="buttonGroup">
- <string>buttonGroup</string>
- </attribute>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="rootModeRadioButton">
- <property name="text">
- <string>Path to Root</string>
- </property>
- <attribute name="buttonGroup">
- <string>buttonGroup</string>
- </attribute>
- </widget>
- </item>
- <item>
- <widget class="QRadioButton" name="pointModeRadioButton">
- <property name="text">
- <string>Point to Point</string>
- </property>
- <attribute name="buttonGroup">
- <string>buttonGroup</string>
- </attribute>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QPushButton" name="setRootButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Minimum" vsizetype="Minimum">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="toolTip">
- <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:'MS Shell Dlg 2'; font-size:8.25pt; 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:8pt;">Enable to select a new root with </span><span style=" font-size:8pt; font-weight:600;">left mouse click</span><span style=" font-size:8pt;"> in the image.</span></p></body></html></string>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="icon">
- <iconset>
- <normaloff>:/QmitkExt/icon_seedpoint.png</normaloff>:/QmitkExt/icon_seedpoint.png</iconset>
- </property>
- <property name="checkable">
- <bool>true</bool>
- </property>
- <property name="flat">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="deselectAllButton">
- <property name="font">
- <font>
- <weight>50</weight>
- <bold>false</bold>
- </font>
- </property>
- <property name="text">
- <string>Deselect All</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="QGroupBox" name="shortInformationGroupBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <weight>50</weight>
- <italic>true</italic>
- <bold>false</bold>
- </font>
- </property>
- <property name="title">
- <string>Short Information about Selection</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_9">
- <item>
- <widget class="QLabel" name="shortInformationLabel">
- <property name="font">
- <font>
- <italic>false</italic>
- </font>
- </property>
- <property name="text">
- <string/>
- </property>
- <property name="alignment">
- <set>Qt::AlignLeading|Qt::AlignLeft|Qt::AlignTop</set>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QTabWidget" name="tubeGraphTabWidget">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="sizePolicy">
- <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="font">
- <font>
- <weight>75</weight>
- <bold>true</bold>
- </font>
- </property>
- <property name="contextMenuPolicy">
- <enum>Qt::DefaultContextMenu</enum>
- </property>
- <property name="autoFillBackground">
- <bool>true</bool>
- </property>
- <property name="locale">
- <locale language="English" country="UnitedStates"/>
- </property>
- <property name="tabShape">
- <enum>QTabWidget::Rounded</enum>
- </property>
- <property name="currentIndex">
- <number>3</number>
- </property>
- <widget class="QWidget" name="attributationTab">
- <attribute name="title">
- <string>Attributation</string>
- </attribute>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <widget class="QToolBox" name="toolBox">
- <widget class="QWidget" name="page">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>343</width>
- <height>282</height>
- </rect>
- </property>
- <attribute name="label">
- <string/>
- </attribute>
- </widget>
- <widget class="QWidget" name="page_2">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>98</width>
- <height>28</height>
- </rect>
- </property>
- <attribute name="label">
- <string/>
- </attribute>
- </widget>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_2">
- <item>
- <widget class="QPushButton" name="addLabelGroupButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>+</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="removeLabelGroupButton">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="text">
- <string>-</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="annotationTab">
- <attribute name="title">
- <string>Annotation</string>
- </attribute>
- <layout class="QVBoxLayout" name="verticalLayout_6">
- <item>
- <widget class="QTableWidget" name="annotationsTableWidget">
- <property name="enabled">
- <bool>true</bool>
- </property>
- <property name="font">
- <font>
- <family>MS Shell Dlg 2</family>
- <kerning>true</kerning>
- </font>
- </property>
- <property name="frameShape">
- <enum>QFrame::WinPanel</enum>
- </property>
- <property name="dragEnabled">
- <bool>false</bool>
- </property>
- <property name="selectionBehavior">
- <enum>QAbstractItemView::SelectRows</enum>
- </property>
- <property name="showGrid">
- <bool>true</bool>
- </property>
- <column>
- <property name="text">
- <string>Name</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Description</string>
- </property>
- </column>
- <column>
- <property name="text">
- <string>Tube</string>
- </property>
- </column>
- </widget>
- </item>
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout_4">
- <item>
- <widget class="QPushButton" name="addAnnotationButton">
- <property name="text">
- <string>+</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="deleteAnnotationButton">
- <property name="text">
- <string>--</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </widget>
- <widget class="QWidget" name="editTab">
- <attribute name="title">
- <string>Edit</string>
- </attribute>
- <layout class="QVBoxLayout" name="verticalLayout_7">
- <item>
- <widget class="QLabel" name="editDescriptionLabel">
- <property name="text">
- <string>Please select the region you want to interact with!</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_2">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Fixed</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="editSelectionNewButton">
- <property name="text">
- <string>Connect</string>
- </property>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer_5">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Fixed</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>40</height>
- </size>
- </property>
- </spacer>
- </item>
- <item>
- <widget class="QPushButton" name="editSelectionSeperateButton">
- <property name="text">
- <string>Separate</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="editSelectionDeleteButton">
- <property name="text">
- <string>Delete</string>
- </property>
- </widget>
- </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 class="QWidget" name="informationTab">
- <attribute name="title">
- <string>Information</string>
- </attribute>
- <layout class="QVBoxLayout" name="verticalLayout_8">
- <item>
- <widget class="QLabel" name="informationLabel">
- <property name="text">
- <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>345</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- </widget>
- </item>
- <item>
- <spacer name="verticalSpacer">
- <property name="orientation">
- <enum>Qt::Vertical</enum>
- </property>
- <property name="sizeType">
- <enum>QSizePolicy::Preferred</enum>
- </property>
- <property name="sizeHint" stdset="0">
- <size>
- <width>20</width>
- <height>20</height>
- </size>
- </property>
- </spacer>
- </item>
- </layout>
- </widget>
- <customwidgets>
- <customwidget>
- <class>QmitkDataStorageComboBox</class>
- <extends>QComboBox</extends>
- <header location="global">QmitkDataStorageComboBox.h</header>
- </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
- <slots>
- <slot>OnActivationModeChanged()</slot>
- </slots>
- <buttongroups>
- <buttongroup name="buttonGroup"/>
- </buttongroups>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkPluginActivator.cpp
deleted file mode 100644
index 7ab0b75d0e..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkPluginActivator.cpp
+++ /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.
-
-============================================================================*/
-
-#include "mitkPluginActivator.h"
-#include "src/internal/QmitkTubeGraphView.h"
-
-namespace mitk
-{
-
- ctkPluginContext* PluginActivator::m_context = nullptr;
-
- void PluginActivator::start(ctkPluginContext* context)
- {
- BERRY_REGISTER_EXTENSION_CLASS(QmitkTubeGraphView, context)
- this->m_context = context;
- }
-
- void PluginActivator::stop(ctkPluginContext*)
- {
- this->m_context = nullptr;
- }
-
- ctkPluginContext* PluginActivator::getContext()
- {
- return m_context;
- }
-
-} //namespace
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkPluginActivator.h
deleted file mode 100644
index 3fde9d75a1..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkPluginActivator.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 mitkPluginActivator_h
-#define mitkPluginActivator_h
-
-// Parent classes
-#include <QObject>
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
- class PluginActivator :
- public QObject, public ctkPluginActivator
- {
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_tubegraph")
- Q_INTERFACES(ctkPluginActivator)
-
- public:
-
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
- static ctkPluginContext* getContext();
-
- private:
-
- static ctkPluginContext* m_context;
- }; // PluginActivator
-
-}
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkTubeGraphDefaultLabelGroups.cpp b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkTubeGraphDefaultLabelGroups.cpp
deleted file mode 100644
index dcf083f9ec..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkTubeGraphDefaultLabelGroups.cpp
+++ /dev/null
@@ -1,181 +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 "mitkTubeGraphDefaultLabelGroups.h"
-
-#include "mitkColorProperty.h"
-
-mitk::TubeGraphDefaultLabelGroups::TubeGraphDefaultLabelGroups()
-{
- mitk::Color color;
-
- auto newLabelGroup = new LabelGroupType();
- newLabelGroup->labelGroupName = "Vessel Type";
-
- auto label = new LabelType();
- label->labelName = "Undefined";
- color[0] = 170; color[1] = 170; color[2] = 169;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "Artery";
- color[0] = 255; color[1] = 0; color[2] = 0;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "Hepatic Vein";
- color[0] = 255; color[1] = 0; color[2] = 0;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "Portal Vein";
- color[0] = 0; color[1] = 0; color[2] = 125;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "Bile Duct";
- color[0] = 0; color[1] = 255; color[2] = 0;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- m_labelGroupsLiver.push_back(newLabelGroup);
- /////////////////////////////////////////////////////////////////
- newLabelGroup = new LabelGroupType();
- newLabelGroup->labelGroupName = "Resection Status";
-
- label = new LabelType();
- label->labelName = "Undefined";
- color[0] = 170; color[1] = 170; color[2] = 169;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "to be resected";
- color[0] = 255; color[1] = 0; color[2] = 0;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "not to be resected";
- color[0] = 0; color[1] = 255; color[2] = 0;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "area at risk";
- color[0] = 255; color[1] = 255; color[2] = 0;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- m_labelGroupsLiver.push_back(newLabelGroup);
- ///////////////////////////////////////////////////////////
- newLabelGroup = new LabelGroupType();
- newLabelGroup->labelGroupName = "Segments (Portal)";
-
- label = new LabelType();
- label->labelName = "Undefined";
- color[0] = 170; color[1] = 170; color[2] = 169;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "I";
- color[0] = 95; color[1] = 158; color[2] = 160;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "II";
- color[0] = 122; color[1] = 197; color[2] = 205;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "III";
- color[0] = 0; color[1] = 154; color[2] =205;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "IVa";
- color[0] = 154; color[1] = 192; color[2] = 205;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "IVb";
- color[0] = 104; color[1] = 131; color[2] = 139;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "V";
- color[0] = 118; color[1] = 238; color[2] = 198;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "VI";
- color[0] = 102; color[1] = 205; color[2] = 170;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "VII";
- color[0] = 69; color[1] = 139; color[2] = 116;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- label = new LabelType();
- label->labelName = "VIII";
- color[0] = 46; color[1] = 139; color[2] = 87;
- label->labelColor = color;
- label->isVisible = true;
- newLabelGroup->labels.push_back(label);
-
- m_labelGroupsLiver.push_back(newLabelGroup);
-}
-mitk::TubeGraphDefaultLabelGroups::~TubeGraphDefaultLabelGroups()
-{
-}
-
-std::vector<mitk::TubeGraphProperty::LabelGroup*> mitk::TubeGraphDefaultLabelGroups::GetLabelGroupForLung()
-{
- return m_labelGroupsLung;
-}
-
-std::vector<mitk::TubeGraphProperty::LabelGroup*> mitk::TubeGraphDefaultLabelGroups::GetLabelGroupForLiver()
-{
- return m_labelGroupsLiver;
-}
diff --git a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkTubeGraphDefaultLabelGroups.h b/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkTubeGraphDefaultLabelGroups.h
deleted file mode 100644
index 72d7c1af4e..0000000000
--- a/Plugins/org.mitk.gui.qt.tubegraph/src/internal/mitkTubeGraphDefaultLabelGroups.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 mitkTubeGraphDefaultLabelGroups_h
-#define mitkTubeGraphDefaultLabelGroups_h
-
-#include "mitkTubeGraphProperty.h"
-
-#include <vector>
-
-namespace mitk
-{
- class TubeGraphDefaultLabelGroups
- {
-
- typedef TubeGraphProperty::LabelGroup LabelGroupType;
- typedef LabelGroupType::Label LabelType;
-
- public:
-
- TubeGraphDefaultLabelGroups();
- virtual ~TubeGraphDefaultLabelGroups();
-
- std::vector<LabelGroupType*> GetLabelGroupForLung();
- std::vector<LabelGroupType*> GetLabelGroupForLiver();
-
- private:
- std::vector<LabelGroupType*> m_labelGroupsLung;
- std::vector<LabelGroupType*> m_labelGroupsLiver;
-
- };
-}//namespace mitk
-#endif
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/CMakeLists.txt b/Plugins/org.mitk.gui.qt.ugvisualization/CMakeLists.txt
deleted file mode 100644
index ed165f14b4..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/CMakeLists.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-project(org_mitk_gui_qt_ugvisualization)
-
-mitk_create_plugin(
- EXPORT_DIRECTIVE UGVISUALIZATION_EXPORT
- EXPORTED_INCLUDE_SUFFIXES src
- MODULE_DEPENDS MitkQtWidgetsExt
-)
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.ugvisualization/documentation/doxygen/modules.dox
deleted file mode 100644
index cee668d667..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/documentation/doxygen/modules.dox
+++ /dev/null
@@ -1,16 +0,0 @@
-/**
- \defgroup org_mitk_gui_qt_ugvisualization org.mitk.gui.qt.ugvisualization
- \ingroup MITKPlugins
-
- \brief Describe your plugin here.
-
-*/
-
-/**
- \defgroup org_mitk_gui_qt_ugvisualization_internal Internal
- \ingroup org_mitk_gui_qt_ugvisualization
-
- \brief This subcategory includes the internal classes of the org.mitk.gui.qt.ugvisualization 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.ugvisualization/files.cmake b/Plugins/org.mitk.gui.qt.ugvisualization/files.cmake
deleted file mode 100644
index 5cb062a6b8..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/files.cmake
+++ /dev/null
@@ -1,37 +0,0 @@
-set(SRC_CPP_FILES
-
-)
-
-set(INTERNAL_CPP_FILES
- QmitkUGVisualizationView.cpp
- mitkPluginActivator.cpp
-)
-
-set(UI_FILES
- src/internal/QmitkUGVisualizationViewControls.ui
-)
-
-set(MOC_H_FILES
- src/internal/QmitkUGVisualizationView.h
- src/internal/mitkPluginActivator.h
-)
-
-set(CACHED_RESOURCE_FILES
- resources/icon.png
- 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.ugvisualization/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.ugvisualization/manifest_headers.cmake
deleted file mode 100644
index 04b75418be..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/manifest_headers.cmake
+++ /dev/null
@@ -1,5 +0,0 @@
-set(Plugin-Name "MITK UG Visualization")
-set(Plugin-Version "0.1")
-set(Plugin-Vendor "German Cancer Research Center (DKFZ)")
-set(Plugin-ContactAddress "https://www.mitk.org")
-set(Require-Plugin org.mitk.gui.qt.common)
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/plugin.xml b/Plugins/org.mitk.gui.qt.ugvisualization/plugin.xml
deleted file mode 100644
index 068fe5adbf..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/plugin.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<?BlueBerry version="0.1"?>
-<plugin>
-
- <extension point="org.blueberry.ui.views">
- <view id="org.mitk.views.ugvisualization"
- name="UG Visualization"
- class="QmitkUGVisualizationView"
- icon="resources/icon.png" />
- </extension>
-
-</plugin>
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/resources/icon.png b/Plugins/org.mitk.gui.qt.ugvisualization/resources/icon.png
deleted file mode 100644
index 329ce3b355..0000000000
Binary files a/Plugins/org.mitk.gui.qt.ugvisualization/resources/icon.png and /dev/null differ
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationView.cpp b/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationView.cpp
deleted file mode 100644
index e9fc1015ac..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationView.cpp
+++ /dev/null
@@ -1,285 +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 "QmitkUGVisualizationView.h"
-
-#include <mitkUnstructuredGrid.h>
-#include <mitkGridRepresentationProperty.h>
-#include <mitkGridVolumeMapperProperty.h>
-#include <mitkVtkScalarModeProperty.h>
-#include <mitkPropertyObserver.h>
-
-#include <QmitkUGCombinedRepresentationPropertyWidget.h>
-#include <QmitkBoolPropertyWidget.h>
-
-#include <QWidgetAction>
-
-#include <QMenu>
-
-
-class UGVisVolumeObserver : public mitk::PropertyView
-{
-public:
-
- UGVisVolumeObserver(mitk::BoolProperty* property, QmitkUGVisualizationView* view)
- : PropertyView(property), m_View(view), m_BoolProperty(property)
- {
- }
-
-protected:
-
- void PropertyChanged() override
- {
- m_View->m_VolumeMode = m_BoolProperty->GetValue();
- m_View->UpdateEnablement();
- }
-
- void PropertyRemoved() override
- {
- m_View->m_VolumeMode = false;
- m_Property = nullptr;
- m_BoolProperty = nullptr;
- }
-
- QmitkUGVisualizationView* m_View;
- mitk::BoolProperty* m_BoolProperty;
-
-};
-
-
-const std::string QmitkUGVisualizationView::VIEW_ID = "org.mitk.views.ugvisualization";
-
-
-QmitkUGVisualizationView::QmitkUGVisualizationView()
-: QmitkAbstractView(), m_Outline2DAction(nullptr), m_Outline2DWidget(nullptr),
- m_LODAction(nullptr), m_ScalarVisibilityAction(nullptr), m_ScalarVisibilityWidget(nullptr),
- m_FirstVolumeRepId(-1), m_ShowTFGeneratorWidget(true), m_ShowScalarOpacityWidget(false),
- m_ShowColorWidget(true), m_ShowGradientOpacityWidget(false), m_ShowTFGeneratorAction(nullptr),
- m_ShowScalarOpacityAction(nullptr), m_ShowColorAction(nullptr), m_ShowGradientOpacityAction(nullptr),
- m_VolumeModeObserver(nullptr)
-{
-}
-
-QmitkUGVisualizationView::~QmitkUGVisualizationView()
-{
- delete m_VolumeModeObserver;
-}
-
-
-void QmitkUGVisualizationView::CreateQtPartControl( QWidget *parent )
-{
- m_Controls.setupUi( parent );
-
- m_Outline2DWidget = new QmitkBoolPropertyWidget("Outline 2D polygons", parent);
- m_Outline2DAction = new QWidgetAction(this);
- m_Outline2DAction->setDefaultWidget(m_Outline2DWidget);
-
- m_LODAction = new QAction("Enable LOD (Level Of Detail)", this);
- m_LODAction->setCheckable(true);
-
- m_ScalarVisibilityWidget = new QmitkBoolPropertyWidget("Visualize scalars", parent);
- m_ScalarVisibilityAction = new QWidgetAction(this);
- m_ScalarVisibilityAction->setDefaultWidget(m_ScalarVisibilityWidget);
-
- m_ShowColorAction = new QAction("Show color transfer function", this);
- m_ShowColorAction->setCheckable(true);
- m_ShowColorAction->setChecked(m_ShowColorWidget);
- m_ShowGradientOpacityAction = new QAction("Show gradient opacity function", this);
- m_ShowGradientOpacityAction->setCheckable(true);
- m_ShowGradientOpacityAction->setChecked(m_ShowGradientOpacityWidget);
- m_ShowScalarOpacityAction = new QAction("Show scalar opacity function", this);
- m_ShowScalarOpacityAction->setCheckable(true);
- m_ShowScalarOpacityAction->setChecked(m_ShowScalarOpacityWidget);
- m_ShowTFGeneratorAction = new QAction("Show transfer function generator", this);
- m_ShowTFGeneratorAction->setCheckable(true);
- m_ShowTFGeneratorAction->setChecked(m_ShowTFGeneratorWidget);
-
- QMenu* menu = new QMenu(parent);
- menu->addAction(m_ScalarVisibilityAction);
- menu->addAction(m_Outline2DAction);
- //menu->addAction(m_LODAction);
- menu->addSeparator();
- menu->addAction(m_ShowTFGeneratorAction);
- menu->addAction(m_ShowScalarOpacityAction);
- menu->addAction(m_ShowColorAction);
- menu->addAction(m_ShowGradientOpacityAction);
-
- m_Controls.m_OptionsButton->setMenu(menu);
-
- m_Controls.m_TransferFunctionWidget->SetScalarLabel("Scalar value");
-
-// const mitk::EnumerationProperty::EnumStringsContainerType& scalarStrings = scalarProp->GetEnumStrings();
-
-// for (mitk::EnumerationProperty::EnumStringsContainerType::const_iterator it = scalarStrings.begin();
-// it != scalarStrings.end(); ++it)
-// {
-// MITK_INFO << "ADding: " << it->first;
-// m_Controls.m_ScalarModeComboBox->addItem(QString::fromStdString(it->first), it->second);
-// }
-
- this->UpdateGUI();
-
- CreateConnections();
-}
-
-void QmitkUGVisualizationView::CreateConnections()
-{
- connect(m_Controls.m_ScalarModeComboBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateRenderWindow()));
- connect(m_Controls.m_RepresentationComboBox, SIGNAL(activated(int)), this, SLOT(UpdateRenderWindow()));
- connect(m_Outline2DWidget, SIGNAL(toggled(bool)), this, SLOT(UpdateRenderWindow()));
- connect(m_ScalarVisibilityWidget, SIGNAL(toggled(bool)), this, SLOT(UpdateRenderWindow()));
- connect(m_Controls.m_TransferFunctionGeneratorWidget, SIGNAL(SignalUpdateCanvas()), m_Controls.m_TransferFunctionWidget, SLOT(OnUpdateCanvas()));
-
- connect(m_ShowColorAction, SIGNAL(triggered(bool)), this, SLOT(ShowColorWidget(bool)));
- connect(m_ShowGradientOpacityAction, SIGNAL(triggered(bool)), this, SLOT(ShowGradientOpacityWidget(bool)));
- connect(m_ShowScalarOpacityAction, SIGNAL(triggered(bool)), this, SLOT(ShowScalarOpacityWidget(bool)));
- connect(m_ShowTFGeneratorAction, SIGNAL(triggered(bool)), this, SLOT(ShowTFGeneratorWidget(bool)));
-}
-
-void QmitkUGVisualizationView::SetFocus()
-{
- m_Controls.m_OptionsButton->setFocus();
-}
-
-void QmitkUGVisualizationView::UpdateRenderWindow()
-{
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void QmitkUGVisualizationView::ShowTFGeneratorWidget(bool show)
-{
- m_ShowTFGeneratorWidget = show;
- UpdateEnablement();
-}
-
-void QmitkUGVisualizationView::ShowScalarOpacityWidget(bool show)
-{
- m_ShowScalarOpacityWidget = show;
- UpdateEnablement();
-}
-
-void QmitkUGVisualizationView::ShowColorWidget(bool show)
-{
- m_ShowColorWidget = show;
- UpdateEnablement();
-}
-
-void QmitkUGVisualizationView::ShowGradientOpacityWidget(bool show)
-{
- m_ShowGradientOpacityWidget = show;
- UpdateEnablement();
-}
-
-void QmitkUGVisualizationView::UpdateEnablement()
-{
- m_Controls.m_TransferFunctionGeneratorWidget->setVisible(m_ShowTFGeneratorWidget);
- m_Controls.m_TransferFunctionWidget->ShowScalarOpacityFunction(m_ShowScalarOpacityWidget);
- m_Controls.m_TransferFunctionWidget->ShowColorFunction(m_ShowColorWidget);
- m_Controls.m_TransferFunctionWidget->ShowGradientOpacityFunction(m_ShowGradientOpacityWidget);
-
- m_Controls.m_TransferFunctionGeneratorWidget->SetThresholdTabEnabled(m_ScalarVisibilityWidget->isChecked());
- m_Controls.m_TransferFunctionGeneratorWidget->SetBellTabEnabled(m_ScalarVisibilityWidget->isChecked());
- m_Controls.m_TransferFunctionWidget->SetScalarOpacityFunctionEnabled(m_ScalarVisibilityWidget->isChecked());
- m_Controls.m_TransferFunctionWidget->SetGradientOpacityFunctionEnabled(m_VolumeMode);
-}
-
-void QmitkUGVisualizationView::UpdateGUI()
-{
- bool enable = false;
-
- mitk::DataNode* node = nullptr;
- auto nodes = this->GetDataManagerSelection();
- if (!nodes.empty())
- {
- node = nodes.front();
-
- if (node)
- {
- // here we have a valid mitk::DataNode
-
- // a node itself is not very useful, we need its data item
- mitk::BaseData* data = node->GetData();
- if (data)
- {
- // test if this data item is an unstructured grid
- enable = dynamic_cast<mitk::UnstructuredGrid*>( data );
- }
- }
- }
-
- m_Controls.m_SelectedLabel->setVisible(enable);
- m_Controls.m_ErrorLabel->setVisible(!enable);
- m_Controls.m_ContainerWidget->setEnabled(enable);
- m_Controls.m_OptionsButton->setEnabled(enable);
-
- if (enable)
- {
- m_VolumeMode = false;
- node->GetBoolProperty("volumerendering", m_VolumeMode);
-
- m_Controls.m_SelectedLabel->setText(QString("Selected UG: ") + node->GetName().c_str());
-
- m_Controls.m_TransferFunctionGeneratorWidget->SetDataNode(node);
- m_Controls.m_TransferFunctionWidget->SetDataNode(node);
-
- mitk::BoolProperty* outlineProp = nullptr;
- node->GetProperty(outlineProp, "outline polygons");
- m_Outline2DWidget->SetProperty(outlineProp);
-
- mitk::BoolProperty* scalarVisProp = nullptr;
- node->GetProperty(scalarVisProp, "scalar visibility");
- m_ScalarVisibilityWidget->SetProperty(scalarVisProp);
-
- mitk::VtkScalarModeProperty* scalarProp = nullptr;
- if (node->GetProperty(scalarProp, "scalar mode"))
- {
- m_Controls.m_ScalarModeComboBox->SetProperty(scalarProp);
- }
-
- mitk::GridRepresentationProperty* gridRepProp = nullptr;
- mitk::GridVolumeMapperProperty* gridVolumeProp = nullptr;
- mitk::BoolProperty* volumeProp = nullptr;
- node->GetProperty(gridRepProp, "grid representation");
- node->GetProperty(gridVolumeProp, "volumerendering.mapper");
- node->GetProperty(volumeProp, "volumerendering");
- m_Controls.m_RepresentationComboBox->SetProperty(gridRepProp, gridVolumeProp, volumeProp);
-
- if (m_VolumeModeObserver)
- {
- delete m_VolumeModeObserver;
- m_VolumeModeObserver = nullptr;
- }
-
- if (volumeProp)
- {
- m_VolumeModeObserver = new UGVisVolumeObserver(volumeProp, this);
- }
- }
-
- UpdateEnablement();
-
-}
-
-
-void QmitkUGVisualizationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList<mitk::DataNode::Pointer>& /*nodes*/)
-{
- UpdateGUI();
-}
-
-
-
-
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationView.h b/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationView.h
deleted file mode 100644
index 5324e380c3..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationView.h
+++ /dev/null
@@ -1,108 +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 QmitkUGVisualizationView_h
-#define QmitkUGVisualizationView_h
-
-#include <berryISelectionListener.h>
-
-#include <QmitkAbstractView.h>
-
-#include "ui_QmitkUGVisualizationViewControls.h"
-
-class QWidgetAction;
-
-class QmitkBoolPropertyWidget;
-
-namespace mitk {
- class PropertyObserver;
-}
-
-/*!
- \brief QmitkUGVisualizationView
-
- \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation.
-*/
-class QmitkUGVisualizationView : 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;
-
- QmitkUGVisualizationView();
- ~QmitkUGVisualizationView() override;
-
- void CreateQtPartControl(QWidget *parent) override;
-
- ///
- /// Sets the focus to an internal widget.
- ///
- void SetFocus() override;
-
- protected slots:
-
- void UpdateRenderWindow();
-
- void ShowTFGeneratorWidget(bool show);
- void ShowScalarOpacityWidget(bool show);
- void ShowColorWidget(bool show);
- void ShowGradientOpacityWidget(bool show);
-
- protected:
-
- /// \brief called by QmitkAbstractView when DataManager's selection has changed
- void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer>& nodes) override;
-
- void CreateConnections();
-
- private:
-
- friend class UGVisVolumeObserver;
-
- void UpdateGUI();
-
- void UpdateEnablement();
-
- Ui::QmitkUGVisualizationViewControls m_Controls;
-
- QWidgetAction* m_Outline2DAction;
- QmitkBoolPropertyWidget* m_Outline2DWidget;
- QAction* m_LODAction;
- QWidgetAction* m_ScalarVisibilityAction;
- QmitkBoolPropertyWidget* m_ScalarVisibilityWidget;
-
- int m_FirstVolumeRepId;
- QHash<int, int> m_MapRepComboToEnumId;
-
- bool m_VolumeMode;
-
- bool m_ShowTFGeneratorWidget;
- bool m_ShowScalarOpacityWidget;
- bool m_ShowColorWidget;
- bool m_ShowGradientOpacityWidget;
-
- QAction* m_ShowTFGeneratorAction;
- QAction* m_ShowScalarOpacityAction;
- QAction* m_ShowColorAction;
- QAction* m_ShowGradientOpacityAction;
-
- mitk::PropertyObserver* m_VolumeModeObserver;
-
-};
-
-
-
-#endif
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationViewControls.ui b/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationViewControls.ui
deleted file mode 100644
index 30fb8ce503..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/QmitkUGVisualizationViewControls.ui
+++ /dev/null
@@ -1,182 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>QmitkUGVisualizationViewControls</class>
- <widget class="QWidget" name="QmitkUGVisualizationViewControls">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>465</width>
- <height>675</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="QWidget" name="widget" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <property name="margin">
- <number>0</number>
- </property>
- <item>
- <widget class="QWidget" name="widget_3" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_3">
- <property name="margin">
- <number>0</number>
- </property>
- <item>
- <widget class="QLabel" name="m_ErrorLabel">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- <property name="styleSheet">
- <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
- </property>
- <property name="text">
- <string>Please select an unstructured grid!</string>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="m_SelectedLabel">
- <property name="text">
- <string/>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="m_OptionsButton">
- <property name="text">
- <string>Options</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QWidget" name="m_ContainerWidget" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <property name="margin">
- <number>0</number>
- </property>
- <item>
- <widget class="QWidget" name="widget_2" native="true">
- <layout class="QGridLayout" name="gridLayout">
- <property name="margin">
- <number>0</number>
- </property>
- <item row="0" column="1">
- <widget class="QmitkUGCombinedRepresentationPropertyWidget" name="m_RepresentationComboBox">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
- <horstretch>1</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item row="1" column="1">
- <widget class="QmitkEnumerationPropertyWidget" name="m_ScalarModeComboBox"/>
- </item>
- <item row="0" column="0">
- <widget class="QLabel" name="label">
- <property name="text">
- <string>Representation</string>
- </property>
- </widget>
- </item>
- <item row="1" column="0">
- <widget class="QLabel" name="label_2">
- <property name="text">
- <string>Scalar mode</string>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- <item>
- <widget class="QmitkTransferFunctionGeneratorWidget" name="m_TransferFunctionGeneratorWidget" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>0</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QmitkTransferFunctionWidget" name="m_TransferFunctionWidget" native="true">
- <property name="sizePolicy">
- <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
- <horstretch>0</horstretch>
- <verstretch>1</verstretch>
- </sizepolicy>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- </item>
- </layout>
- </widget>
- <layoutdefault spacing="6" margin="11"/>
- <customwidgets>
- <customwidget>
- <class>QmitkTransferFunctionWidget</class>
- <extends>QWidget</extends>
- <header location="global">QmitkTransferFunctionWidget.h</header>
- </customwidget>
- <customwidget>
- <class>QmitkTransferFunctionGeneratorWidget</class>
- <extends>QWidget</extends>
- <header location="global">QmitkTransferFunctionGeneratorWidget.h</header>
- <container>1</container>
- </customwidget>
- <customwidget>
- <class>QmitkEnumerationPropertyWidget</class>
- <extends>QComboBox</extends>
- <header location="global">QmitkEnumerationPropertyWidget.h</header>
- </customwidget>
- <customwidget>
- <class>QmitkUGCombinedRepresentationPropertyWidget</class>
- <extends>QComboBox</extends>
- <header location="global">QmitkUGCombinedRepresentationPropertyWidget.h</header>
- </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/mitkPluginActivator.cpp
deleted file mode 100644
index 84778c5f95..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/mitkPluginActivator.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 "mitkPluginActivator.h"
-#include "QmitkUGVisualizationView.h"
-
-namespace mitk {
-
-void PluginActivator::start(ctkPluginContext* context)
-{
- BERRY_REGISTER_EXTENSION_CLASS(QmitkUGVisualizationView, context)
-}
-
-void PluginActivator::stop(ctkPluginContext* context)
-{
- Q_UNUSED(context)
-}
-
-}
diff --git a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/mitkPluginActivator.h
deleted file mode 100644
index f822ca8e0a..0000000000
--- a/Plugins/org.mitk.gui.qt.ugvisualization/src/internal/mitkPluginActivator.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 mitkPluginActivator_h
-#define mitkPluginActivator_h
-
-#include <ctkPluginActivator.h>
-
-namespace mitk {
-
-class PluginActivator :
- public QObject, public ctkPluginActivator
-{
- Q_OBJECT
- Q_PLUGIN_METADATA(IID "org_mitk_gui_qt_ugvisualization")
- Q_INTERFACES(ctkPluginActivator)
-
-public:
-
- void start(ctkPluginContext* context) override;
- void stop(ctkPluginContext* context) override;
-
-}; // PluginActivator
-
-}
-
-#endif
diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index d3e5e55ac7..bd06fe812e 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -1,509 +1,508 @@
#-----------------------------------------------------------------------------
# Convenient macro allowing to download a file
#-----------------------------------------------------------------------------
if(NOT MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL)
set(MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL https://www.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 ${EXTERNAL_MITK_DATA_DIR})
endif()
endif()
#-----------------------------------------------------------------------------
# External project settings
#-----------------------------------------------------------------------------
include(ExternalProject)
include(mitkMacroQueryCustomEPVars)
include(mitkFunctionInstallExternalCMakeProject)
include(mitkFunctionCleanExternalProject)
option(MITK_AUTOCLEAN_EXTERNAL_PROJECTS "Experimental: Clean external project builds if updated" ON)
set(ep_prefix "${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()
# 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")
if(Qt6_DIR)
set(_install_rpath_linkflag "${_install_rpath_linkflag}:${Qt6_DIR}/../..")
endif()
set(_install_rpath_linkflag "${_install_rpath_linkflag}'")
endif()
endif()
set(_install_rpath)
if(APPLE)
set(_install_rpath "@loader_path/../lib")
elseif(UNIX)
# this work for libraries as well as executables
set(_install_rpath "\$ORIGIN/../lib")
if(Qt6_DIR)
set(_install_rpath "${_install_rpath}:${Qt6_DIR}/../..")
endif()
endif()
set(ep_common_args
-DCMAKE_POLICY_DEFAULT_CMP0091:STRING=OLD
-DCMAKE_CXX_EXTENSIONS:STRING=${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} ${MITK_CXX${MITK_CXX_STANDARD}_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_Qt6
MITK_USE_SYSTEM_Boost
MITK_USE_BLUEBERRY
- MITK_USE_OpenCL
MITK_USE_OpenMP
)
#-----------------------------------------------------------------------------
# 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()
if(MITK_USE_OpenCV)
list(APPEND mitk_optional_cache_args "-DCMAKE_CONFIGURATION_TYPES:STRING=Debug$<SEMICOLON>Release")
endif()
# Optional python variables
if(MITK_USE_Python3)
list(APPEND mitk_optional_cache_args
-DMITK_USE_Python3:BOOL=${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}
-DQt6_DIR:PATH=${Qt6_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
)